@article {pmid40579258, year = {2025}, author = {Weckwerth, W and Chaturvedi, P and Ghatak, A and Kerou, M and Garg, V and Bohra, A and Subbarao, GV and Stein, L and Schleper, C and Varshney, RK and Snapp, S}, title = {Natural variation of the holobiont for sustainable agroecosystems.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2025.05.006}, pmid = {40579258}, issn = {1878-4372}, abstract = {Plant evolution is largely driven by plant-microbe interactions, yet the ecology of the plant holobiont is not well understood at a molecular level. However, these relationships hold diverse benefits for sustainable agriculture as nature-based solutions (NbS). We propose a workflow to enhance understanding of natural variation in the plant-soil microbiome holobiont, addressing key challenges like growth promotion, stress resilience, nitrogen use efficiency (NUE), biological nitrification inhibition (BNI), healthy soils, and improving fertilization practices towards a more natural agroecosystem. We discuss a panome-wide association study (PWAS) approach to discover and incorporate novel genetic diversity from exotic germplasm into breeding populations. Ultimately, understanding natural variation of the holobiont in agroecosystems will contribute to the development of novel climate-resilient crop varieties for food security.}, }
@article {pmid40578184, year = {2025}, author = {Debat, H and Paolinelli, M and Escoriaza, G and Garcia-Lampasona, S and Gomez-Talquenca, S and Bejerman, N}, title = {Grapevine holobiome metatranscriptomics provides a glimpse into the wood mycovirome.}, journal = {Virology}, volume = {610}, number = {}, pages = {110604}, doi = {10.1016/j.virol.2025.110604}, pmid = {40578184}, issn = {1096-0341}, abstract = {Given the agronomic and economic importance of viticulture, grapevine has been shown to host the largest number of viruses among plants to date. Nevertheless, studies assessing the grapevine-associated holobiont remain scarce. In this context, the viral component of this ecological niche is understudied. In this work, through metatranscriptomics of wood samples from individual grapevines that were either healthy or exhibited symptoms of grapevine trunk disease from Argentina, we provide a glimpse into the wood linked virome. Virus discovery from high-throughput sequencing data resulted in the identification and reconstruction of 123 novel virus sequences. Genetic and phylogenetic insights suggest that these sequences correspond to 78 novel virus species. Structural and functional annotation of the viruses showed a great diversity of genomic organizations, with the presence of dsRNA, ssRNA(-) and ssRNA(+) viruses belonging to more than 15 virus families. Some highly divergent viruses resembling narnaviruses, ophioviruses, deltaflexiviruses and bunyaviruses could be accommodated within new genera or even new virus families. The differential detection and variable RNA levels across samples suggest complex dynamics and prevalence patterns of those novel viruses. The viral profile described here provides a first insight into the multifaceted South American grapevine wood holobiont mycovirome.}, }
@article {pmid40568303, year = {2025}, author = {Wiederkehr, F and Engelhardt, KE and Vetter, J and Ruscheweyh, HJ and Salazar, G and O'Brien, J and Priest, T and Ziegler, M and Sunagawa, S}, title = {Host-level biodiversity shapes the dynamics and networks within the coral reef microbiome.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf097}, pmid = {40568303}, issn = {2730-6151}, abstract = {Coral reefs face severe threats from human activity, resulting in drastic biodiversity loss. Despite the urgency of safeguarding these ecosystems, we know little about the ecological impacts of losing coral reef host-associated microbial communities (microbiomes). Here, we experimentally studied the microbiomes attached to or released from seven benthic reef hosts belonging to the functional groups of stony corals, soft corals, macroalgae, and sponges while manipulating the coral reef metacommunity to mimic biodiverse or degraded reef habitats. Developing an ecological framework, we found host species and functional groups to show distinct patterns of interacting with the environment (i.e. by exuding, maintaining, acquiring, or exchanging microbiome members), with habitat biodiversity primarily influencing microbial acquisition. In a degraded compared to a biodiverse habitat, the microbiomes of stony corals were less connected to soft corals and sponges, while those of soft corals, macroalgae, and sponges became more tightly linked. Our study demonstrates that a decline in metacommunity biodiversity is not merely associated with a proportional loss in microbial diversity; rather, it triggers complex changes in the microbial interactions among the persisting hosts with each other and the environment. These results emphasize the importance of conserving coral reef host biodiversity to preserve the intricately linked microbiomes-and with them the ecosystem functions and services coral reefs provide.}, }
@article {pmid40555367, year = {2025}, author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM}, title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250729}, doi = {10.1098/rspb.2025.0729}, pmid = {40555367}, issn = {1471-2954}, support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; }, mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.}, }
@article {pmid40545364, year = {2025}, author = {Nakanishi, E and Cornette, R and Shimura, S and Kikawada, T}, title = {Microbiome Associated with Polypedilum sp. (Diptera; Chironomidae), a Midge Adapted to an Extremely Acidic Environment.}, journal = {Microbes and environments}, volume = {40}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME24090}, pmid = {40545364}, issn = {1347-4405}, abstract = {Chironomids (Diptera; Chironomidae), non-biting midges, are a highly diverse family of holometabolous insects, many of which are known for their tolerance to extreme environmental conditions, such as desiccation, pollution, and high acidity. The contribution of microbial symbionts to these adaptations was recently suggested. Therefore, we herein exami-ned the microbiome associated with the larvae of the undescribed acid-tolerant chironomid species, Polypedilum sp., which inhabits the Yukawa River (Gunma, Japan), an environment that is characterized by an extremely low pH (≤2) and high concentrations of heavy metal ions (including arsenic). Amplicon sequencing of the 16S rRNA gene revealed a distinct larval microbiome with a lower alpha diversity value and more enriched and specific bacterial taxa than the surrounding river water and detritus. Full-length 16S rRNA gene sequencing using nanopore long-read technology identified several previously undescribed operational taxonomic units (OTUs), among which OTU_Bacillaceae_Yukawa was consistently present in larvae reared in the laboratory for more than 4 months, suggesting persistent, possibly vertically transmitted, symbiosis. An inferred pathway ana-lysis suggested the contribution of the larval microbiome to host nutritional physiology. The possibly acid-sensitive OTU_Bacillaceae_Yukawa localized to midgut segments, indicating internal pH-buffered niches for microbial survival. These results provide novel insights into the ecology of acid-tolerant chironomids and lay the groundwork for further examinations of holobiont-based stress tolerance.}, }
@article {pmid40542287, year = {2025}, author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C}, title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {40542287}, issn = {2058-5276}, support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; }, abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.}, }
@article {pmid40528245, year = {2025}, author = {Yang, Q and Zhang, H and Qiu, JW and Huang, D and Zhou, X and Zheng, X}, title = {Symbiotic Symbiodiniaceae mediate coral-associated bacterial communities along a natural thermal gradient.}, journal = {Environmental microbiome}, volume = {20}, number = {1}, pages = {72}, pmid = {40528245}, issn = {2524-6372}, support = {2022YFC3102003//National Key Research and Development Program of China/ ; 2020017//he Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 42376110//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; }, abstract = {The coral-associated microbiome plays a vital role in the holobiont, enabling coral adaptation to diverse environments by modulating its composition and mediating interactions among its constituents. However, the responses of coral microbiomes, particularly the interactions between Symbiodiniaceae and bacteria, to environmental changes remain unclear. To fill this knowledge gap, we examined Pocillopora acuta, an environmentally sensitive coral species, collected from three sites along the southeastern coast of Hainan which exhibit moderate environmental differences. We measured the physiological characteristics of Symbiodiniaceae and conducted amplicon sequencing to analyze the structure of Symbiodiniaceae and bacterial communities. Our results revealed that P. acuta in southeastern Hainan maintains stable symbiosis with Symbiodiniaceae sub-clades such as C1, C42.1, C3, D1, D4, and D6, as evidenced by ΔF/Fm' values ranging from 0.45 for P. acuta dominated by Durusdinium (PaD) to 0.6 for counterparts dominated by Cladocopium (PaC). However, the composition of Symbiodiniaceae varied among the three sites, primarily due to differences in the abundance of dominant sub-clades. These variations may reflect adaptations to distinct environmental conditions, which in turn significantly influence the associated bacterial communities. Notably, our results suggest that Symbiodiniaceae may exert a greater regulatory role on the coral-associated bacterial community than environmental differences. Specific bacteria, such as Endozoicomonas and Synechococcus_CC9902, exhibit strong correlations with particular Symbiodiniaceae genera or sub-clades, indicating that the dominant Symbiodiniaceae shape bacterial community dynamics. Despite the observed variations, we identified modular co-occurrence patterns in bacterial networks, with PaC exhibiting a more complex and stable structure. Overall, these results highlight the critical role of various Symbiodiniaceae genera in influencing bacterial community dynamics, emphasizing their importance in maintaining coral health and resilience in the face of changing environmental conditions.}, }
@article {pmid40527464, year = {2025}, author = {Titelboim, D and Dedman, CJ and Hodgson, RP and Knowles, LS and Liu, X and Lenzi, L and Tudor, J and Vamos, E and Rickaby, REM}, title = {Exogenous diatoms ameliorate thermal bleaching of symbiont bearing benthic foraminifera.}, journal = {Proceedings. Biological sciences}, volume = {292}, number = {2049}, pages = {20250596}, doi = {10.1098/rspb.2025.0596}, pmid = {40527464}, issn = {1471-2954}, support = {/ERC_/European Research Council/International ; //H2020 Marie Skłodowska-Curie Actions/ ; }, mesh = {*Foraminifera/physiology ; *Symbiosis ; *Diatoms/physiology ; Temperature ; Hot Temperature ; }, abstract = {Many marine calcifiers engage in obligatory algal symbiosis which is threatened by ocean warming. Large benthic foraminifera are prominent carbonate and sand producers in shallow environments with a wide range of species-specific thermal tolerances assumed to be related to their diverse algal symbionts. We examine two diatom-bearing benthic foraminifera species which differ in their thermal physiological tolerance and symbiont community composition. Our findings demonstrate that the less thermally tolerant host, Amphistegina lobifera Larsen, 1976, 'shuffles' the dominant players of the internal symbiont community with increasing temperature while the more thermally tolerant host Pararotalia calcariformata McCulloch, 1977, is dominated by Arcocellulus cornucervis Medlin, 1990, at all temperatures. Although this diatom species was present in A. lobifera from all treatments, it became more abundant only under the most severe temperature stress. Symbionts were isolated from the thermally tolerant foraminifera P. calcariformata, with only one species of symbiont surviving at 35°C, while the others failed to survive at 32°C. Supplementation of isolated symbionts reduced bleaching of A. lobifera under heat stress suggesting that while increased temperature creates shuffling at the family level, heat tolerance of the holobiont is related to changes at the species level of the symbiont algae.}, }
@article {pmid40526476, year = {2025}, author = {Tignat-Perrier, R and Bramanti, L and Giordano, B and van de Water, JAJM and Manea, E and Allemand, D and Ferrier-Pagès, C}, title = {Microbiome Dynamics in Early Life Stages of the Precious Mediterranean Red Coral Corallium rubrum.}, journal = {Environmental microbiology reports}, volume = {17}, number = {3}, pages = {e70127}, doi = {10.1111/1758-2229.70127}, pmid = {40526476}, issn = {1758-2229}, support = {//Fondation CHANEL/ ; //Government of the Principality of Monaco/ ; //Prince Albert II of Monaco Foundation/ ; //COST Action CA20102 Marine Animal Forests of the World/ ; 101062275//Marie Curie Actions, the project RESTORE/ ; }, mesh = {Animals ; *Anthozoa/microbiology/growth & development ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Larva/microbiology ; Phylogeny ; Mediterranean Sea ; Coral Reefs ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial colonisation in the early life stages of corals plays a critical role in their fitness, but the mechanisms by which microbial symbionts are acquired-whether from parental colonies, the environment, or both-remain poorly understood, particularly in octocorals. Although they are the second most abundant coral group on tropical reefs and contribute significantly to the structural complexity of Mediterranean coral reefs, their microbial dynamics are largely unexplored. In this study, we investigated the acquisition of the bacterial microbiota in the red coral Corallium rubrum, a precious coral. By analysing the composition of the bacterial community at different early life stages, including newly released larvae, 5- and 10-day-old larvae, 3-month-old settlers, 1-year-old recruits and 3-year-old juveniles, we are gaining new insights into the development of its microbiome. Using a direct PCR-based 16S rRNA metabarcoding approach, we performed high-resolution microbiome analyses at the level of individual larvae and settlers. Our results show that the bacterial microbiota of C. rubrum matures after the first year of life. Notably, dominant symbionts, such as Spirochaetaceae and BD72BR169 Gammaproteobacteria, were absent in larvae, settlers and recruits, suggesting that they were likely acquired horizontally from the environment. These findings improve our understanding of the microbial colonisation and development of C. rubrum and shed light on the potential role of its bacterial community in holobiont function.}, }
@article {pmid40523116, year = {2025}, author = {Preising, SE and Heck, ML}, title = {Potato Leafroll Virus in the Aphid Holobiont: Interactions Shaping Vector Biology.}, journal = {Annual review of virology}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-virology-092623-103226}, pmid = {40523116}, issn = {2327-0578}, abstract = {The aphid holobiont includes the aphid host and aphid-associated microorganisms, including pathogenic plant viruses. The polerovirus potato leafroll virus (PLRV) is transmitted exclusively by aphids and one of the most economically significant viruses infecting potatoes. In potato plants, PLRV infection results in stunting, leaf rolling, and net necrosis on tubers. PLRV threatens global potato cultivation, especially in regions where vector management options are limited. In this review, we describe the effect of PLRV on the aphid holobiont and highlight studies of the evolutionary and mechanistic ways in which PLRV influences the aphid holobiont during plant infection. We explore ideas to address the pressing need for aphid and PLRV management strategies by targeting interactions within the holobiont. Approaching PLRV-aphid interactions research through the lens of the holobiont allows a systems-level analysis of host, plant, and microbial effects that influence virus transmission. In turn, this knowledge can be leveraged to develop new virus management strategies.}, }
@article {pmid40508259, year = {2025}, author = {Gorvel, S and Walter, B and Taylor, JD and Unsworth, RKF}, title = {Functional Roles of the Seagrass (Zostera marina) Holobiont Change with Plant Development.}, journal = {Plants (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/plants14111584}, pmid = {40508259}, issn = {2223-7747}, abstract = {Seagrass meadows play a critical role in biogeochemical cycling, especially in nitrogen and sulphur processes, driven by their associated microbiome. This study provides a novel functional analysis of microbial communities in seagrass (Zostera marina) rhizosphere and endosphere, comparing seedlings and mature plants. While nitrogen-fixing bacteria are more abundant in seedlings, mature plants exhibit greater microbial diversity and stability. Sediment samples show higher microbial diversity than roots, suggesting distinct niche environments in seagrass roots. Key microbial taxa (sulphur-oxidizing and nitrogen-cycling bacteria) were observed across developmental stages, with rapid establishment in seedlings aiding survival in sulphide-rich, anoxic sediments. Chromatiales, which oxidize sulphur, are hypothesized to support juvenile plant growth by mitigating sulphide toxicity, a key stressor in early development. Additionally, sulfate-reducing bacteria (SRB), though potentially harmful due to H2S production, may also aid in nitrogen fixation by producing ammonium. The study underscores the dynamic relationship between seagrass and its microbiome, especially the differences in microbial community structure and function between juvenile and mature plants. The study emphasizes the need for a deeper understanding of microbial roles within the seagrass holobiont to aid with Blue Carbon stores and to improve restoration success, particularly for juvenile plants struggling to establish effective microbiomes.}, }
@article {pmid40499768, year = {2025}, author = {Levasseur, M and Trac, A and Clavereau, I and Zannini, F and Estevez, Y and Amusant, N and Gelhaye, É and Pollet, N and Houël, E and Touboul, D and Eparvier, V}, title = {Reverse chemical ecology to study the defense of the plant host Sextonia rubra and the chemical mediators of its endophyte Fusarium falciforme against phytopathogen Trametes versicolor.}, journal = {Phytochemistry}, volume = {}, number = {}, pages = {114577}, doi = {10.1016/j.phytochem.2025.114577}, pmid = {40499768}, issn = {1873-3700}, abstract = {Sextonia rubra is a tropical tree endemic to the Guiana Shield and the Brazilian Amazon. Despite its renowned wood durability, it remains susceptible to degradation by white-rot fungi such as Trametes versicolor. To mitigate biotic stresses, plants can rely on their associated microbial communities, including endophytes, which play a crucial role in their defense mechanisms. In this study, we explored the cultivable microbiota of S. rubra, considering it a holobiont. Endophytic strains were isolated from the bark, sapwood and heartwood of S. rubra, and metabolome were extracted. We used a reverse chemical ecology approach to elucidate the mechanisms underlying these extracts' fungicidal activity. In this context, glutathione-S-transferases (GST), key detoxification enzymes of the lignivorous fungus T. versicolor, were chosen as targets. GST tests confirmed the presence of antifungal compounds in extracts from 13 of the 152 endophytes. Two isolates of Fusarium falciforme and one isolate of Fusarium graminearum were selected for co-culture experiments with T. versicolor. A comprehensive metabolic analysis of the confrontation zones using RPLC-ESI(+)-HRMS/MS and molecular networking revealed that the antifungal activity against T. versicolor was primarily mediated by cyclopeptides, and the observed contact inhibition was attributed to fusarins. These findings shed new light on the role of endophytic fungi in the chemical defense strategies of S. rubra, highlighting their potential as a source of bioactive compounds with antifungal properties.}, }
@article {pmid40480235, year = {2025}, author = {Glynn, VM and de Barros Marangoni, LF and Guglielmetti, M and Tapia, ER and Ali, V and Quintero, H and Rodriguez Guerra, EC and Yuval, M and Kline, DI and Leray, M and Connolly, SR and Barrett, RDH}, title = {The role of holobiont composition and environmental history in thermotolerance of Tropical Eastern Pacific corals.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.05.035}, pmid = {40480235}, issn = {1879-0445}, abstract = {Coral reefs support approximately 25% of all marine life, making it essential to understand the factors impacting their ability to withstand climate change. Corals' response mechanisms encompass both the host's own potential and that of a diverse microbial community, collectively known as the holobiont. Research investigating how these co-evolved taxa affect each other during thermal stress has revealed both the vulnerability and resilience of coral reefs, but the precise mechanisms underlying different bleaching trajectories are still poorly understood. We implemented a standardized acute thermal stress assay to investigate how seasonal upwelling in Panama's Tropical Eastern Pacific (TEP) influences Pocillopora coral's host-microbiome configurations, and we tested holobionts' resistance to increasing temperatures. Despite little host genetic differentiation, algal community shifts were modulated by both region and genetic lineage. This pattern strongly contrasted with temperature-driven dysbiosis for the prokaryotic community. Host stress responses differed among regions during acute thermal stress. Regional variation in total antioxidant capacity suggested that corals from the region with seasonal upwelling experience more stressful baseline conditions, which may contribute to their higher predicted thermal thresholds as estimated via host protein concentrations. Furthermore, shifts in algal microbiomes were associated with changes in host thermotolerance, as captured by host physiology and oxidative metabolism, suggesting a possible link between microbiome composition and host physiological performance. By leveraging the natural laboratory created by Panama's TEP, we demonstrate that coral holobionts from nearby gulfs with different thermal dynamics differ in their ability to withstand thermal stress, providing new insights into the factors driving coral thermotolerance.}, }
@article {pmid40471452, year = {2025}, author = {Turanoglu, C and Ancel, H and Lann, CL and Van Baaren, J and Bazin, O and Declerck, S and Fort, F and Breton, TF and Vandenkoornhuyse, P and Mony, C}, title = {Functional traits of Asteraceae species vary with arbuscular mycorrhizal fungal identity and phylogeny.}, journal = {Mycorrhiza}, volume = {35}, number = {3}, pages = {40}, pmid = {40471452}, issn = {1432-1890}, mesh = {*Mycorrhizae/physiology/classification/genetics ; *Phylogeny ; *Asteraceae/microbiology/physiology/growth & development ; Plant Roots/microbiology/growth & development ; Phenotype ; Symbiosis ; }, abstract = {Plants interact closely with arbuscular mycorrhizal (AM) fungi. They allocate photosynthates to AM fungi in exchange for nutrients, thereby influencing plant fitness. Although plant phenotypes result from multiple traits constrained by trade-offs, the effects of AM fungi on plants are often studied using one trait. Plant response to AM fungi therefore needs to be analysed using multiple traits. Four Asteraceae species were inoculated with ten AM fungal strains using a factorial design in the greenhouse. The effect of AM fungal inoculation and their taxonomic identity on plants vegetative and reproductive traits were assessed. The predictability of the effects was evaluated based on AM fungal phylogenetic relatedness. The effect of the inoculation depended on the trait considered. Compared with the non-inoculated control, biomass allocation to roots decreased, while allocations to shoots or reproduction increased depending on the AM fungi or the plant. Significant differences were observed among AM fungi inoculates used, whether looking at separate traits, trade-offs between vegetative or reproductive growth, and the trait syndrome. In Centaurea cyanus, changes in plant phenotype were associated with the phylogenetic distance between AM fungi. These results underline the importance of using multi-trait approaches to understand AM fungal effects on plant phenotype. In accordance with the holobiont concept, the outcomes of this interaction depended on both the host plant and the AM fungus involved. It contributes to a better understanding of the biological effectors shaping the reaction norm (i.e., the range of phenotypic variation of a given host genotype) within the plant holobiont.}, }
@article {pmid40467557, year = {2025}, author = {Alexander, A and Iglesias-Carrasco, M and Lozano, M and Garcia-Gonzalez, F}, title = {Monogamy removes constraints on reproductive tissue investment imposed by intense sexual selection.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {19646}, pmid = {40467557}, issn = {2045-2322}, support = {CGL2016-76173-P//Ministerio de Ciencia e Innovación/ ; }, mesh = {Animals ; Male ; Female ; Reproduction/physiology ; *Sexual Selection ; *Sexual Behavior, Animal/physiology ; Biological Evolution ; *Mating Preference, Animal ; }, abstract = {A key factor influencing the reproductive success and fitness of an individual is the allocation of resources to reproductive tissue. Previous research has documented positive influences of sexual selection on the evolution of male traits such as testes size. However, few studies have focused on whether sexual selection shapes overall reproductive tissue investment patterns, and even fewer have studied it in both males and females. Furthermore, whether the ecological/demographic context modulates these effects is not known. We used experimental evolution on an insect model system to assess the independent and interactive effects of sexual selection intensity (intense [polygamy] vs. relaxed [monogamy]) and metapopulation structure (absent vs. present) on reproductive tissue investment in both sexes. Counterintuitively, we found that both males and females evolving under monogamy had higher relative reproductive tissue investment than individuals evolving under polygamy. We found no independent effect of metapopulation structure or any interactive effect with sexual selection on reproductive tissue investment of either sex. Our findings suggest that trade-offs between pre- and post-copulatory sexual selection may constrain reproductive tissue investment under intense sexual selection, and that selection under monogamy removes this constraint. Generally, our study underscores the complexities underpinning the evolution of reproductive allocation strategies.}, }
@article {pmid40467297, year = {2025}, author = {Waterworth, SC and Egbert, S and Sorensen, J and O'Keefe, BR and Beutler, JA}, title = {A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont.}, journal = {Environmental microbiology}, volume = {27}, number = {6}, pages = {e70112}, doi = {10.1111/1462-2920.70112}, pmid = {40467297}, issn = {1462-2920}, support = {//Natural Sciences and Engineering Research Council of Canada/ ; ZIA BC 011471/CA/NCI NIH HHS/United States ; ZIA BC 011469/CA/NCI NIH HHS/United States ; }, mesh = {*Lichens/microbiology/classification/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Biosynthetic Pathways/genetics ; Phylogeny ; Secondary Metabolism ; Metagenomics ; Metagenome ; Symbiosis ; }, abstract = {Lichens are pioneer species in several ecosystems, and as such are found in a variety of geographic regions and environments. Here, inspection of metagenomic data from 794 lichen samples from 34 countries reveals the presence of a complex holobiont harbouring remarkable biosynthetic capabilities, particularly in the bacterial consortia, a component that has been somewhat underappreciated. While bacteria were consistently present, their abundance varied among lichen taxa. Common bacterial genera included Microbacterium, Terribacillus, and JABEUN01 (an Acidimicrobiaceae bacterium awaiting Latin binomial naming assignment) albeit in low abundance. Lichenihabitans and Sphingomonas genera were moderately abundant, present in approximately 30% of samples, and exhibited an enrichment in the number of biosynthetic gene clusters (BGCs) predicted to encode secondary metabolites (biosynthetic potential). We found that both fungal and bacterial biosynthetic repertoires appeared to follow genus-specific patterns but that there was greater relative homogeneity of BGCs in the fungal genera. The substantial biosynthetic diversity within lichen holobionts is evident in our findings, with the lichen-associated bacteria emerging as a promising potential source for sustainable drug discovery.}, }
@article {pmid40463963, year = {2025}, author = {Coblentz, M and Evans, JD and Kothe, CI and Mak, T and Valerón, NR and Chwalek, P and Wejendorp, K and Garg, S and Pless, L and Mak, S and Sörensen, PM and Jahn, LJ and Ekblaw, A}, title = {Food fermentation in space: Opportunities and challenges.}, journal = {iScience}, volume = {28}, number = {4}, pages = {112189}, pmid = {40463963}, issn = {2589-0042}, abstract = {Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here, we investigate whether food fermentation in space is possible and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days and compared it with two earthbound controls. Based on environmental metadata, shotgun metagenomics, whole-genome sequencing, untargeted metabolomics, colorimetry, and sensory analysis, we found that overall, the space miso is recognizable as a miso, indicating fermentation in space is possible. We also found some key microbiological and sensory differences in the space miso, which suggest distinctive features of the space environment. These findings can be harnessed to create more flavorful, nourishing foods for long-term space missions and invite further research questions across science, health, technology, and society.}, }
@article {pmid40454874, year = {2025}, author = {Pfister, CA and Berlinghof, J and Bogan, M and Cardini, U and Gobet, A and Hamon-Giraud, P and Hart, J and Jimenez, N and Siegel, A and Stanfield, E and Vallet, M and Leblanc, C and Rousseau, C and Thomas, F and Stock, W and Dittami, SM}, title = {Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0099624}, doi = {10.1128/msphere.00996-24}, pmid = {40454874}, issn = {2379-5042}, abstract = {UNLABELLED: Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana-associated microbes, while only Ascophyllum nodosum-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.<br><br>IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.}, }
@article {pmid40450335, year = {2025}, author = {Cerca, J and Díaz, PJ and Goubert, C and Yang, H and Bieker, VC and Fernández-Mazuecos, M and Vargas, P and Schley, R and Li, S and Guevara-Andino, JE and Petersen, B and Petersen, G and Sinha, NR and Nielsen, LR and Leebens-Mack, JH and Rivas-Torres, G and Rieseberg, LH and Martin, MD}, title = {No evidence of transposable element bursts in the Galápagos Scalesia adaptive radiation despite hybridization, diversification and ecological niche shifts.}, journal = {Mobile DNA}, volume = {16}, number = {1}, pages = {23}, pmid = {40450335}, issn = {1759-8753}, abstract = {Transposable elements (TEs) have been hypothesized to play a pivotal role in driving diversification by facilitating the emergence of novel phenotypes and the accumulation of divergence between species. Hybridization and adaptation to novel niches have been proposed to destabilize mechanisms constraining TE proliferation, potentially inducing a 'TE burst' that promotes TE accumulation on the genome. The rapid speciation and ecological diversification characteristic of adaptive radiations offer a unique opportunity to examine the link between TE accumulation and speciation, diversification, hybridization and adaptation. Here, focusing on all 15 species of the genus Scalesia (Asteraceae), a radiation endemic to the Galápagos Islands, we test whether diversification, hybridization, or shifts in ecological niche are associated with changes in TE accumulation in genomes. Our analyses reveal little to no variation in TE accumulation among Scalesia species nor its hybrid populations. Shifts in ecological niches, linked to climatic variation, did not result in discernible changes in TE accumulation, a surprising finding given the anticipated selective pressure imposed by aridity, a factor often linked to genome size reduction. We found no distinct patterns in the temporal accumulation of TEs, and no effects at the class or superfamily level. Our findings suggest that while TEs may play a key role in evolution at the locus level, their macroevolutionary association with diversification or speciation appears weak. Rather than actively driving evolutionary diversification, TEs may simply be'along for the ride.}, }
@article {pmid40448582, year = {2025}, author = {Hall, LA and Scott, KD and Webster, N and Kerkhof, LJ and Häggblom, MM}, title = {Dehalogenating Desulfoluna spp. are Ubiquitous in Host-Specific Sponge Microbiomes of the Great Barrier Reef.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wraf113}, pmid = {40448582}, issn = {1751-7370}, abstract = {Marine sponge holobionts are important contributors to numerous biogeochemical cycles, including the natural organohalogen cycle. Sponges produce diverse brominated secondary metabolites, which select for a population of anaerobic debrominating bacteria within the sponge body. Sponge microbiomes can be host-specific, but the selection and host-specificity of debrominating bacteria are unknown currently. In this study, we used nanopore long-read sequencing of nearly full-length ribosomal RNA operons to evaluate host-specificity of the Great Barrier Reef sponge microbiomes at the strain level and to determine if host specificity extends to sponge-associated dehalogenating bacteria. Reductive debromination activity was observed in anaerobic enrichment cultures established from all Great Barrier Reef sponges. Even though other bacterial symbionts of interest, including Nitrospira spp. and Ca. Synechococcus spp. demonstrated strong host-specificity, Desulfoluna spp., a key sponge-associated dehalogenating bacterium showed no evidence of host-specificity. This suggests different modes of transmission and/or retention of different members of the sponge microbiome residing within the same host species. These findings expand our understanding of how sponge microbiomes are assembled and the relationship between the host and individual bacterial strains.}, }
@article {pmid40441134, year = {2025}, author = {Huffmyer, AS and Wong, KH and Becker, DM and Strand, E and Mass, T and Putnam, HM}, title = {Shifts and critical periods in coral metabolism reveal energetic vulnerability during development.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2025.05.013}, pmid = {40441134}, issn = {1879-0445}, abstract = {Climate change accelerates coral reef decline and jeopardizes recruitment essential for ecosystem recovery. Adult corals rely on a vital nutritional exchange with their symbiotic algae (Symbiodiniaceae), but the dynamics of reliance from fertilization to recruitment are understudied. We investigated the physiological, metabolomic, and transcriptomic changes across 13 developmental stages of Montipora capitata, a coral in Hawai'i that inherits symbionts from parent to egg. We found that embryonic development depends on maternally provisioned mRNAs and lipids, with a rapid shift to symbiont-derived nutrition in late developmental stages. Symbiont density and photosynthesis peak in swimming larvae to fuel pelagic dispersal. By contrast, respiratory demand increases significantly during metamorphosis and settlement, reflecting this energy-intensive morphological reorganization. Symbiont proliferation is driven by symbiont ammonium assimilation in larval stages with little evidence of nitrogen metabolism in the coral host. As development progresses, the host enhances nitrogen sequestration, regulating symbiont populations, and ensuring the transfer of fixed carbon to support metamorphosis, with both metabolomic and transcriptomic indicators of increased carbohydrate availability. Although algal symbiont community composition remained stable, bacterial communities shifted with ontogeny, associated with holobiont metabolic reorganization. Our study reveals extensive metabolic changes during development with increasing reliance on symbiont nutrition. Metamorphosis and settlement emerge as critical periods of energetic vulnerability to projected climate scenarios that destabilize symbiosis. This highly detailed characterization of symbiotic nutritional exchange during sensitive early life stages provides essential knowledge for understanding and forecasting the function of nutritional symbioses and, specifically, coral survival and recruitment in a future of climate change.}, }
@article {pmid40434804, year = {2025}, author = {Kohl, KD}, title = {Through the microbial looking glass: our shifting understanding of the holobiont and microbes as mediators of organismal biology.}, journal = {Integrative and comparative biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/icb/icaf059}, pmid = {40434804}, issn = {1557-7023}, abstract = {Our understanding and appreciation for the role of microbial symbioses in the evolution and speciation of macro-organisms has fluctuated over time. Even in contemporary times our collective understanding of the microbiome has shifted from an adaptationist focus on beneficial interactions, to better incorporate ecological, stochastic, and neutral interactions. From the 1900s to today, the holobiont concept has repeatedly been proposed as a guiding hypothesis and principle. However, it has also received continuous dispute and critique, often regarding the universality of processes, fidelity of partnerships, and lack of explicit delineation of holobionts from individual units. Modern interpretation of the holobiont is meant to be an extension of multilevel selection theory, and natural selection need not always act at this collective level. The solution may be for scientists to remove conceptual mind blocks and consider a hazy, flexible, and dynamic definition of the holobiont. Such a frame of mind will be similar to the lack of clarity generally surrounding the biological species concept - a muddled yet unifying concept. Viewing the world through the "microbial looking glass" of the holobiont will offer a more accurate understanding of biological systems and will facilitate research progress.}, }
@article {pmid40405248, year = {2025}, author = {Cornejo-Granados, F and Gallardo-Becerra, L and Romero-Hidalgo, S and Lopez-Zavala, AA and Cota-Huízar, A and Cervantes-Echeverría, M and Sotelo-Mundo, RR and Ochoa-Leyva, A}, title = {Host genome drives the microbiota enrichment of beneficial microbes in shrimp: exploring the hologenome perspective.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {50}, pmid = {40405248}, issn = {2524-4671}, support = {Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; Fronteras de la Ciencia CF2019-G-263986//Consejo Nacional de Innovaci&#xf3;n, Ciencia y Tecnolog&#xed;a/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; IN219723//Direcci&#xf3;n General de Asuntos del Personal Acad&#xe9;mico (DGAPA)/ ; }, abstract = {BACKGROUND: Pacific Whiteleg shrimp (Litopenaeus vannamei) is an important model for breeding programs to improve global aquaculture productivity. However, the interaction between host genetics and microbiota in enhancing productivity remains poorly understood. We investigated the effect of two shrimp genetic lines, Fast-Growth (Gen1) and Disease-Resistant (Gen2), on the microbiota of L. vannamei.<br><br>RESULTS: Using genome-wide SNP microarray analysis, we confirmed that Gen1 and Gen2 represented distinct genetic populations. After confirming that&#xa0;the rearing pond did not significantly influence the microbiota composition, we determined that genetic differences explained 15.8% of the microbiota variability, with a stronger selective pressure in the hepatopancreas than in the intestine. Gen1, which exhibited better farm productivity, fostered a microbiota with greater richness, diversity, and resilience than Gen2, along with a higher abundance of beneficial microbes. Further, we demonstrated that a higher abundance of beneficial microbes was associated with healthier shrimp vs. diseased specimens, suggesting that Gen1 could improve shrimp's health and productivity by promoting beneficial microbes. Finally, we determined that the microbiota of both genetic lines was significantly different from their wild-type counterparts, suggesting farm environments and selective breeding programs strongly alter the natural microbiome.<br><br>CONCLUSIONS: This study highlights the importance of exploring the hologenome perspective, where integrating host genetics and microbiome composition can enhance breeding programs and farming practices.}, }
@article {pmid40402820, year = {2025}, author = {Alberdi, A and Limborg, MT and Groussin, M and Aizpurua, O and Gilbert, MTP}, title = {Metagenomic spaces: a framework to study the effect of microbiome variation on animal ecology and evolution.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voaf063}, pmid = {40402820}, issn = {1420-9101}, abstract = {Microorganisms are essential for the normal functioning of most vertebrates. Hence, identifying and measuring the factors that shape host-associated microbial communities is necessary to understand ecological and evolutionary implications of host-microbiota associations. We propose a framework, built on the so-called 'metagenomic space' concept, which incorporates multiple definitions and quantifiable features relating to the variation of microbial communities that are associated with vertebrate hosts. By drawing on diverse theories and concepts developed in different fields of biology, our framework sets a conceptual landscape that transcends the mere characterisation of microbial communities. This provides the basis to study more complex attributes, such as 'potential' and 'fundamental metagenomic spaces', 'metagenomic plasticity' and 'metagenomic evolvability', which we argue are essential for understanding the microbial contribution to vertebrate host ecology and evolution-and hold considerable promise for advancing applied research and innovation. In doing so, we hope to contribute to an improved understanding of the impact of spatio-temporal variation of vertebrate host-microbiota associations, and inspire new approaches to address testable hypotheses related to ecological, evolutionary and applied processes.}, }
@article {pmid40399165, year = {2025}, author = {Hussain, M and Heuer, H}, title = {Rice diterpenoids rewire microbiome to fight plant-parasitic nematodes.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2025.05.001}, pmid = {40399165}, issn = {1471-5007}, abstract = {Microorganisms associated with plant roots can protect the host from plant-parasitic nematodes. Kudjordjie et al. recently demonstrated that rice diterpenoid phytoalexins are involved in the assembly of beneficial root microbiota for nematode suppression. The discovery of phytochemical-mediated modulation of plant-microbe interactions offers an innovative approach to sustainable nematode management.}, }
@article {pmid40397361, year = {2025}, author = {Lin, YY and Ho, HC and Chou, JY}, title = {Effects of lichen symbiotic bacteria-derived indole-3-acetic acid on the stress responses of an algal-fungal symbiont.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {40397361}, issn = {1678-4405}, support = {MOST 111-2621-B-018-001//National Science Council/ ; }, abstract = {Lichens, comprising filamentous fungi and algae/cyanobacteria engaged in mutualistic symbiosis, exhibit remarkable adaptability to environmental challenges. While fungi safeguard algae from dry conditions, their ability to mitigate other stresses remains uncertain. Additionally, the functions of coexisting bacteria within lichen communities remain relatively unexplored. This study investigates the potential of indole-3-acetic acid (IAA) as a stress-response signaling molecule in lichen symbiosis. We subjected IAA-treated monocultures of algae and co-cultures of the fungal-algal complex to various stress conditions. IAA's role in bolstering resilience was evident, as demonstrated by the release of IAA (0-500 µM) by bacteria isolated from the lichen Parmelia tinctorum. This IAA was subsequently utilized by the lichen photobionts to alleviate oxidative stress. IAA acted as a communication signal, priming algal cells to defend against impending stressors. Further microscopic examinations unveiled that only the fibrous extensions were exposed in fungal cells that were in direct physical contact with viable algal cells. Co-cultivation and subsequent microscopic observations revealed that the algal cells were protected from diverse stressors by a barrier of fungal hyphae. Our findings underscore the significance of IAA in enhancing stress resistance within the context of lichen symbiosis, thereby advancing our understanding of the adaptability of these unique organisms. Further exploration of bacterial functions in lichen symbiosis holds promise for uncovering novel insights into their ecology and biology.}, }
@article {pmid40387602, year = {2025}, author = {Bonacolta, AM and Krause-Massaguer, J and Unuma, T and Del Campo, J}, title = {The Sea Cucumber-Infecting Parasite Apostichocystis gudetama gen. nov. sp. nov. Expands Marine-Host-Specific Clade of Apicomplexans.}, journal = {The Journal of eukaryotic microbiology}, volume = {72}, number = {3}, pages = {e70013}, pmid = {40387602}, issn = {1550-7408}, support = {//University of Miami/ ; PID2020-118836GA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021 SGR 00420//Departament de Recerca i Universitats de la Generalitat de Catalunya/ ; }, mesh = {Animals ; Phylogeny ; *Sea Cucumbers/parasitology ; *Apicomplexa/genetics/classification/isolation &amp; purification ; Host Specificity ; Female ; Host-Parasite Interactions ; Genome, Mitochondrial ; }, abstract = {Unknown ellipsoid bodies, later classified as apicomplexan cysts, are prevalent in the ovaries of Japanese sea cucumbers (Apostichopus japonicus), where they can lead to lower fecundity in infected individuals and adverse effects on wild populations as well as aquaculture efforts for this endangered species. Apicomplexans are widespread and essential to marine environments, where they can affect the health and fitness of host populations. We performed genomic sequencing of recovered cysts to gain more ecological and evolutionary information on this parasite. We recovered this apicomplexan's complete nuclear ribosomal RNA (rrn) operon, the entire mitochondrial genome, and a partial apicoplast (relic chloroplast) genome. The rrn operon phylogeny revealed this parasite as being closely related to coccidian-like parasites of marine fish (ichthyocolids) and cnidarians (corallicolids), while organelle phylogenomics hint at a closer relation to the protococcidian Eleutheroschizon. Using this new phylogenetic context and previous morphological descriptions, we describe this parasite as Apostichocystis gudetama gen. nov. sp. nov. Mining available microbiomes reveal the presence of Apostichocystis spp. beyond its host range, alluding to other potential hosts or cryptic, closely related lineages. Its phylogenetic placement has important implications concerning the evolution of parasitism within Apicomplexa and the divergence of a marine-host-specific clade of coccidian-like parasites.}, }
@article {pmid40385307, year = {2025}, author = {McLaren, GC and Farrell, MV and Shikuma, NJ and Tran, C}, title = {Photosynthetic dependence and filament production in physical bacterial-Symbiodiniaceae interactions.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf070}, pmid = {40385307}, issn = {2730-6151}, abstract = {The cnidarian microbiome consists of a wide variety of beneficial microbes that play vital roles in maintaining and fortifying host health. Photosynthesis from symbiotic dinoflagellates (in the family Symbiodiniaceae) is crucial for their symbiosis establishment with the cnidarian host. Although more is known regarding interactions between the host and its associated bacteria and dinoflagellates, there has been little investigation into the relationship between the two microbes themselves and whether photosynthesis plays a role. Through two different methods of photosynthetic inhibition of dinoflagellates (incubation in the dark or pre-treatment with a photosystem II inhibitor), we investigated how pathogenic versus beneficial bacteria physically interact with three Symbiodiniaceae strains (symbiotic and free-living). The beneficial bacterium Tritonibacter mobilis appears to interact with photosynthesizing algae only. In the absence of photosynthesis, little to no physical interactions were observed between Symbiodiniaceae and T. mobilis. Bacterial congregation around individual dinoflagellate cells was significantly lower when photosynthesis was impaired, suggesting photosynthesis is a key facilitator of interactions between T. mobilis and all three Symbiodiniaceae strains. We also investigated whether photosynthesis affects interactions between Symbiodiniaceae and the pathogen Vibrio alginolyticus. Although no discernable impacts of photosynthetic inhibition were observed with the pathogen, scanning electron microscopy uncovered various mechanisms of interaction between Symbiodiniaceae and both bacteria, one of which includes the production of filaments not previously described. Overall, our research highlights the importance of photosynthesis in initiating interactions between bacteria and both free-living and symbiotic dinoflagellates, and opens a door to new questions regarding cell-surface interactions among individual microbes.}, }
@article {pmid40382475, year = {2025}, author = {Yang, Q and Downey, R and Stark, JS and Johnstone, GJ and Mitchell, JG}, title = {The Microbial Ecology of Antarctic Sponges.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {44}, pmid = {40382475}, issn = {1432-184X}, mesh = {*Porifera/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Archaea/classification/genetics/isolation &amp; purification ; Ecosystem ; Fungi/classification/genetics/isolation &amp; purification ; }, abstract = {Microbial communities in Antarctic marine sponges have distinct taxonomic and functional profiles due to low temperatures, seasonal days and nights, and geographic isolation. These sponge holobionts contribute to nutrient cycling, structural habitat formation, and benthic ecosystem resilience. We review Antarctic sponge holobiont knowledge, integrating culture-based and molecular data across environmental and taxonomic gradients. Although microbiome data exist for only a fraction of the region's 593 known sponge species, these hosts support diverse symbionts spanning at least 63 bacterial, 5 archaeal, and 6 fungal phyla, highlighting the complexity and ecological significance of these understudied polar microbiomes. A conserved core microbiome, dominated by Proteobacteria, Bacteroidetes, Nitrospinae, and Planctomycetes, occurs across Antarctic sponges, alongside taxa shaped by host identity, depth, and environment. Metagenomic data indicate microbial nitrogen cycling, chemoautotrophic carbon fixation, and stress tolerance. Despite these advances, major knowledge gaps remain, particularly in deep-sea and sub-Antarctic regions, along with challenges in taxonomy, methodological biases, and limited functional insights. We identify key research priorities, including developing standardised methodologies, expanded sampling across ecological and depth gradients, and integrating multi-omics with environmental and host metadata. Antarctic sponge holobionts provide a tractable model for investigating microbial symbiosis, functional adaptation, and ecosystem processes in one of Earth's most rapidly changing marine environments.}, }
@article {pmid40375625, year = {2025}, author = {Maillet, L and Norest, M and Kautsky, A and Geraci, A and Oddo, E and Troia, A and Guillerm-Erckelboudt, AY and Falentin, C and Rousseau-Gueutin, M and Chèvre, AM and Istace, B and Cruaud, C and Belser, C and Aury, JM and Schicchi, R and Frachon, L and Bartoli, C}, title = {Plant Genetic Bases Associated With Microbiota Descriptors Shed Light Into a Novel Holobiont Generalist Genes Theory.}, journal = {Environmental microbiology}, volume = {27}, number = {5}, pages = {e70108}, pmid = {40375625}, issn = {1462-2920}, support = {//Commissariat &#xe0; l'Energie Atomique et aux Energies Alternatives (CEA)" and "France G&#xe9;nomique (ANR-10-INBS-09-08)"/ ; 101039541/ERC_/European Research Council/International ; //Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Ecosymb/ ; }, mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Fungi/genetics/classification/isolation &amp; purification ; *Brassica rapa/microbiology/genetics ; Rhizosphere ; Plant Roots/microbiology ; Symbiosis ; Italy ; France ; Genome, Plant ; }, abstract = {Plants as animals are associated with a cortege of microbes influencing their health, fitness and evolution. Scientists refer to all living organisms as holobionts, complex genetic units that coevolve simultaneously. This is what has been recently proposed as the hologenome theory. This exciting theory has important implications on animal and plant health; however, it still needs consistent proof to be validated. Indeed, holobionts are still poorly studied in their natural habitats where coevolution processes occur. Compared to animals, wild plant populations are an excellent model to explore the hologenome theory. These sessile holobionts have coevolved with their microbiota for decades, and natural selection and adaptive processes acting on wild plants are likely to regulate the plant-microbe interactions. Here, we conducted a microbiota survey, plant genome sequencing and genome-environmental analysis (GEA) of 26 natural populations of the plant species Brassica rapa. We collected plants over two seasons in Italy and France and analysed the root and rhizosphere microbiota. When conducting GEA, we evidenced neat peaks of association correlating with both fungal and bacterial microbiota. Surprisingly, we found 13 common genes between fungal and bacterial diversity descriptors that we referred to under the name of holobiont generalist genes (HGGs).}, }
@article {pmid40360784, year = {2025}, author = {Voolstra, CR and Schlotheuber, M and Camp, EF and Nitschke, MR and Szereday, S and Bejarano, S}, title = {Spatially restricted coral bleaching as an ecological manifestation of within-colony heterogeneity.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {740}, pmid = {40360784}, issn = {2399-3642}, support = {468583787//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Anthozoa/physiology/microbiology ; Coral Reefs ; *Coral Bleaching ; Symbiosis ; Ecosystem ; Dinoflagellida/physiology ; }, abstract = {Coral bleaching is a widespread stress response of reef-building corals to elevated sea temperatures, resulting in the loss of symbiotic algae and often leading to coral death and reef degradation. Although coral bleaching occurs globally, not all reefs, species, colonies, or polyps bleach equally. Understanding intra-colony bleaching heterogeneity is crucial to anticipate the extent of coral loss at 2°C warming and harness variability to inform restorative interventions. Partially bleached coral colonies are commonly documented yet rarely tracked to determine whether they reflect ecologically distinct heterogeneity (e.g., in thermal tolerance) or eventually bleach completely. Focusing on bleaching that appears restricted to certain areas within a coral colony, we examine its putative basis in the spatial variability of the holobiont. A coral's three-dimensional structure creates mosaics of microenvironments. Adaptations to these microenvironments are underpinned by intra-colony differences in Symbiodiniaceae association, microbiome assemblage, and nutritional status, giving rise to microhabitats. Genetic mosaicism and epigenetic changes further contribue to intra-colony phenotypic heterogeneity. We pinpoint methodologies to align spatially restricted bleaching to different forms of coral surface heterogeneity, examine the common assumption that coral fragments represent entire colonies, and illuminate implications for coral biology and restoration.}, }
@article {pmid40357708, year = {2025}, author = {Pawlik, JR}, title = {Ecosystem engineers on tropical reefs in transition: giant barrel sponges in the Anthropocene.}, journal = {The Journal of experimental biology}, volume = {228}, number = {10}, pages = {}, doi = {10.1242/jeb.250082}, pmid = {40357708}, issn = {1477-9145}, support = {//National Science Foundation/ ; //National Oceanic and Atmospheric Administration/ ; }, mesh = {Animals ; *Coral Reefs ; *Porifera/physiology/anatomy &amp; histology ; Climate Change ; *Ecosystem ; Tropical Climate ; Seawater ; }, abstract = {Tropical coral reef ecosystems are changing rapidly to an alternative state in which sponges are the dominant living habitat, with giant barrel sponges (GBSs, Xestospongia spp.) representing the largest biomass. Unlike other benthic reef organisms, GBSs are ecosystem engineers that pump large volumes of seawater, disrupting the benthic boundary layer and directing flow away from the reef surface and into the water column. The morphology and size of GBSs have made them particularly good experimental subjects to study the hydraulics of sponge pumping and the transformation that occurs as seawater is processed by the sponge holobiont (sponge cells and microbial symbionts). This Review is part of a series marking the 100th birthday of The Company of Biologists, which was founded by marine biologist George Parker Bidder III, who primarily worked on sponges. The Review provides an integrative assessment of research on GBSs with comparisons with what is known about other marine sponges. Recent discoveries suggest that ancient lineages of morphologically indistinguishable GBSs are responding to environmental changes over sub-decadal time periods to rapidly populate reefs stripped of coral cover by climate change. If GBSs remain robust to rising seawater temperatures, they will become the greatest source of habitat complexity on reefs of the future, so knowledge of their biology and physiology will be important to our understanding of these ecosystems.}, }
@article {pmid40357403, year = {2025}, author = {Mejías, S and Jiménez, NE and Conca, C and Salgado, JC and Gerdtzen, ZP}, title = {Unveiling Wolbachia transcriptomic signature in the arboviral vector Aedes aegypti.}, journal = {Frontiers in cellular and infection microbiology}, volume = {15}, number = {}, pages = {1538459}, pmid = {40357403}, issn = {2235-2988}, mesh = {Animals ; *Wolbachia/genetics/physiology ; *Aedes/microbiology/genetics/virology ; *Mosquito Vectors/microbiology/genetics/virology ; Symbiosis/genetics ; *Transcriptome ; Gene Expression Profiling ; Female ; }, abstract = {INTRODUCTION: The mosquito Aedes aegypti is the main vector of arboviral diseases such as dengue and imposes a global health burden. A promising control strategy is to infect A. aegypti populations with Wolbachia, a genus of intracellular bacteria capable of blocking arboviral infections. Enhancing and preserving the efficacy of this method will depend on a solid mechanistic knowledge of the A. aegypti-Wolbachia symbiosis. By identifying differences between Wolbachia-infected and uninfected A. aegypti, previous transcriptomic studies proposed a wide range of symbiotic interactions, but a systematic identification of consistent effects across datasets is still missing.<br><br>METHODS: To identify A. aegypti genes and functions consistently affected by Wolbachia, we performed differential expression and functional enrichment analysis on published transcriptomic datasets, followed by a meta-analysis of the obtained p-values using the maxP method. Six datasets were retrieved from Gene Expression Omnibus, Sequence Read Archive and ArrayExpress (last searched in July 2024, considering lack of replication as the exclusion criteria). After discarding one dataset from wAlbB-infected cell line due to poor mapping to the A. aegypti genome, the data comprised adult female A. aegypti heads, muscles, carcasses, midguts and bodies, and Wolbachia strains wMel and wMelPop.<br><br>RESULTS AND DISCUSSION: Meta-analysis revealed 10 and 21 consistently down- and upregulated host genes, some of which have escaped the focus of previous research, including the consistently downregulated exonuclease AAEL009650 which has a pro-dengue virus homolog in Drosophila. At the function level, we found consistent upregulation of electron transport chain (ETC), carbohydrate transport and serine-type peptidase activity and inhibition, and downregulation of DNA replication. ETC upregulation suggests an alternative mechanism for Wolbachia's induction of antiviral oxidative stress, previously attributed to dual- and NADPH-oxidases which here showed downregulation or no regulation. Through analysis of previously published datasets, this work identifies promising molecular and functional targets for future studies aimed at elucidating the most fundamental mechanisms of the A. aegypti-Wolbachia symbiosis.}, }
@article {pmid40351403, year = {2025}, author = {Millard, A and Denise, R and Lestido, M and Thomas, MT and Webster, D and Turner, D and Sicheritz-Pontén, T}, title = {taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {6}, number = {1}, pages = {5-11}, pmid = {40351403}, issn = {2641-6549}, abstract = {BACKGROUND: Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee on the Taxonomy of Viruses. With the rapid increase in phage genomic data there is a growing need for automated classification systems that can handle large-scale genome analyses and place phages into new or existing genera and species.<br><br>MATERIALS AND METHODS: We developed taxMyPhage, a tool system for the rapid automated classification of dsDNA bacteriophage genomes. The system integrates a MASH database, built from ICTV-classified phage genomes to identify closely related phages, followed by BLASTn to calculate intergenomic similarity, conforming to ICTV guidelines for genus and species classification. taxMyPhage is available as a git repository at https://github.com/amillard/tax_myPHAGE, a conda package, a pip-installable tool, and a web service at https://phagecompass.ku.dk.<br><br>RESULTS: taxMyPhage enables rapid classification of bacteriophages to the genus and species level. Benchmarking on 705 genomes pending ICTV classification showed a 96.7% accuracy at the genus level and 97.9% accuracy at the species level. The system also detected inconsistencies in current ICTV classifications, identifying cases where genera did not adhere to ICTV's 70% average nucleotide identity (ANI) threshold for genus classification or 95% ANI for species. The command line version classified 705 genomes within 48 h, demonstrating its scalability for large datasets.<br><br>CONCLUSIONS: taxMyPhage significantly enhances the speed and accuracy of bacteriophage genome classification at the genus and species levels, making it compatible with current sequencing outputs. The tool facilitates the integration of bacteriophage classification into standard workflows, thereby accelerating research and ensuring consistent taxonomy.}, }
@article {pmid40343087, year = {2025}, author = {Vázquez-Rosas-Landa, M and Pérez-Ceballos, R and Zaldívar-Jiménez, A and Hereira, S and Pérez González, L and Prieto-Davó, A and Celis-Hernández, O and Canales-Delgadillo, JC}, title = {Impact of seasonal flooding and hydrological connectivity loss on microbial community dynamics in mangrove sediments of the southern Gulf of Mexico.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19371}, pmid = {40343087}, issn = {2167-8359}, mesh = {Gulf of Mexico ; *Geologic Sediments/microbiology ; *Seasons ; RNA, Ribosomal, 16S/genetics ; *Floods ; *Wetlands ; *Microbiota ; Biodiversity ; Hydrology ; Ecosystem ; }, abstract = {BACKGROUND: Mangrove ecosystems play essential roles in coastal resilience, carbon sequestration, and biodiversity but are under increasing threat from anthropogenic pressures. This study explores the impact of hydrological variability on microbial communities in mangrove sediments of the southern Gulf of Mexico.<br><br>METHODS: We employed 16S rRNA sequencing to assess microbial diversity and function across different hydrological zones, seasons, and sediment depths at Estero Pargo.<br><br>RESULTS: Our results show that microbial community composition is significantly influenced by hydrological conditions, with distinct microbial assemblages observed across the fringe, basin, and impaired zones. Seasonal variations were particularly pronounced, with higher microbial diversity during the flood season compared to the dry season. Depth also played a critical role, with surface layers (5 cm) predominantly featuring aerobic microbial communities, while deeper layers (20-40 cm) harbored anaerobic taxa such as Bathyarchaeota and Thermococcaceae. Notably, the impaired zone showed enrichment in genes related to denitrification and sulfur oxidation pathways, indicating strong microbial adaptation to reduced environments. These findings highlight the intricate interactions between microbial dynamics and environmental factors in mangrove ecosystems. Understanding these relationships is crucial for developing effective conservation and management strategies that enhance mangrove resilience in the face of global environmental changes.}, }
@article {pmid40342594, year = {2025}, author = {R J Clokie, M and Sicheritz-Pontén, T}, title = {Unveiling and Classifying the Hidden Potential of Bacteriophages.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {6}, number = {1}, pages = {1}, doi = {10.1089/phage.2025.7130}, pmid = {40342594}, issn = {2641-6549}, }
@article {pmid40341944, year = {2025}, author = {Iglesias-Carrasco, M and Tamburrino, G and Lozano, M and Broggi, J and Garcia-Gonzalez, F}, title = {Sexual selection and population spatial structure interact to shape sex-specific evolutionary responses in physiology.}, journal = {Journal of evolutionary biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jeb/voaf052}, pmid = {40341944}, issn = {1420-9101}, abstract = {Different selection pressures acting on females and males arising from sexual selection and sexual conflict may lead to sex-specific phenotypic expression of physiological traits. Importantly, sexual selection is affected by ecological and demographic factors. We explored whether population spatial structure modulates the effect of sexual selection on male and female standard metabolic rates and oxidative stress. For this purpose, we used selection lines of the seed beetle Callosobruchus maculatus subjected to divergent evolutionary regimes in the intensity of sexual selection (high vs. low, in polygamous vs. enforced monogamous populations, respectively) and the presence of metapopulation structure (absent vs. present). We found that the evolutionary treatments impacted physiological traits in a complex way. While in the selection regimes simulating metapopulation structure (i.e., divided populations) both sexes had similar metabolic rates, in undivided (unstructured) populations males had lower rates than females. Males from polygamous and undivided populations showed the lowest levels of antioxidant enzymes quantified as SOD, resulting in strong sexual dimorphism in SOD levels in this selection regime. The oxidative damage to lipids measured as TBARS levels, instead, were highest for both males and females from monogamous and undivided populations. On the whole, our results reveal two key insights. First, physiological traits evolve differently in females and males in response to sexual selection intensity and population spatial structure. Second, such sex-specific physiological responses are linked to selective pressures acting mostly on males. We highlight the importance of considering ecological and demographic factors when evaluating whether sexual selection drives sex-specific trait evolution.}, }
@article {pmid40335917, year = {2025}, author = {Lan, M and Gao, K and Qin, Z and Li, Z and Meng, R and Wei, L and Chen, B and Yu, X and Xu, L and Wang, Y and Yu, K}, title = {Coral microbiome in estuary coral community of Pearl River Estuary: insights into variation in coral holobiont adaptability to low-salinity conditions.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {278}, pmid = {40335917}, issn = {1471-2180}, support = {42206157//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; GXLSCRSCS2022103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; 2022GXNSFBA035449//Natural Science Foundation of Guangxi Province/ ; PM-zx703-202004-143//Central Public-Interest Scientific Institution Basal Research Fund/ ; }, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Estuaries ; *Microbiota ; Salinity ; *Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Rivers ; Biodiversity ; Phylogeny ; Adaptation, Physiological ; RNA, Ribosomal, 16S/genetics ; Dinoflagellida/genetics/classification/physiology ; Ecosystem ; China ; }, abstract = {BACKGROUND: Low salinity is a crucial environmental stressor that affects estuarine coral ecosystems considerably. However, few studies have focused on the effects of low-salinity conditions on coral-associated microorganisms and the adaptability of coral holobionts.<br><br>METHODS: We explored the community structure of coral symbiotic Symbiodiniaceae and associated bacteria in low-salinity conditions using samples of six coral species from the Pearl River Estuary and analyzed the adaptability of coral holobionts in estuaries.<br><br>RESULTS: The symbiotic Symbiodiniaceae of all six studied coral species were dominated by Cladocopium, but, the Symbiodiniaceae subclades differed among these coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of symbiotic Symbiodiniaceae but low Symbiodiniaceae density, with different adaptability to low-salinity stress in the Pearl River Estuary. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by associating with specific Symbiodiniaceae subclades and with high Symbiodiniaceae density under low-salinity stress. The microbiome associated with the coral species were dominated by Proteobacteria, Chloroflexi, and Bacteroidetes; however, its diversity and composition varied among coral species. Some coral species (e.g., Acropora solitaryensis) had a high diversity of associated bacteria, with different adaptability owing to low-salinity stress. Other coral species (e.g., Plesiastrea versipora) potentially increased their resistance by having minority bacterial dominance under low-salinity stress.<br><br>CONCLUSIONS: High Symbiodiniaceae density and high bacterial diversity may be conducive to increase the tolerance of coral holobiont to low-salinity environments. Different coral species have distinct ways of adapting to low-salinity stress, and this difference is mainly through the dynamic regulation of the coral microbiome by corals.}, }
@article {pmid40318223, year = {2025}, author = {Granit, L and Levi, R and Lifshitz, N and Banc-Prandi, G and Zelinger, E and Ronen, B and Kraut-Cohen, J and Naqib, A and Green, SJ and Fine, M and Yarden, O}, title = {Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistilatta.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40318223}, issn = {1751-7370}, support = {888/19//Israel Science Foundation/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; Symbiosis ; Indian Ocean ; *Mycobiome ; Stachybotrys/isolation &amp; purification/physiology ; Temperature ; Phylogeny ; *Ascomycota/isolation &amp; purification/physiology/genetics ; }, abstract = {The presence of fungi in the coral microbiome is increasingly recognized, yet their potential impact on the holobiont's health, particularly under stress conditions, remains underexplored. To address this gap, we isolated over 200 strains (predominantly Ascomycota) from the common scleractinian Red Sea coral, Stylophora pistillata. Using conidia from a rare (Stachybotrys chlorohalonata) and a common (Cladosporium halotolerans) fungal symbiont, we investigated their effects on coral fragments maintained at ambient (25°C) and elevated (33°C) sea temperatures. Inoculation with S. chlorohalonata resulted in significant tissue loss, across both water temperature treatments. Conversely, inoculation with C. halotolerans did not result in visible effects at ambient temperature, but mitigated tissue loss at elevated temperature. This protective effect was accompanied by reduced expression of stress-induced peroxiredoxin-6 and Rad51 host genes, yet not that of Hsp70. Additionally, potential algal symbiont photosynthetic efficiency was higher by over 25% in the elevated temperature treatment, concurrent with higher bacterial diversity, including a marked reduction (>3-fold) in the proliferation of Vibrionaceae in the C. halotolerans-treated coral nubbins. These findings reveal the contrasting impacts of fungal symbionts on coral health, highlighting the dual roles of the mycobiome in influencing holobiont resilience under environmental stress.}, }
@article {pmid40301674, year = {2025}, author = {Osman, EO and Garcias-Bonet, N and Cardoso, PM and Rosado, PM and García, FC and Ferrier-Pagès, C and Peixoto, RS}, title = {Phototrophic bacteria as potential probiotics for corals.}, journal = {npj biodiversity}, volume = {4}, number = {1}, pages = {16}, pmid = {40301674}, issn = {2731-4243}, abstract = {Coral-associated microorganisms provide crucial nutritional, protective, and developmental benefits, yet many functional traits remain unexplored. Phototrophic bacteria may enhance coral nutrition and reduce oxidative stress during bleaching via photosynthesis and antioxidant production. Despite this potential, their role in the holobiont's energy budget and heat stress resilience is understudied. This review explores the functional traits and potential of phototrophic bacteria to enhance coral health and resilience under environmental stress.}, }
@article {pmid40299544, year = {2025}, author = {Veenhof, RJ and McGrath, AH and Champion, C and Dworjanyn, SA and Marzinelli, EM and Coleman, MA}, title = {The role of microbiota in kelp gametophyte development and resilience to thermal stress.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.70018}, pmid = {40299544}, issn = {1529-8817}, support = {//The University of Sydney/ ; DP200100201//Australian Research Council/ ; //NSW Climate Change Fund/ ; //Holsworth Wildlife Research Endowment/ ; }, abstract = {Ocean warming is driving profound changes in the ecology of marine habitat formers such as kelps, with negative implications for the biodiversity and ecosystem services they support. Thermal stress can disturb associated microbiota that are essential to the healthy functioning of kelp, but little is known about how this process influences early-life stages. Because kelps have a biphasic life cycle, thermal stress dynamics of adult sporophyte microbiota may not reflect those of the free-living haploid gametophyte. We investigated the role of microbial disruption under thermal stress on gametophytes of the kelp Ecklonia radiata and compared sporophyte and gametophyte microbiota. The microbiota of gametophytes changed significantly when the microbiome was disrupted and under increased temperature (26°C), in which putative generalist bacterial taxa proliferated and bacterial families associated with nitrogen fixation decreased. Concurrently, the survival of gametophytes decreased to <10%, and surviving gametophytes did not become fertile when the microbiome was disrupted. The length of gametophytes decreased under both microbial disruption and thermal stress. Taken together, this suggests that the associated microbiota of Ecklonia gametophytes is important for their survival, fertility, and response to warming. Gametophyte and parental sporophyte microbiota were also distinct from the water column but not each other, suggesting vertical transmission of microbiota from one life stage to the next. This study furthers our understanding of the role of microbiota in gametophyte stress tolerance as well as the acquisition of microbiota, which may prove vital in protecting and increasing the stress resilience of these foundation species.}, }
@article {pmid40284718, year = {2025}, author = {Wu, X and Liao, H and Zhang, X and Ma, Z and Fu, Z}, title = {Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome.}, journal = {Microorganisms}, volume = {13}, number = {4}, pages = {}, pmid = {40284718}, issn = {2076-2607}, support = {2022GXNSFBA035473//Natural Science Foundation of Guangxi Province China/ ; 2023A1515011859//Guangdong Natural Science Foundation of China/ ; 2021KJQD18//Guangxi&#xa0;Minzu&#xa0;University&#xa0;Research&#xa0;Fund/ ; }, abstract = {Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m[2]) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.}, }
@article {pmid40273425, year = {2025}, author = {Bonacolta, AM and Weiler, BA and Grimes, CJ and Trznadel, M and Vermeij, MJA and Keeling, PJ and Del Campo, J}, title = {Fireworms are a reservoir and potential vector for coral-infecting apicomplexans.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40273425}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/parasitology ; Coral Reefs ; Phylogeny ; Sequence Analysis, DNA ; Ecosystem ; }, abstract = {Corals (Cnidaria; Anthozoa) play critical roles as habitat-forming species with a wide range, from warm shallow-water tropical coral reefs to cold-water ecosystems. They also represent a complex ecosystem as intricate holobionts made up of microbes from all domains of the Tree of Life that can play significant roles in host health and fitness. The corallicolids are a clade of apicomplexans that infect a wide variety of anthozoans worldwide and can influence the thermal tolerance of habitat-forming corals. Despite their potentially important impacts on reef ecosystems, much of the basic biology and ecology of corallicolids remains unclear. Apicomplexans often have a closed life cycle, with minimal environmental exposure and sometimes multiple hosts. Corallicolids have only been documented in anthozoan hosts, with no known secondary/reservoir hosts or vectors. Here, we show that abundant corallicolid sequences are recovered from bearded fireworms (Hermodice carunculata) in tropical reef habitats off Curaçao and that they are distinct from corallicolids infecting the corals on which the fireworms were feeding at the time of their collection. These data are consistent with a fireworm-specific corallicolid infection, not merely a byproduct of the worms feeding on infected corals. Furthermore, we suggest that H. carunculata is potentially a vector moving corallicolids among coral hosts through its feces. These findings not only expand our understanding of the ecological interactions within coral reef ecosystems but also highlight the potential role of host-associated parasites in shaping the resilience of reef habitats.}, }
@article {pmid40269580, year = {2025}, author = {Ahrar, M and Glenn, L and Held, M and Jackson, A and Kus, K and Hurst, GDD and Chrostek, E}, title = {Development of Antisense Tools to Study Bodo saltans and Its Intracellular Symbiont.}, journal = {MicrobiologyOpen}, volume = {14}, number = {2}, pages = {e70018}, pmid = {40269580}, issn = {2045-8827}, support = {//This study was funded by Gordon and Betty Moore Foundation's Symbiosis in Aquatic Systems Initiative, Grant ID: #9357 (10.37807/GBMF9357), awarded to G.H., E.C., and A.J./ ; }, mesh = {*Symbiosis/genetics ; Animals ; *Kinetoplastida/microbiology/genetics/physiology ; *RNA, Antisense/genetics ; }, abstract = {Obligate symbioses are common in nature and present a particular challenge for functional genetic analysis. In many cases, the host is a non-model species with poor tools for genetic manipulation, and the symbiont cannot be cultured or its gene expression manipulated to investigate function. Here, we investigated the potential for using antisense inhibition to analyze host and symbiont gene function within an obligate aquatic symbiosis. We focused on the kinetoplastid host Bodo saltans and its bacterial symbiont, Candidatus Bodocaedibacter vickermanii, a member of Rickettsiales. We conclude that antisense inhibition is not feasible in the Bodo saltans and its symbiont, as the holobiont feeds on the antisense molecules-and increases in numbers-upon treatment with the antisense construct. Although our approach has proven unsuccessful, we have developed an array of protocols that can be used to study the biology of this microeukaryote and its microbial associates.}, }
@article {pmid40268344, year = {2025}, author = {Förster, F and Sauzéat, L and Ferrier-Pagès, C and Reynaud, S and Sheldrake, TE}, title = {Redox-sensitive δ65Cu isotopic fractionation in the tissue of the scleractinian coral Stylophora pistillata: a biomarker of holobiont photophysiology following volcanic ash exposure.}, journal = {Metallomics : integrated biometal science}, volume = {17}, number = {5}, pages = {}, pmid = {40268344}, issn = {1756-591X}, support = {PCEFP2_194204/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Animals ; *Anthozoa/metabolism/chemistry/physiology ; Oxidation-Reduction ; *Volcanic Eruptions ; Biomarkers/metabolism/analysis ; Photosynthesis ; *Copper/metabolism/analysis ; Isotopes/analysis ; Symbiosis ; }, abstract = {Volcanic ash is a significant source of micronutrients including iron (Fe), copper (Cu), and zinc (Zn) in oligotrophic tropical waters. These bioactive metals enhance primary productivity, influencing local and global biogeochemical cycles. This study explores how volcanic ash exposure affects trace metal uptake and photophysiological response, and how redox-sensitive metal stable isotope measurements in the tissues of the scleractinian coral Stylophora pistillata can provide crucial information on coral health. Controlled coral culture experiments were conducted in which coral nubbins were exposed to varying intensity and duration of volcanic ash. Throughout the experiment, coral symbionts showed enhanced photosynthetic performance irrespective of intensity or duration of ash exposure. Stable isotopes, such as δ65Cu and δ56Fe, in the coral tissue are marked by systematic variations, not associated with intensity or duration of ash exposure. Instead, we suggest biologically modulated redox-sensitive fractionation associated with ash exposure, linked to the coral host's oxidative stress state. This is evidenced by significant correlations between δ65Cu in coral hosts and photophysiology, with lighter Cu isotope ratios associated with higher photosynthetic performances. Hence, we propose that δ65Cu, and more generally redox-sensitive isotopic ratios (i.e. δ56Fe), in coral hosts serves as an indicator of the physiological state of symbiotic corals.}, }
@article {pmid40266833, year = {2025}, author = {Huang, YH and Wang, M and Chang, XP and Ke, YL and Li, ZQ}, title = {Comparison Between Worker and Soldier Transcriptomes of Termite Neotermes binovatus Reveals Caste Specialization of Host-Flagellate Symbiotic System.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266833}, issn = {2075-4450}, support = {2023A1515011424//Natural Science Foundation of Guangdong Province of China/ ; }, abstract = {Termites are eusocial insects with functionally specialized workers and soldiers, both sharing the same genotype. Additionally, lower termites host flagellates in their hindguts that assist in wood digestion. However, worker-biased and soldier-biased gene expression patterns of the host-flagellate symbiotic system remain underexplored in most taxonomic groups. In this study, we sequenced high-depth transcriptomes from the workers and soldiers of a lower termite, Neotermes binovatus (Kalotermitidae), to investigate the differentially expressed termite transcripts, flagellate transcript abundance, and co-expression patterns of the host-flagellate transcript pairs in both castes. The worker-biased transcripts were enriched in functions related to cuticle development, nervous system regulation, pheromone biosynthesis, and metabolism, whereas the soldier-biased transcripts were predominantly involved in muscle development and kinesis, body morphogenesis, protein modification, and aggression. Flagellate transcripts from the orders Cristamonadida, Trichomonadida, Tritrichomonadida, and Oxymonadida were identified in both workers and soldiers, with the abundance of most flagellate transcripts tending to be higher in workers than in soldiers. Furthermore, we observed a much larger number of strong co-expression correlations between the termite and flagellate transcripts in workers than in soldiers, suggesting the possibility that soldiers depend more on food processed by worker holobionts than on their own symbiotic system. This research provides insights into the functional specialization of the host-flagellate symbiotic system in the worker and soldier castes of termites, supporting the workers' roles in nest maintenance, preliminary food processing, and communication, while emphasizing the defensive role of soldiers. Additionally, it offers new perspectives on the potential termite-flagellate interactions and underscores the need for whole-genome data of termite flagellates in further studies.}, }
@article {pmid40266732, year = {2025}, author = {Duque-Granda, D and Vivero-Gómez, RJ and González Ceballos, LA and Junca, H and Duque, SR and Aroca Aguilera, MC and Castañeda-Espinosa, A and Cadavid-Restrepo, G and Gómez, GF and Moreno-Herrera, CX}, title = {Exploring the Diversity of Microbial Communities Associated with Two Anopheles Species During Dry Season in an Indigenous Community from the Colombian Amazon.}, journal = {Insects}, volume = {16}, number = {3}, pages = {}, pmid = {40266732}, issn = {2075-4450}, support = {Hermes 57545//Universidad Nacional de Colombia/ ; }, abstract = {Malaria disease affects millions of people annually, making the Amazon Basin a major hotspot in the Americas. While traditional control strategies rely on physical and chemical methods, the Anopheles microbiome offers a promising avenue for biological control, as certain bacteria can inhibit parasite development and alter vector immune and reproductive systems, disrupting the transmission cycle. For this reason, this study aimed to explore the bacterial communities in An. darlingi and An. triannulatus s.l., including breeding sites, immature stages, and adults from San Pedro de los Lagos (Leticia, Amazonas) through next-generation sequencing of the 16S rRNA gene. The results revealed a higher bacterial genus richness in the L1-L2 larvae of An. triannulatus s.l. Aeromonas and Enterobacter were prevalent in most samples, with abundances of 52.51% in L3-L4 larvae and 48.88% in pupae of An. triannulatus s.l., respectively. In breeding site water, Verrucomicrobiota bacteria were the most dominant (52.39%). We also identified Delftia (15.46%) in An. triannulatus s.l. pupae and Asaia (98.22%) in An. triannulatus, linked to Plasmodium inhibition, and Elizabethkingia, in low abundances, along with Klebsiella and Serratia, known for paratransgenesis potential. Considering the high bacterial diversity observed across the different mosquito life stages, identifying bacterial composition is the first step towards developing new strategies for malaria control. However, the specific roles of these bacteria in anophelines and the malaria transmission cycle remain to be elucidated.}, }
@article {pmid40256745, year = {2025}, author = {Ruiz-Toquica, J and Franco Herrera, A and Medina, M}, title = {Endozoicomonas dominance and Vibrionaceae stability underpin resilience in urban coral Madracis auretenra.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e19226}, pmid = {40256745}, issn = {2167-8359}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Colombia ; Ecosystem ; Seasons ; }, abstract = {Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra, a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats-urban and protected-using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas, along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats.}, }
@article {pmid40252635, year = {2025}, author = {Taylor, H and Uhlig, HH and Powrie, F}, title = {Autoimmunity in inflammatory bowel disease: a holobiont perspective.}, journal = {Current opinion in immunology}, volume = {94}, number = {}, pages = {102557}, doi = {10.1016/j.coi.2025.102557}, pmid = {40252635}, issn = {1879-0372}, mesh = {Humans ; *Inflammatory Bowel Diseases/immunology/microbiology ; *Autoimmunity ; Animals ; *Gastrointestinal Microbiome/immunology ; Autoantigens/immunology ; Autoantibodies/immunology ; Adaptive Immunity ; Immunity, Mucosal ; }, abstract = {Adaptive immunity towards self-antigens (autoimmunity) and intestinal commensal microbiota is a key feature of inflammatory bowel disease (IBD). Considering mucosal adaptive immunity from a holobiont perspective, where the host and its microbiome form a single physiological unit, emphasises the challenge of avoiding damaging responses to self-antigen and symbiotic microbial communities in the gut while protecting against potential pathogens. Intestinal tolerance mechanisms prevent maladaptive T and B cell responses to microbial, environmental, and self-antigens, which drive inflammation. We discuss the spectrum of antimicrobial and autoantibody responses and highlight mechanisms by which common IBD-associated adaptive immune responses contribute to disease.}, }
@article {pmid40251276, year = {2025}, author = {Al-Kaisy, R and Bhatt, S and Duchêne, DA}, title = {Distinct evolutionary regimes across domains of the Plasmodium falciparum CSP gene.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {13507}, pmid = {40251276}, issn = {2045-2322}, support = {NNF23OC0084647//Novo Nordisk Fonden/ ; NNF20OC0059309//Novo Nordisk Fonden/ ; DNRF160//Danish National Research Foundation/ ; G-22-63345//The Eric and Wendy Schmidt Fund/ ; NIHR200908//UK National Institute for Health Research/ ; }, mesh = {*Plasmodium falciparum/genetics ; *Protozoan Proteins/genetics/chemistry ; *Evolution, Molecular ; Phylogeny ; Malaria, Falciparum/parasitology ; Humans ; Protein Domains ; }, abstract = {Malaria disease caused by parasites of genus Plasmodium places an enormous disease burden across tropical regions of the world. The circumsporozoite protein (CSP) of Plasmodium has several key functions in binding and accessing host cells, with functions subdivided across multiple protein regions. While its key roles during infection make the gene a primary target for malaria vaccine development, the evolutionary dynamics that could affect the forecasting of useful strains remain poorly understood. We tested whether the gene undergoes multiple DNA substitution processes and whether these are divided across gene regions using a phylogenetic mixture model, and a global sample of CSP sequences specific to P. falciparum. These analyses reveal evolutionary processes unique to the central repeat region and the C-terminus. The central repeat region is dominated by synonymous substitutions (putatively neutral) and heavy C-T substitution bias, while the C-terminus undergoes mostly non-synonymous changes. These evolutionary processes are not strongly geographically restricted, and lineages from Africa and Asia where the parasite is most abundant appear to drive evolution across all CSP gene regions. We propose that insights about DNA substitution processes can help forecast the variants of importance to vaccine development, aided by state-of-the-art evolutionary modelling.}, }
@article {pmid40247696, year = {2025}, author = {Tortorelli, G and Rosset, SL and Sullivan, CES and Woo, S and Johnston, EC and Walker, NS and Hancock, JR and Caruso, C and Varela, AC and Hughes, K and Martin, C and Quinn, RA and Drury, C}, title = {Heat-induced stress modulates cell surface glycans and membrane lipids of coral symbionts.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40247696}, issn = {1751-7370}, support = {2307516//The National Science Foundation Organismal Response to Climate Change/ ; }, mesh = {Animals ; *Anthozoa/physiology/parasitology/microbiology ; *Symbiosis ; *Polysaccharides/metabolism/analysis ; *Membrane Lipids/metabolism/analysis ; *Dinoflagellida/physiology/genetics/chemistry ; *Heat-Shock Response ; Hot Temperature ; Oxidative Stress ; }, abstract = {The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an 8-day heat stress. Symbionts' cell surface glycan composition differed between genera and was significantly affected by temperature and oxidative stress. The metabolic profile of coral holobionts was primarily shaped by symbionts identity, but was also strongly responsive to oxidative stress. At peak temperature stress, betaine lipids in Cladocopium were remodeled to more closely resemble the abundance and saturation state of Durusdinium symbionts, which paralleled a larger metabolic shift in Cladocopium. Exploring how Symbiodiniaceae members regulate stress and host-symbiont affinity helps identify the traits contributing to coral resilience under climate change.}, }
@article {pmid40216077, year = {2025}, author = {Armengaud, J and Cardon, T and Cristobal, S and Matallana-Surget, S and Bertile, F}, title = {Novel model organisms and proteomics for a better biological understanding.}, journal = {Journal of proteomics}, volume = {316}, number = {}, pages = {105441}, doi = {10.1016/j.jprot.2025.105441}, pmid = {40216077}, issn = {1876-7737}, mesh = {*Proteomics/methods ; Animals ; Bacteria/metabolism ; Humans ; }, abstract = {The concept of « model organisms » is being revisited in the light of the latest advances in multi-omics technologies that can now capture the full range of molecular events that occur over time, regardless of the organism studied. Classic, well-studied models, such as Escherichia coli, Saccharomyces cerevisiae, to name a few, have long been valuable for hypothesis testing, reproducibility, and sharing common platforms among researchers. However, they are not suitable for all types of research. The complexity of unanswered questions in biology demands more elaborated systems, particularly to study plant and animal biodiversity, microbial ecosystems and their interactions with their hosts if any. More integrated systems, known as « holobionts », are emerging to describe and unify host organisms and associated microorganisms, providing an overview of all their possible interactions and trajectories. Comparative evolutionary proteomics offers interesting prospects for extrapolating knowledge from a few selected model organisms to others. This approach enables a deeper characterization of the diversity of proteins and proteoforms across the three branches of the tree of life, i.e. Bacteria, Archaea, and Eukarya. It also provides a powerful means to address remaining biological questions, such as identifying the key molecular players in organisms when they are confronted to environmental challenges, like anthropogenic toxicants, pathogens, dietary shifts or climate stressors, and proposing long-term sustainable solutions. SIGNIFICANCE: In this commentary, we reevaluated the concept of "model organisms" in light of advancements in multi-omics technologies. Traditional models have proven invaluable for hypothesis testing, reproducibility, and fostering shared research frameworks. However, we discussed that they are not universally applicable. To address complexities such as biodiversity and understand microbial ecosystems and their host interactions, integrated systems like "holobionts," which encompass host organisms and their associated microbes, are gaining prominence. Comparative evolutionary proteomics further enhances our understanding by enabling detailed exploration of protein diversity across organisms. This approach also facilitates the identification of critical molecular players in organisms facing environmental challenges, such as pollutants, pathogens, dietary changes, or climate stress, and contributes to developing sustainable long-term solutions.}, }
@article {pmid40215444, year = {2025}, author = {Kerwin, AH and Ohdera, A and Bier, J and Goodman, D and Mammone, M and Sharp, V and Echeandía, A and Medina, M}, title = {Cassiopea xamachana microbiome across anatomy, development, and geography.}, journal = {PloS one}, volume = {20}, number = {4}, pages = {e0319944}, pmid = {40215444}, issn = {1932-6203}, mesh = {Animals ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Larva/microbiology ; *Hydrozoa/microbiology/growth &amp; development/anatomy &amp; histology ; Female ; Phylogeny ; Symbiosis ; Male ; Geography ; }, abstract = {The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.}, }
@article {pmid40208324, year = {2025}, author = {Mazzella, V and Zahn, G and Dell'Anno, A and Pons, LN}, title = {Marine Mycobiomes Colonize Mediterranean Sponge Hosts in a Random Fashion.}, journal = {Microbial ecology}, volume = {88}, number = {1}, pages = {25}, pmid = {40208324}, issn = {1432-184X}, support = {C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; C63C22000520001//National Recovery and Resilience Plan (NRRP)/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; Mediterranean Sea ; *Mycobiome ; *Seawater/microbiology ; Phylogeny ; Biodiversity ; DNA Barcoding, Taxonomic ; DNA, Fungal/genetics ; Ecosystem ; }, abstract = {Marine sponges are widespread, sessile, filter-feeding animals, known for living in association with complex prokaryotic communities structured by host species. Though marine fungi are ubiquitous across marine environments, little is known about sponge-associated fungal communities (mycobiome). Indeed, aside from a few studies based on the isolation of fungal strains for biotechnological purposes, little information is available to understand the diversity and structure of sponge mycobiome. Here, a metabarcoding approach based on the ITS1 marker was applied to examine the structure and composition of fungal communities associated with four Mediterranean sponges. The species: Petrosia ficiformis, Chondrosia reniformis, Crambe crambe, and Chondrilla nucula were analyzed along with the surrounding seawater, revealing Aspergillus (1-56%), Cladosporium (1-75%), Malassezia (1-38.5%), and Pennicillium (1.5-36%) as the most represented fungal genera. Our data showed high intra-specific variability and no clear core mycobiome within each of the sponge species host, suggesting stochastic and perhaps transient community membership. This study sheds light on one of the most abundant yet least understood components of the marine ecosystem. Unraveling the dynamics of fungal interactions within sponge holobionts is essential to advance our understanding of their ecological roles and functions. By addressing the enigmatic nature of sponge-associated fungi, this research opens new avenues for exploring their contributions to marine ecosystems and resolving the many unanswered questions in this field.}, }
@article {pmid40205751, year = {2025}, author = {Dho, M and Montagna, M and Liu, C and Magoga, G and Forni, G and Alma, A and Gonella, E}, title = {Multilocus sequence typing of the invasive pest Halyomorpha halys (Hemiptera: Pentatomidae) and associated endosymbiont reveals unexplored diversity.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70034}, pmid = {40205751}, issn = {1744-7917}, abstract = {Halyomorpha halys is an invasive pest affecting a wide range of crops in many regions of the world. Rapid and cost-effective methods to reconstruct its invasion routes are crucial for implementing strategies to prevent further spread. The mitochondrial markers COI and COII and the pseudogene ΔybgF of the primary symbiont "Candidatus Pantoea carbekii" have been analyzed to track the spread of H. halys. However, these markers do not provide sufficient resolution to fully elucidate invasion routes. Here, H. halys individuals from native and invasive populations were analyzed to identify new DNA markers and evaluate their effectiveness in a multilocus sequence typing (MLST) framework. Three new nuclear markers for H. halys (Hh_KsPi, Hh_UP1, Hh_D3PDh) and three new markers for P. carbekii (Pc_TamA, Pc_SucA, Pc_SurA) were identified. Hh_D3PDh was the most informative marker for H. halys, describing two more haplotypes than COI. By integrating Hh_D3PDh with mitochondrial markers, 30 distinct haplotypes were identified, with each of the populations studied exhibiting multiple haplotypes. Pc_SucA was the most informative symbiont marker, and when all P. carbekii markers were combined, symbiont diversity was greatly increased. The low network specialization between the novel nuclear markers and both mitochondrial and symbiont markers underlined the higher power of nuclear markers. Interestingly, perfect network specialization between H. halys COI and symbiont markers was found in populations from invaded areas, suggesting that some holobiont variants may contribute to enhanced invasive ability. A MLST workflow is proposed as a new tool for population genetics analysis and reconstruction of H. halys invasion.}, }
@article {pmid40194944, year = {2025}, author = {Wilson, I and Perry, T and Eisenhofer, R and Rismiller, P and Shaw, M and Grutzner, F}, title = {Microbiota changes in lactation in the short-beaked echidna (Tachyglossus aculeatus).}, journal = {FEMS microbiology ecology}, volume = {101}, number = {5}, pages = {}, pmid = {40194944}, issn = {1574-6941}, support = {//University of Adelaide/ ; }, mesh = {Animals ; Female ; *Lactation ; *Tachyglossidae/microbiology/physiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Animals, Zoo/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Reproduction ; }, abstract = {Monotreme and marsupial development is characterized by a short gestation, with young exposed to the environment at an early developmental stage and supported by a long lactation in the pouch, pseudo-pouch, or burrow. The lack of a functional adaptive immune system in these altricial young raises questions about how they survive in a microbe-rich environment. Previous studies on marsupial pouches have revealed changes to pouch microbe composition during lactation, but no information is available in monotremes. We investigated changes in the echidna pseudo-pouch microbiota (n = 22) during different stages of the reproductive cycle and whether this differs between wild and zoo-managed animals. Metataxonomic profiling using 16S rRNA gene sequencing revealed that pseudo-pouch microbial communities undergo dramatic changes during lactation, with significant differences in taxonomic composition compared with samples taken outside of breeding season or during courtship and mating. This suggests that the echidna pseudo-pouch environment changes during lactation to accommodate young that lack a functional adaptive immune system. Furthermore, captivity was not found to have a significant effect on pseudo-pouch microbiota. This study pioneers pouch microbiota research in monotremes, provides new biological information on echidna reproduction, and may also provide information about the effects of captive management to inform breeding programmes in the future.}, }
@article {pmid40175359, year = {2025}, author = {Sipos, A and Kerekes, &#xc9; and Szeőcs, D and Szarvas, F and Schwarcz, S and Tóth, E and Ujlaki, G and Mikó, E and Bai, P}, title = {Ursodeoxycholic acid prompts glycolytic dominance, reductive stress and epithelial-to-mesenchymal transition in ovarian cancer cells through NRF2 activation.}, journal = {Cell death discovery}, volume = {11}, number = {1}, pages = {134}, pmid = {40175359}, issn = {2058-7716}, support = {K142141//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; FK146 852//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; FK 128 387//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal (NKFI Office)/ ; }, abstract = {Numerous secreted bacterial metabolites were identified with bioactivity in various neoplasias, including ovarian cancer. One such metabolite is ursodeoxycholic acid (UDCA), a secondary bile acid that has widespread beneficial effects in neoplasias. Hereby, we assessed the bioactivity of UDCA in cell models of ovarian cancer, by applying UDCA in concentrations corresponding to the serum reference concentrations of UDCA (300 nM). UDCA induced epithelial-to-mesenchymal transition (EMT), increased the flux of glycolysis and reduced the naturally occurring oxidative stress in ovarian cancer cells. These changes were dependent on the activation of NRF2. The tumoral overexpression of UDCA-induced genes in humans correlated with worse survival. These results point out that bacterial metabolites may have opposite effects in different neoplasias and raise the possibility that UDCA-containing remedies on the long run may support cancer progression in ovarian cancer patients.}, }
@article {pmid40171541, year = {2025}, author = {Robert, C and Alves Monteiro, HJ and Le Moan, A and Tanguy, A and Laugen, AT and Hemmer-Hansen, J and Strand, &#xc5; and De Wit, P}, title = {Fine Scale Patterns of Population Structure and Connectivity in Scandinavian Flat Oysters in Scandinavia (Ostrea edulis L.).}, journal = {Evolutionary applications}, volume = {18}, number = {4}, pages = {e70096}, pmid = {40171541}, issn = {1752-4571}, abstract = {Stocks of the European flat oyster, Ostrea edulis, have collapsed due to overfishing, habitat destruction, and pathogen outbreaks across most of their distribution range. Nonetheless, as a result of lower exploitation pressure and the absence of pathogens in the most northern part of the range, a large part of the remaining wild population can be found in relatively high densities in Scandinavia, a region in Northern Europe. However, despite recent studies focusing on flat oyster population structure along the European coast, little is known about the population structure of oysters in the Skagerrak marginal sea in Scandinavia, and how it is related to neighbouring regions. This study, therefore, aimed to investigate the population structure of flat oysters in Scandinavia, with a special emphasis on the Skagerrak. We gathered low-coverage whole-genome sequencing data from oysters in Sweden, Norway, and Denmark, the three countries that border the Skagerrak. Genetic diversity appeared to be homogeneously distributed over the sampled area in the Skagerrak, while samples collected from the east coast of Denmark and from a location with known historical farming activity on the Norwegian West Coast were genetically distinct from Skagerrak samples. A genetic barrier analysis indicated barriers to gene flow in the Baltic Sea transition zone and on the west coast of Norway. Overall, our results suggest that flat oysters from the Swedish Skagerrak coasts form a single panmictic population that is distinct from neighbouring seas, potentially allowing for regional management of stocks and restoration translocations in the area. However, the genetic composition of donor and recipient stocks should be assessed on a case-by-case basis, genetic diversity effects of hatchery practices should be monitored, and biosecurity measures need to be considered prior to any movement of stock.}, }
@article {pmid40165613, year = {2025}, author = {Fialas, PC and Santini, L and Russo, D and Amorim, F and Rebelo, H and Novella-Fernandez, R and Marques, F and Domer, A and Vella, A and Martinoli, A and Figurek, A and Tsoar, A and Sandor, A and Ibanez, C and Korine, C and Kerbiriou, C and Voigt, C and Mifsud, C and Jére, C and Ridha, D and Preatoni, D and Hamidović, D and Tidenberg, EM and Çoraman, E and Mathews, F and Lison, F and Joanna, F and Petersons, G and Loumassine, H and Garin, I and Csősz, I and Liira, J and Juste, J and Julien, JF and van der Kooij, J and Darija, J and Aihartza, J and Eldegard, K and Phelps, K and Olival, KJ and Marina, K and Ancillotto, L and Grzegorz, L and Barti, L and Salazar, LC and Bosso, L and Rodrigues, L and Hamel, L and Uhrin, M and Mas, M and Cerekovic, N and Toshkova, N and Roche, N and Kalda, O and Aizpurua, O and Georgiakakis, P and Kanuch, P and Presetnik, P and Bilgin, R and McKay, RA and Dina, R and Goran, R and Ireneusz, R and Sørås, R and Robert, S and Aulagnier, S and Kramer-Schadt, S and Gazaryan, S and Bücs, SL and Yorulmaz, T and Stjernberg, T and Liukko, UM and Nistreanu, V and Vintulis, V and Radchuk, V and Puig-Montserrat, X and Bas, Y and Zagmajster, M and Zegarek, M and Vida, Z and Razgour, O}, title = {Changes in community composition and functional diversity of European bats under climate change.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e70025}, doi = {10.1111/cobi.70025}, pmid = {40165613}, issn = {1523-1739}, support = {//Natural Environment Research Council/ ; //NE/M018660/1, NE/S007504/1/ ; //COST ACTION CA18107 'Climate change and bats: from science to conservation - ClimBats' (https://climbats.eu/)/ ; }, abstract = {Climate change is predicted to drive geographical range shifts that will result in changes in species diversity and functional composition and have potential repercussions for ecosystem functioning. However, the effect of these changes on species composition and functional diversity (FD) remains unclear, especially for mammals, specifically bats. We used species distribution models and a comprehensive ecological and morphometrical trait database to estimate how projected future climate and land-use changes could influence the distribution, composition, and FD of the European bat community. Future bat assemblages were predicted to undergo substantial shifts in geographic range and trait structure. Range suitability decreased substantially in southern Europe and increased in northern latitudes. Our findings highlight the potential for climate change to drive shifts in bat FD, which has implications for ecosystem function and resilience at a continental scale. It is important to incorporate FD in conservation strategies. These efforts should target species with key functional traits predicted to be lost and areas expected to experience losses in FD. Conservation strategies should include habitat and roost protection, enhancing landscape connectivity, and international monitoring to preserve bat populations and their ecosystem services.}, }
@article {pmid40159998, year = {2025}, author = {Iglesias-Carrasco, M and Torres, J and Cruz-Dubon, A and Candolin, U and Wong, BBM and Velo-Antón, G}, title = {Global impacts of exotic eucalypt plantations on wildlife.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.70022}, pmid = {40159998}, issn = {1469-185X}, support = {PID2022-137901NB-I00//Spanish Ministry of Science, Innovation and Universities/ ; DOC_00453//Junta de Andalucia/ ; }, abstract = {The establishment of exotic tree plantations poses a pervasive threat to wildlife across the globe. Among the most important tree species used for forestry purposes worldwide are members of the genus Eucalyptus, which have now been established in at least 107 countries outside of their native range. When introduced into non-native areas, eucalypt plantations are associated with myriad novel challenges for native fauna, and have often been associated with reductions in the biodiversity of local communities. However, similar to other anthropogenic habitats, eucalypt plantations can also create novel opportunities for species that can allow them to survive and thrive in these novel environments. In this review, we use eucalypt plantations as a case study for understanding the ecological and evolutionary responses of wildlife to anthropogenic habitat loss and change. We begin by summarising the main avenues of research addressing the study of wildlife responses at the individual, community, and ecosystem levels, and highlight critical research gaps. We also consider the characteristics of different types of eucalypt plantations and how such attributes are linked with the ability of animals to respond appropriately to the establishment of plantations, and summarise important considerations for the conservation of animal communities in these human-altered habitats.}, }
@article {pmid40154760, year = {2025}, author = {Sutcliffe, EI and Irvine, A and Rooney, J and Smith, D and Northcote, HM and McKenzie, D and Bakshi, S and Nisbet, AJ and Price, D and Graham, R and Morphew, R and Atkinson, L and Mousley, A and Cantacessi, C}, title = {Antimicrobial peptides in nematode secretions - Unveiling biotechnological opportunities for therapeutics and beyond.}, journal = {Biotechnology advances}, volume = {81}, number = {}, pages = {108572}, doi = {10.1016/j.biotechadv.2025.108572}, pmid = {40154760}, issn = {1873-1899}, mesh = {Animals ; *Antimicrobial Peptides/therapeutic use/chemistry/pharmacology/metabolism ; *Nematoda/metabolism ; Humans ; *Biotechnology ; *Nematode Infections/drug therapy/parasitology ; Drug Discovery ; }, abstract = {Gastrointestinal (GI) parasitic nematodes threaten food security and affect human health and animal welfare globally. Current anthelmintics for use in humans and livestock are challenged by continuous re-infections and the emergence and spread of multidrug resistance, underscoring an urgent need to identify novel control targets for therapeutic exploitation. Recent evidence has highlighted the occurrence of complex interplay between GI parasitic nematodes of humans and livestock and the resident host gut microbiota. Antimicrobial peptides (AMPs) found within nematode biofluids have emerged as potential effectors of these interactions. This review delves into the occurrence, structure, and function of nematode AMPs, highlighting their potential as targets for drug discovery and development. We argue that an integrated approach combining advanced analytical techniques, scalable production methods, and innovative experimental models is needed to unlock the full potential of nematode AMPs and pave the way for the discovery and development of sustainable parasite control strategies.}, }
@article {pmid40151579, year = {2025}, author = {de Breuyn, M and Ostendarp, M and El-Khaled, YC and Garcias-Bonet, N and Carvalho, S and Wild, C and Peixoto, RS}, title = {Probiotics prevent mortality of thermal-sensitive corals exposed to short-term heat stress.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf039}, pmid = {40151579}, issn = {2730-6151}, abstract = {The use of coral probiotics, i.e. beneficial microorganisms for corals (BMCs), is a novel approach to enhancing coral health under heat stress. While BMCs mitigate coral bleaching and mortality during prolonged heat stress conditions, their effectiveness in mitigating short-term acute heat stress remains understudied. This study investigates the effects of BMCs on two Red Sea hard coral species, Acropora cf. hemprichii and Pocillopora verrucosa, during short-term heat stress. Twelve coral fragments per species were allocated to each treatment across two temperature regimes (26°C and 32°C) for 48 hours, with half receiving BMC inoculation and half serving as controls. Results show BMC supplementation significantly prevented mortality in Acropora cf. hemprichii at 32°C, contrasting with a 100% mortality observed in the control group. Specifically, probiotic-inoculated Acropora cf. hemprichii at 32°C exhibited preserved primary production, a 12-13 fold increase in algal cell densities, 4-5 times higher FV/Fm ratios, and 4-5 and 2-3 times higher chlorophyll a and c2 concentrations, respectively, compared to their untreated conspecifics. All P. verrucosa colonies survived the 32°C exposure without tissue loss or reduced holobiont function in both control and BMC treatments. These findings underscore the rapid effects of BMC inoculation, initiated just 2 hours prior to acute heat stress, in protecting heat-sensitive Acropora cf. hemprichii against mortality and adverse photo-physiological changes, with beneficial effects visible within 2 days. Recognizing the critical timeframe for beneficial effects is paramount for management strategies to address heat-sensitive corals on natural reefs, such as implementing probiotic interventions before anticipated marine heatwaves.}, }
@article {pmid40143859, year = {2025}, author = {Abou Jaoudé, R and Luziatelli, F and Ficca, AG and Ruzzi, M}, title = {Soil microbiome transplantation to enhance the drought response of Salvia officinalis L.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1553922}, pmid = {40143859}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil microbiome transplantation is a promising technique for enhancing plant holobiont response to abiotic and biotic stresses. However, the rapid assessment of microbiome-plant functional integration in short-term experiments remains a challenge.<br><br>METHODS: This study investigates the potential of three evergreen sclerophyll species, Pistacia lentiscus (PL), Rosmarinus officinalis (RO), and Juniperus phoenicea (JP), to serve as a reservoir for microbial communities able to confer enhanced tolerance to drought in Salvia officinalis cultivated under water shortage, by analyzing biomass production, plant phenotype, plant ecophysiological responses, and leaf metabolome.<br><br>RESULTS: Our results showed that the inoculation with the three rhizomicrobiomes did not enhance total plant biomass, while it significantly influenced plant architecture, ecophysiology, and metabolic responses. The inoculation with the JP rhizomicrobiome led to a significant increase in root biomass, resulting in smaller leaves and a higher leaf number. These morphological changes suggest improved water acquisition and thermoregulation strategies. Furthermore, distinct stomatal conductance patterns were observed in plants inoculated with microbiomes from PJ and PL, indicating altered responses to drought stress. The metabolome analysis demonstrated that rhizomicrobiome transplantation significantly influenced the leaf metabolome of S. officinalis. All three rhizomicrobiomes promoted the accumulation of phenolic compounds, terpenoids, and alkaloids, known to play crucial roles in plant defense and stress response. Five molecules (genkwanin, beta-ionone, sumatrol, beta-peltatin-A-methyl ester, and cinnamoyl-beta-D-glucoside) were commonly accumulated in leaves of inoculated sage, independently of the microbiome. Furthermore, unique metabolic alterations were observed depending on the specific inoculated rhizomicrobiome, highlighting the specialized nature of plant-microbe interactions and the possible use of these specific molecules as biomarkers to monitor the recruitment of beneficial microorganisms.<br><br>DISCUSSION: This study provides compelling evidence that microbiome transplantation can induce phenotypic and metabolic changes in recipient plants, potentially enhancing their resilience to water scarcity. Our findings emphasize the importance of considering multiple factors, including biomass, physiology, and metabolomics, when evaluating the effectiveness of microbiome engineering for improving plant stress tolerance.}, }
@article {pmid40139064, year = {2025}, author = {Yang, H and Yuan, D and Zhou, Z and Zhao, H}, title = {Nitrate enrichment exacerbates microbiome and metabolism disturbances of the coral holobiont under heat stress.}, journal = {Marine environmental research}, volume = {208}, number = {}, pages = {107098}, doi = {10.1016/j.marenvres.2025.107098}, pmid = {40139064}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/physiology/microbiology ; *Microbiota/drug effects ; *Nitrates ; *Hot Temperature ; Coral Reefs ; *Heat-Shock Response ; Symbiosis ; }, abstract = {Coral reef ecosystems are facing severe deterioration due to escalating global temperatures and human-induced activities. Combined nitrate and heat stress can exacerbate coral bleaching, however, the underlying mechanism is still unclear. In the present study, we assessed the bleaching status of Acropora hyacinthus, a reef-building coral species, under high temperature and nitrate stress conditions using chemostat cultivation. We observed nitrate enrichment (9 μM) induced a significant reduction in photosystem efficiency (Fv/Fm) of Symbiodiniaceae and an increased thermal bleaching of corals under high temperature (30 °C). Nitrate exposure promoted the proliferation of Enterobacteriaceae and Vibrionaceae, which are bacterial families, potentially augmenting the coral's susceptibility to disease while exerting negligible effects on the fungal community. Alterations were observed in the metabolic pathways of both the coral hosts and Symbiodiniaceae, including down-regulated folate biosynthesis and inflammatory mediator regulation of TRP channels. Our findings indicate that nitrate enrichment under heat stress disrupts the metabolism of coral holobionts through altering bacterial communities, ultimately leading to increased coral bleaching.}, }
@article {pmid40132032, year = {2025}, author = {Ostendarp, M and de Breuyn, M and El-Khaled, YC and Garcias-Bonet, N and Carvalho, S and Peixoto, RS and Wild, C}, title = {Temperature-dependent responses of the hard corals Acropora sp. and Pocillopora verrucosa to molecular hydrogen.}, journal = {PloS one}, volume = {20}, number = {3}, pages = {e0308894}, pmid = {40132032}, issn = {1932-6203}, mesh = {Animals ; *Anthozoa/physiology/drug effects ; *Hydrogen/pharmacology ; *Temperature ; Photosynthesis/drug effects ; Coral Reefs ; Global Warming ; Electron Transport ; Seawater ; Indian Ocean ; }, abstract = {Coral reefs are increasingly threatened by mass bleaching events due to global ocean warming. Novel management strategies are urgently needed to support coral survival until global efforts can mitigate ocean warming. Given the strong antioxidant, anti-inflammatory and anti-apoptotic properties of molecular hydrogen, our study explores its potential to alleviate the negative effects of heat stress on corals. We investigated the ecophysiological responses of two common hard corals (Acropora sp. and Pocillopora verrucosa) from the Central Red Sea under ambient (26 °C) and elevated seawater temperatures (32 °C), with and without hydrogen addition (~ 150 µ M H2) over 48 h. Our results showed that at 32 °C without hydrogen addition, P. verrucosa exhibited high temperature tolerance, whereas Acropora sp. showed significant reductions in photosynthetic efficiency and maximum electron transport rate compared to the ambient condition (26 °C). The addition of hydrogen at 32 °C increased the maximum electron transport rate of Acropora sp. by 28%, maintaining it at levels compared to those at 26 °C. In contrast, the addition of hydrogen at 26 °C caused a significant decrease in the photophysiology of both Acropora sp. and P. verrucosa. This suggests that the short-term response of the coral holobiont to molecular hydrogen is temperature-dependent, potentially benefiting the coral holobiont under heat stress, while impairing the photophysiology under ambient temperatures. Our findings therefore provide the foundation for future long-term studies uncovering the mechanisms behind molecular hydrogen, potentially informing the development of new management strategies to enhance coral resilience to ocean warming.}, }
@article {pmid40130423, year = {2025}, author = {Silver, LW and Farquharson, KA and Peel, E and Gilbert, MTP and Belov, K and Morales, HE and Hogg, CJ}, title = {Temporal Loss of Genome-Wide and Immunogenetic Diversity in a Near-Extinct Parrot.}, journal = {Molecular ecology}, volume = {34}, number = {9}, pages = {e17746}, pmid = {40130423}, issn = {1365-294X}, support = {CE200100012//Australian Research Council/ ; }, mesh = {Animals ; *Parrots/genetics/immunology ; *Genetic Variation ; Genome ; Male ; Female ; Genetics, Population ; *Extinction, Biological ; Alleles ; Endangered Species ; Immunogenetics ; }, abstract = {Loss of genetic diversity threatens a species' adaptive potential and long-term resilience. Predicted to be extinct by 2038, the orange-bellied parrot (Neophema chrysogaster) is a critically endangered migratory bird threatened by numerous viral, bacterial and fungal diseases. The species has undergone multiple population crashes, reaching a low of three wild-born females and 13 males in 2016, and is now represented by only a single wild population and individuals in the captive breeding program. Here we used our high-quality long-read reference genome, and contemporary (N = 19) and historical (N = 16) resequenced genomes from as early as 1829, to track the long-term genomic erosion and immunogenetic diversity decline in this species. 62% of genomic diversity was lost between historical (mean autosomal heterozygosity = 0.00149 ± 0.000699 SD) and contemporary (0.00057 ± 0.000026) parrots. A greater number and length of runs of homozygosity in contemporary samples were also observed. A temporal reduction in the number of alleles at Toll-like receptor genes was found (historical average alleles = 5.78 ± 2.73; contemporary = 3.89 ± 2.10), potentially exacerbating disease susceptibility in the contemporary population. Of particular concern is the new threat of avian influenza strain (HPAI) to Australia. We discuss the conservation implications of our findings and propose that hybridisation and synthetic biology may be required to address the catastrophic loss of genetic diversity that has occurred in this species in order to prevent extinction.}, }
@article {pmid40123705, year = {2025}, author = {Hasnain, SE and Ahmed, N}, title = {Rethinking Conservation in the Anthropocene-The Case of Holobionts.}, journal = {Disease biology, genetics, and socioecology}, volume = {1}, number = {1}, pages = {}, pmid = {40123705}, support = {R01 AI116471/AI/NIAID NIH HHS/United States ; }, }
@article {pmid40116496, year = {2025}, author = {Baa-Puyoulet, P and Gerlin, L and Parisot, N and Peignier, S and Renoz, F and Calevro, F and Charles, H}, title = {ArtSymbioCyc, a metabolic network database collection dedicated to arthropod symbioses: a case study, the tripartite cooperation in Sipha maydis.}, journal = {mSystems}, volume = {10}, number = {4}, pages = {e0014025}, pmid = {40116496}, issn = {2379-5077}, support = {ANR-16-CE02-0014//Agence Nationale de la Recherche/ ; PrANR-21-CE35-0011//Agence Nationale de la Recherche/ ; }, mesh = {*Symbiosis ; Animals ; *Metabolic Networks and Pathways ; Amino Acids/metabolism ; *Aphids/microbiology/metabolism ; *Arthropods/microbiology ; *Bacteria/metabolism/genetics ; *Databases, Factual ; }, abstract = {Most arthropods live in close association with bacteria. The genomes of associated partners have co-evolved, creating situations of interdependence that are complex to decipher despite the availability of their complete sequences. We developed ArtSymbioCyc, a metabolism-oriented database collection gathering genomic resources for arthropods and their associated bacteria. ArtSymbioCyc uses the powerful tools of the BioCyc community to produce high-quality annotations and to analyze and compare metabolic networks on a genome-wide scale. We used ArtSymbioCyc to study the case of the tripartite symbiosis of the cereal aphid Sipha maydis focusing on amino acid and vitamin metabolisms, as these compounds are known to be important in this strictly phloemophagous insect. We showed that the metabolic pathways of the insect host and its two obligate bacterial associates are interdependent and specialized in the exploitation of Poaceae phloem, particularly for the biosynthesis of sulfur-containing amino acids and most vitamins. This demonstrates that ArtSymbioCyc does not only reveal the individual metabolic capacities of each partner and their respective contributions to the holobiont they constitute but also allows to predict the essential inputs that must come from host nutrition.IMPORTANCEThe evolution has driven the emergence of complex arthropod-microbe symbiotic systems, whose metabolic integration is difficult to unravel. With its user-friendly interface, ArtSymbioCyc (https://artsymbiocyc.cycadsys.org) eases and speeds up the analysis of metabolic networks by enabling precise inference of compound exchanges between associated partners and helps unveil the adaptive potential of arthropods in contexts such as conservation or agricultural control.}, }
@article {pmid40113967, year = {2025}, author = {Mannaa, M and Park, AR and Kim, JC and Seo, YS}, title = {Microbial allies recruited by Bacillus subtilis JCK-1398 to defend pine trees against pinewood nematode.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {9670}, pmid = {40113967}, issn = {2045-2322}, mesh = {Animals ; *Bacillus subtilis/physiology ; *Pinus/parasitology/microbiology ; *Plant Diseases/parasitology/prevention &amp; control/microbiology ; *Nematoda ; Rhizosphere ; Microbiota ; Disease Resistance ; Soil Microbiology ; Pantoea ; }, abstract = {Pine wilt disease (PWD) is a devastating disease caused by the pinewood nematode (Bursaphelenchus xylophilus). Its substantial ecological disruption harms global forestry and poses serious economic challenges. Although previous research has demonstrated that Bacillus subtilis JCK-1398 has the potential to induce systemic resistance in pine trees, the ecological mechanisms underlying its biocontrol efficacy remain underexplored. This study investigated how JCK-1398 treatment influences rhizosphere- and nematode-associated microbial communities to mitigate PWD. Metabarcoding analyses revealed that JCK-1398 treatment increased the abundance of beneficial microbial taxa (e.g., Nocardioides and Mesorhizobium) in the rhizosphere microbiome. Concurrently, nematode-associated microbial communities became dominated by Pantoea, a genus with known nematicidal properties. Isolation and characterization of Pantoea dispersa BC11 confirmed that it significantly limits nematode viability. These findings highlight the multifaceted defense that JCK-1398 offers, not only inducing systemic resistance, but also orchestrating beneficial microbiome dynamics. This study emphasizes the potential of manipulating a microbial holobiont for eco-friendly and sustainable disease management. The ability of JCK-1398 to recruit and enhance microbial allies offers a novel framework for developing biocontrol agents, with implications for managing PWD and other plant-pathogen systems.}, }
@article {pmid40111689, year = {2025}, author = {Mattos, MCO and Vivacqua, A and Carneiro, VMA and Grisi, DC and Guimarães, MDCM}, title = {Interaction of the Systemic Inflammatory State, Inflammatory Mediators, and the Oral Microbiome.}, journal = {Advances in experimental medicine and biology}, volume = {1472}, number = {}, pages = {121-132}, pmid = {40111689}, issn = {0065-2598}, mesh = {Humans ; *Microbiota ; *Mouth/microbiology/immunology ; *Periodontitis/microbiology/immunology ; *Inflammation/microbiology/immunology/metabolism ; *Inflammation Mediators/metabolism/immunology ; Gingivitis/microbiology ; }, abstract = {Humans are biological units that host numerous microbial symbionts and their genomes, which together form a superorganism or holobiont. Changes in the balance of the oral ecosystem can have consequences for both general and oral health, such as cavities, gingivitis, and periodontitis. Periodontitis is initiated by a synergistic and dysbiotic microbial community that causes local inflammation and destruction of the tooth's supporting tissues, potentially leading to systemic inflammation. This inflammation caused by periodontal disease has been associated with various systemic alterations, and the immune system is largely responsible for the body's exacerbated response, which can induce and exacerbate chronic conditions. Studies indicate that subgingival microorganisms found in periodontitis reach the bloodstream and are distributed throughout the body and, therefore, can be found in distant tissues and organs. Among all diseases associated with periodontal disease, diabetes mellitus presents the strongest and most elucidated link, and its bidirectional relationship has already been demonstrated. Chronic hyperglycemia favors the worsening of periodontal parameters, while the aggravation of periodontal parameters can promote an increase in glycemic indexes. Other systemic diseases have been related to periodontitis, such as Alzheimer's, chronic kidney disease, atherosclerosis, and respiratory diseases. The importance of periodontal control may suggest a reduction in the chances of developing chronic inflammatory diseases because these two alterations often share inflammatory pathways and, for this reason, may influence each other.}, }
@article {pmid40108459, year = {2025}, author = {Duchêne, DA and Chowdhury, AA and Yang, J and Iglesias-Carrasco, M and Stiller, J and Feng, S and Bhatt, S and Gilbert, MTP and Zhang, G and Tobias, JA and Ho, SYW}, title = {Drivers of avian genomic change revealed by evolutionary rate decomposition.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {40108459}, issn = {1476-4687}, abstract = {Modern birds have diversified into a striking array of forms, behaviours and ecological roles. Analyses of molecular evolutionary rates can reveal the links between genomic and phenotypic change[1-4], but disentangling the drivers of rate variation at the whole-genome scale has been difficult. Using comprehensive estimates of traits and evolutionary rates across a family-level phylogeny of birds[5,6], we find that genome-wide mutation rates across lineages are predominantly explained by clutch size and generation length, whereas rate variation across genes is driven by the content of guanine and cytosine. Here, to find the subsets of genes and lineages that dominate evolutionary rate variation in birds, we estimated the influence of individual lineages on decomposed axes of gene-specific evolutionary rates. We find that most of the rate variation occurs along recent branches of the tree, associated with present-day families of birds. Additional tests on axes of rate variation show rapid changes in microchromosomes immediately after the Cretaceous-Palaeogene transition. These apparent pulses of evolution are consistent with major changes in the genetic machineries for meiosis, heart performance, and RNA splicing, surveillance and translation, and correlate with the ecological diversity reflected in increased tarsus length. Collectively, our analyses paint a nuanced picture of avian evolution, revealing that the ancestors of the most diverse lineages of birds underwent major genomic changes related to mutation, gene usage and niche expansion in the early Palaeogene period.}, }
@article {pmid40092220, year = {2025}, author = {Bhatia, A and Sharma, D and Mehta, J and Kumarasamy, V and Begum, MY and Siddiqua, A and Sekar, M and Subramaniyan, V and Wong, LS and Mat Rani, NNI}, title = {Probiotics and Synbiotics: Applications, Benefits, and Mechanisms for the Improvement of Human and Ecological Health.}, journal = {Journal of multidisciplinary healthcare}, volume = {18}, number = {}, pages = {1493-1510}, pmid = {40092220}, issn = {1178-2390}, abstract = {This review explores the multifaceted roles and applications of probiotics, emphasizing their significance in maintaining and enhancing host health through microbial interactions. It includes the concept of holobionts and the symbiotic relationships between hosts and their microbiomes, illustrating how various microbiota can enhance immunity, support growth, and prevent diseases. It delves into the customization of probiotics using molecular and genomic techniques, focusing Enterococcus, Bifidobacterium, and Lactobacillus species. Furthermore, it discusses the symbiotic effects of symbiotics which aids in enhancing the survivability and beneficial effects of probiotics. The role beneficial microbes in gut is emphasized, noting its impact on preventing diseases and maintaining a stable microbial community. The potential therapeutic value of probiotics includes the ability to treat gastrointestinal diseases, as well as to strengthen the immune system and reduce the number of free radicals that are present in the body. Additionally, it explores secondary metabolites produced by bacteria in the gut, such as bacteriocins and exopolysaccharides, and their effect on the health of human, particularly in the gastrointestinal tract. The review concludes by addressing the use of probiotics in traditional medicine and their potential in novel therapeutic applications, including the treatment of endangered wildlife species and various human ailments.}, }
@article {pmid40081757, year = {2025}, author = {Armengaud, J}, title = {The dawn of the revolution that will allow us to precisely describe how microbiomes function.}, journal = {Journal of proteomics}, volume = {316}, number = {}, pages = {105430}, doi = {10.1016/j.jprot.2025.105430}, pmid = {40081757}, issn = {1876-7737}, mesh = {Humans ; *Proteomics/methods ; *Microbiota/physiology ; Metabolomics/methods ; *Metagenomics/methods ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The community of microorganisms inhabiting a specific environment, such as the human gut - including bacteria, fungi, archaea, viruses, protozoa, and others - is known as the microbiota. A holobiont, in turn, refers to an integrated ecological unit where microbial communities function and interact with their host, thus is a more integrative concept. To understand the processes involved, the diversity of microorganisms present must be identified and their molecular components quantified, especially proteins. Indeed, proteins - through their roles as catalytic units, structural components, and signaling molecules - are the main drivers of biological processes. Metagenomics has significantly expanded what we know about the genetic material present in microbiota, revealing their functional potential; metabolomics delivers an overall snapshot of the metabolites produced by the community. But metaproteomics offers a complementary approach to explore microbiome and holobiont functionality by focusing on the active proteins and functional pathways from each taxon. Significant recent advances in high-resolution tandem mass spectrometry have greatly expanded the catalog of peptide sequences accessible in each sample, creating the conditions for unprecedented taxonomical profiling, while also providing more accurate biomass quantification, more detailed protein characterization, and a greater capacity to monitor abundance and distinguish host biomarkers. By integrating artificial intelligence into the metaproteomics pipeline, extended datasets can now be efficiently mined to gain a more comprehensive functional view of complex biological systems, paving the way for next-generation metaproteomics. In this perspective, I discuss the transformative potential of this methodology. We are on the cusp of a remarkable omic revolution that promises to uncover the intricate workings of microbiomes by producing a vast array of new knowledge with multiple applications. SIGNIFICANCE: Metaproteomics provides a powerful lens to investigate microbiome and holobiont functionality by identifying and quantifying active proteins and functional pathways within each taxon. Recent breakthroughs in high-resolution tandem mass spectrometry have dramatically expanded the repertoire of peptide sequences detectable per sample. This progress enables unprecedented taxonomic resolution for microbial identification, more precise biomass quantification, comprehensive protein characterization, abundance monitoring, and the unique identification of host biomarkers. In this commentary, I delve into the distinctive features that make metaproteomics a transformative tool. I discuss the recent advancements in tandem mass spectrometry and argue that the primary challenge in analyzing complex samples is shifting from data acquisition to data interpretation. With the integration of artificial intelligence, I believe next-generation metaproteomics is poised to become the next Big Thing in microbiome research, unlocking profound insights into microbial functionality and ecosystem dynamics.}, }
@article {pmid40077904, year = {2025}, author = {Brunet, M and Le Duff, N and Barbeyron, T and Thomas, F}, title = {Year-Round Quantification, Structure and Dynamics of Epibacterial Communities From Diverse Macroalgae Reveal a Persistent Core Microbiota and Strong Host Specificities.}, journal = {Environmental microbiology reports}, volume = {17}, number = {2}, pages = {e70077}, pmid = {40077904}, issn = {1758-2229}, support = {ANR-10-BTBR-04//Agence Nationale de la Recherche/ ; ANR-18-CE02-0001-01//Agence Nationale de la Recherche/ ; }, mesh = {*Seaweed/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Host Specificity ; Seasons ; Rhodophyta/microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Ecosystem ; }, abstract = {Macroalgae-bacteria interactions play pivotal ecological roles in coastal ecosystems. Previous characterisation of surface microbiota from various macroalgae evidenced fluctuations based on host tissues, physicochemical and environmental parameters. However, the dynamics and degree of similarity of epibacterial communities colonising phylogenetically distant algae from the same habitat are still elusive. We conducted a year-long monthly epimicrobiota sampling on five algal species inhabiting an English Channel rocky shore: Laminaria digitata, Ascophyllum nodosum, Fucus serratus (brown algae), Palmaria palmata (red alga) and Ulva sp. (green alga). To go beyond relative compositional data and estimate absolute variations in taxa abundance, we combined qPCR measurements of 16S rRNA gene copies with amplicon metabarcoding. A core microbiome composed of 10 genera was consistently found year-round on all algae. Notably, the abundant genus Granulosicoccus stood out for being the only one present in all samples and displayed an important microdiversity. Algal host emerged as the primary driver of epibacterial community composition, before seasonality, and bacterial taxa specifically associated with one or several algae were identified. Moreover, the impact of seasons on the epimicrobiota varied depending on algal tissues. Overall, this study provides an extensive characterisation of the microbiota of intertidal macroalgae and enhances our understanding of algal-bacteria holobionts.}, }
@article {pmid40071145, year = {2025}, author = {Prioux, C and Ferrier-Pagès, C and Del Campo, J and Guillou, L and Estaque, T and Allemand, D and Tignat-Perrier, R}, title = {Unraveling the impact of marine heatwaves on the Eukaryome of the emblematic Mediterranean red coral Corallium rubrum.}, journal = {ISME communications}, volume = {5}, number = {1}, pages = {ycaf035}, pmid = {40071145}, issn = {2730-6151}, abstract = {Global warming is intensifying heatwaves worldwide, leading to more frequent and severe temperature extremes. This study investigates the impact of the unprecedented 2022 Mediterranean heatwaves on the coral eukaryome, which has received little attention despite its known importance to coral holobiont functioning. Fifty-six colonies of the iconic red coral Corallium rubrum from the Mediterranean Sea were collected at different sites, depths, and health states. The microeukaryotic communities were analyzed using an 18S rRNA gene metabarcoding approach. Primers were designed to reduce amplification of the 18S rRNA gene sequences of the red coral while being universal for amplification of microeukaryotes. Our results showed that the red coral eukaryome was dominated by Dino-Group I, Licnophoridae, and Labyrinthulomycetes in the control sites that were not affected by the heat waves. In the heat-affected colonies, the composition of the coral eukaryome changed, with the relative abundances of Ephelotidae, Exobasidiomycetes, Corallicolidae, Labyrinthulomycetes, and/or the epibionts Phaeophyceae increasing depending on the intensity of heat stress experienced by the colonies. It was thus possible to link colony health to changes in the eukaryome. Finally, we illustrated putative interactions (competition, predator-prey relationship, and parasitism) occurring within C. rubrum eukaryome that could explain the compositional changes observed in the microeukaryotic communities under heat stress. Our findings improve our understanding of the ecological effects of heatwaves on marine ecosystems.}, }
@article {pmid40060185, year = {2025}, author = {Khattak, AA and Huang, Y and Afzal, M and Wang, X}, title = {MHZ3: a key regulator of ethylene signaling in rice.}, journal = {aBIOTECH}, volume = {6}, number = {1}, pages = {133-138}, pmid = {40060185}, issn = {2662-1738}, abstract = {The plant hormone ethylene regulates plant growth, development, and stress responses. Recent studies on early signaling events following ethylene perception in rice (Oryza sativa) have identified MAO HU ZI 3 (MHZ3) as a stabilizer of the ethylene receptors ETHYLENE RESPONSE SENSOR 2 (OsERS2) and ETHYLENE RECEPTOR 2 (OsETR2). MHZ3 ensures the interaction of these receptors with CONSTITUTIVE TRIPLE RESPONSE 2 (OsCTR2), thereby maintaining OsCTR2 activity. Ethylene treatment disrupts the interactions within the MHZ3/receptors/OsCTR2 protein complex, leading to decreased OsCTR2 phosphorylation and the initiation of downstream signaling. Recent studies have established MHZ3 as the primary regulator and switch for OsCTR2 phosphorylation. In this review, we explore the role of MHZ3 in regulating ethylene signaling and highlight its effects on plant growth, development, and stress responses at the plant holobiont level.}, }
@article {pmid40057976, year = {2025}, author = {Nikitashina, V and Bartels, B and Mansour, JS and LeKieffre, C and Decelle, J and Hertweck, C and Not, F and Pohnert, G}, title = {Metabolic interdependence and rewiring in radiolaria-microalgae photosymbioses.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40057976}, issn = {1751-7370}, support = {//European Union/ ; 2022FGI0010//European Regional Development Fund/ ; }, mesh = {*Symbiosis ; *Microalgae/metabolism/physiology ; Metabolome ; Photosynthesis ; }, abstract = {Marine planktonic Radiolaria harboring symbiotic microalgae are ubiquitous in the oceans and abundant in oligotrophic areas. In these low-nutrient environments, they are among the most important primary producers. Systematic studies of radiolarian biology are limited because radiolaria are non-culturable and prone to damage during sampling. To obtain insight into the mechanistic basis of radiolarian photosymbiosis, we address here the metabolic contributions of the partners to the performance of the holobiont. Therefore, we describe the metabolic inventory of two highly abundant photosymbiotic radiolaria-colony-forming Collodaria and single-celled Acantharia and compare their metabolomes to metabolomes of respective free-living algae. Most of the metabolites detected in the symbiosis are not present in the free-living algae, suggesting a significant transformation of symbionts' metabolites by the host. The metabolites identified in the holobiont and the free-living algae encompass molecules of primary metabolism and a number of osmolytes, including dimethylsulfoniopropionate. Mass spectrometry imaging revealed the presence of dimethylsulfoniopropionate in the symbionts and host cells, indicating that the algae provide osmolytic protection to the host. Furthermore, our findings suggest a possible dependence of Collodaria on symbiotic vitamin B3. Distinctive differences in phospholipid composition between free-living and symbiotic stages indicate that the algal cell membrane may undergo rearrangement in the symbiosis. Our results demonstrate a strong interdependence and rewiring of the algal metabolism underlying radiolaria-microalgae photosymbioses.}, }
@article {pmid40057975, year = {2025}, author = {Adomako, MO and Wu, J and Yu, FH}, title = {Ecological and evolutionary responses of earthworm holobionts to environmental changes.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {40057975}, issn = {1751-7370}, support = {W2433081//National Science Foundation of China/ ; }, mesh = {Animals ; *Oligochaeta/microbiology/physiology ; *Biological Evolution ; *Microbiota ; Soil Microbiology ; Host Microbial Interactions ; Soil/chemistry ; Ecosystem ; *Climate Change ; Symbiosis ; }, abstract = {Global environmental change substantially affects soil detritivores, including earthworms, impacting host-microbiota interactions and altering key soil biogeochemical processes such as litter decomposition. As microbial communities are inherently capable of rapid evolution, responses of earthworms and associated microbiota (i.e. earthworm holobionts) to global environmental change may likely involve the interplay of ecological and evolutionary processes and feedback. Although species-level responses of earthworms to global environmental change are well studied, the potential ecological and evolutionary responses of earthworm holobionts to environmental change remain unexplored. Here, we provide a conceptual framework to elaborate on the complex network of earthworm host-microbiota interactions that modify their traits in response to global environmental change, jointly shaping their ecology and evolution. Based on the literature, we synthesize evidence of global environmental change impacts on earthworm host-microbiota and discuss evidence of their ecological and evolutionary responses to environmental change. Lastly, we highlight the agro- and eco-system-level consequences of environmental change-mediated shift in earthworm host-microbiota functions. Soil legacies of environmental change have cascading detrimental impacts on the abundance, diversity, and functional dynamics of earthworm host-microbiota interactions in agriculture and ecosystems. The primary mechanisms driving such responses of earthworm hosts and associated microbial communities to environmental change include altered litter quality and host dietary preferences, competitive interactions and exclusion, habitat homogenization, and a shift in soil physicochemical and biological processes. Therefore, advancing knowledge of the intricate animal-microorganism interactions is crucial for belowground biodiversity management in a changing global environment.}, }
@article {pmid40054578, year = {2025}, author = {Zeng, Y and Lu, X and Wang, M and Chen, R and Li, Q and Zhu, J and Su, Z and Lin, F}, title = {Endophyte Acrocalymma vagum establishes the holobiont with rice to attract beneficial microorganisms and promote disease resistance.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2025.03.008}, pmid = {40054578}, issn = {2090-1224}, abstract = {INTRODUCTION: Endophytic fungi are essential microorganisms in promoting plant health. However, the mechanism of endophytic fungi regulating root microbiota to enhance crop production and resistance remains unclear.<br><br>OBJECTIVES: We aimed i) to explore the microbial alteration driven by endophytic Acrocalymma vagum in developing crop yield and rice resistance; ii) to reveal the mechanism of root-released compound stimulated by A. vagum in recruiting benefit microbes.<br><br>METHODS: The microbiome was applied in a culture-dependent and culture-independent method to study the microbial communities of the A. vagum-rice holobiont using 16S rRNA and ITS gene metabarcoding. Non-target metabolome identified distinct metabolites responsible for community variations. Label-free proteomic analyses investigated the association between primary genes related to the holobiont formation. CRISPR/Cas9 technique and homologous recombination replacement were used to characterize the functions of putative genes.<br><br>RESULTS: A. vagum enhanced cultivated rice yield by 5.73&#xa0;&#xb1;&#xa0;1.76&#xa0;% and induced 83.24&#xa0;&#xb1;&#xa0;9.86&#xa0;% control efficiency against rice blast. We discovered that A. vagum simplified rice microbial structure based on co-occurrence networks, by lowering the proportion of potentially pathogenic predominant Burkholderia and driving rice to recruit beneficial Lactobacillus, Sarocladium and Nigrospora to promote rice growth with the increases of 44.41&#xa0;&#xb1;&#xa0;5.10&#xa0;% shoot height and 70.21&#xa0;&#xb1;&#xa0;9.57&#xa0;% shoot biomass. Moreover, the holobiont released coumaric and trans-ferulic acids to attract beneficial microbes. 206 rice proteins were notably up-regulated in the holobiont, particularly the OsPrxs. CRISPR/Cas9-edited mutants of OsPRX70 and OsPRX95 reduced the promotion effect of A. vagum on rice growth. Furthermore, the pathways of 39 overexpressed proteins in A. vagum were enriched in invading the host and inducing resistance. The knockouts of AvGH3, AvGH7, AvMFS1, and AvCBA transformed A. vagum role from endophyte to pathogen.<br><br>CONCLUSIONS: The A. vagum-rice holobiont releases recruitment signals and improves the rice community structure. We provide ecological and molecular evidence to confirm the mutualism of endophyte-plant-promoting growth and disease resistance.}, }
@article {pmid40054249, year = {2025}, author = {Walling, LK and Gamache, MH and González-Pech, RA and Harwood, VJ and Ibrahim-Hashim, A and Jung, JH and Lewis, DB and Margres, MJ and McMinds, R and Rasheed, K and Reis, F and van Riemsdijk, I and Santiago-Alarcon, D and Sarmiento, C and Whelan, CJ and Zalamea, PC and Parkinson, JE and Richards, CL}, title = {Incorporating microbiome analyses can enhance conservation of threatened species and ecosystem functions.}, journal = {The Science of the total environment}, volume = {970}, number = {}, pages = {178826}, doi = {10.1016/j.scitotenv.2025.178826}, pmid = {40054249}, issn = {1879-1026}, mesh = {*Conservation of Natural Resources/methods ; *Microbiota ; *Ecosystem ; *Endangered Species ; Biodiversity ; Genomics ; }, abstract = {Conservation genomics is a rapidly growing subdiscipline of conservation biology that uses genome-wide information to inform management of biodiversity at all levels. Such efforts typically focus on species or systems of conservation interest, but rarely consider associated microbes. At least three major approaches have been used to study how microorganisms broadly contribute to conservation areas: (1) diversity surveys map out microbial species distribution patterns in a variety of hosts, natural environments or regions; (2) functional surveys associate microbial communities with factors of interest, such as host health, symbiotic interactions, environmental characteristics, ecosystem processes, and biological invasions; and (3) manipulative experiments examine the response of changes to microbial communities or determine the functional roles of specific microbes within hosts or communities by adding, removing, or genetically modifying microbes. In practice, multiple approaches are often applied simultaneously. The results from all three conservation genomics approaches can be used to help design practical interventions and improve management actions, some of which we highlight below. However, experimental manipulations allow for more robust causal inferences and should be the ultimate goal of future work. Here we discuss how further integration of microbial research of a host's microbiome and of free living microbes into conservation biology will be an essential advancement for conservation of charismatic organisms and ecosystem functions in light of ongoing global environmental change.}, }
@article {pmid40054197, year = {2025}, author = {Jiang, S and He, L and Cao, L and Sun, R and Dai, Z and Liang, YQ and Ren, L and Sun, S and Li, C}, title = {Unraveling individual and combined toxicity of microplastics and tetracycline at environment-related concentrations to coral holobionts.}, journal = {Journal of hazardous materials}, volume = {490}, number = {}, pages = {137823}, doi = {10.1016/j.jhazmat.2025.137823}, pmid = {40054197}, issn = {1873-3336}, mesh = {Animals ; *Anthozoa/drug effects/metabolism/microbiology ; *Microplastics/toxicity ; *Tetracycline/toxicity ; *Water Pollutants, Chemical/toxicity ; *Anti-Bacterial Agents/toxicity ; Coral Reefs ; Bacteria/drug effects ; Microbiota/drug effects ; Symbiosis/drug effects ; }, abstract = {Coral holobionts constitute the foundational organisms of coral reef ecosystems. As an emerging pollutant, the projected accumulated levels of microplastics (MPs) are expected to continue increasing. Meanwhile, due to their properties, MPs can absorb multiple other marine pollutants, such as antibiotics (ATs). However, the co-toxicity mechanism of MPs and ATs to coral holobionts remains to be explored. Here, using Zoanthus sociatus as a model organism, we investigate the individual and combined toxicity of MPs and tetracycline (TC) at environment-related concentrations to coral holobionts. Microbiomics indicate that MPs and TC increase coral holobionts bacterial species richness while concurrently reducing the microbial community structure stability. The key metabolites and enzyme activity results demonstrated that the impacts of MPs and TC on corals encompassed antioxidant capacity, detoxification capability, immune function, and lipid metabolism. Transcriptomics shows that MPs and TC disrupt coral-algae relationships mainly through host nutrition limitation and inhibition of symbiotic algae carbon/nitrogen metabolism, respectively. A synergistic effect between MPs and TC has also been observed. In contrast, coral holobionts have shown adaptability through activating coral-symbiodiniaceae-bacteria interactions, mainly including: 1) enhancing the abundance of BMCs (beneficial microorganisms for corals); 2) enhancing host lipid accumulation; 3) immunoregulation; 4) symbiotic regulation. Overall, our findings provide new insights into the co-toxicity of MPs and TC, and highlight those MPs and TC at current environment concentration and predicted for most oceans in the coming decades, can ultimately cause coral bleaching.}, }
@article {pmid40048537, year = {2025}, author = {Kistler, L and de Oliveira Freitas, F and Gutaker, RM and Maezumi, SY and Ramos-Madrigal, J and Simon, MF and Mendoza F, JM and Drovetski, SV and Loiselle, H and de Oliveira, EJ and Vieira, EA and Carvalho, LJCB and Ellis Perez, M and Lin, AT and Liu, HL and Miller, R and Przelomska, NAS and Ratan, A and Wales, N and Wann, K and Zhang, S and García, M and Valenzuela, D and Rothhammer, F and Santoro, CM and Domic, AI and Capriles, JM and Allaby, RG}, title = {Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.}, journal = {Science (New York, N.Y.)}, volume = {387}, number = {6738}, pages = {eadq0018}, doi = {10.1126/science.adq0018}, pmid = {40048537}, issn = {1095-9203}, mesh = {*Genome, Plant ; *Manihot/genetics/growth &amp; development/classification ; *Genetic Variation ; Brazil ; Domestication ; *Crops, Agricultural/genetics ; Heterozygote ; }, abstract = {Manioc-also called cassava and yuca-is among the world's most important crops, originating in South America in the early Holocene. Domestication for its starchy roots involved a near-total shift from sexual to clonal propagation, and almost all manioc worldwide is now grown from stem cuttings. In this work, we analyze 573 new and published genomes, focusing on traditional varieties from the Americas and wild relatives from herbaria, to reveal the effects of this shift to clonality. We observe kinship over large distances, maintenance of high genetic diversity, intergenerational heterozygosity enrichment, and genomic mosaics of identity-by-descent haploblocks that connect all manioc worldwide. Interviews with Indigenous traditional farmers in the Brazilian Cerrado illuminate how traditional management strategies for sustaining, diversifying, and sharing the gene pool have shaped manioc diversity.}, }
@article {pmid40038092, year = {2025}, author = {Million, WC and Voolstra, CR and Perna, G and Puntin, G and Rowe, K and Ziegler, M}, title = {Resolving Symbiodiniaceae Diversity Across Coral Microhabitats and Reef Niches.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70065}, pmid = {40038092}, issn = {1462-2920}, support = {//German Academic Exchange Service/ ; 469364832//Deutsche Forschungsgemeinschaft/ ; SPP 2299/441832482//Deutsche Forschungsgemeinschaft/ ; //King Abdullah University of Science and Technology/ ; }, mesh = {Animals ; *Anthozoa/parasitology ; *Coral Reefs ; *Ecosystem ; *Dinoflagellida/genetics/classification/isolation &amp; purification ; *Biodiversity ; Indian Ocean ; Symbiosis ; Phylogeny ; Seawater/parasitology/microbiology ; Sequence Analysis, DNA ; }, abstract = {Dinoflagellates of the family Symbiodiniaceae are important symbionts of diverse marine animals and they also occupy different environmental niches on coral reefs. The link between diversity at ecosystem-scale to microhabitats of Symbiodiniaceae within the coral holobiont is largely unknown. Using ITS2-amplicon sequencing, we compared Symbiodiniaceae communities across four environments (seawater, near-reef vs. distant sediments and turf algae) and two coral microhabitats (tissue, mucus) on a coral reef in the Red Sea. We found that coral and environmental habitats were both dominated by the genera Symbiodinium, Cladocopium and Durusdinium, but environmental habitats additionally harboured Fugacium, Gerakladium and Halluxium. Each environmental habitat harboured a distinct Symbiodiniaceae community. Nonetheless, 17 ITS2 sequences were shared among coral and environmental habitats and were also part of nearly half of the ITS2 type profiles in coral-based communities. Tissues and mucus of 49 coral colonies from 17 genera had largely identical Symbiodiniaceae communities. Together with the large difference between environmental Symbiodiniaceae communities and those in the coral tissue and mucus, our results indicate a clear barrier between host-associated and environmental Symbiodiniaceae communities marked by only few shared complete type profiles. Monitoring coral colonies after mucus sampling confirmed its suitability for long-term monitoring of coral-associated Symbiodiniaceae communities.}, }
@article {pmid40037084, year = {2025}, author = {Zhang, J and Liu, C and Ling, J and Zhou, W and Wang, Y and Cheng, H and Huang, X and Yang, Q and Zhang, W and Liang, T and Zhang, Y and Dong, J}, title = {Revealing the potential of biochar for heavy metal polluted seagrass remediation from microbial perspective.}, journal = {Ecotoxicology and environmental safety}, volume = {292}, number = {}, pages = {117991}, doi = {10.1016/j.ecoenv.2025.117991}, pmid = {40037084}, issn = {1090-2414}, mesh = {*Charcoal/chemistry ; *Water Pollutants, Chemical/toxicity/metabolism/analysis ; *Metals, Heavy/analysis/metabolism/toxicity ; *Environmental Restoration and Remediation/methods ; *Hydrocharitaceae/microbiology/drug effects ; Microbiota/drug effects ; Biodegradation, Environmental ; }, abstract = {Seagrass meadows are under threat due to climate change and human activities, including heavy metal contamination, which can accumulate in seagrass tissues and harm their health and productivity. Despite extensive research, effective remediation strategies are lacking. This study investigated biochar's potential as a remediation agent for seagrass meadows affected by heavy metal pollution. Heavy metal pollution was simulated by adding copper (Cu) and chromium (Cd) to seagrass Thalassia hemprichii, and the remediation effects of biochar were evaluated by monitoring seagrass physiology, root-associated microbial communities, and heavy metal concentrations. Seagrasses can accumulate heavy metals, which adversely affect their health and alter microbial communities. Seagrasses may resist heavy metal stress by releasing dissolved organic carbon (DOC) and recruiting beneficial bacteria. Biochar reduced heavy metal bioavailability and restored seagrass ecosystem health, as evidenced by restored microbial community dynamics. This study highlights biochar's promising role in seagrass meadow restoration impacted by heavy metal pollution.}, }
@article {pmid40034670, year = {2025}, author = {Adair, MG and Tolley, KA and van Vuuren, BJ and da Silva, JM}, title = {Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion).}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18811}, pmid = {40034670}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Lizards/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Anthropogenic Effects ; Ecosystem ; Bacteria/genetics/classification ; }, abstract = {Exploration of the microbiome has been referred to as a final frontier in biological research. This is due to its precedence for generating insights on the holistic functioning of organismal biology by exploring the interactions between hosts and their associated symbiotic organisms. The microbiomes of many vertebrate groups still require exploration to advance current knowledge and fill previous knowledge gaps. This study generated initial descriptions of the bacterial microbiomes of three species of dwarf chameleon (Bradypodion) from the 16S rRNA gene region targeting the V3 and V4 hypervariable regions. This led to the successful identification of 1,073 and 4,502 independent amplicon sequence variants from buccal swab and faecal material samples, respectively. This newly acquired information is intended as a baseline for future work incorporating holobiont information. The diversity of microbial taxa suggests that the total dwarf chameleon microbiome is similar to other squamates investigated to date, as well as chelonians (Testudines). Microbial frequency differences were noted in comparison to crocodilians (Archosauria) and mammalian groups. Furthermore, this study aimed to examine the influence of habitat transformation on the composition of the microbiome in dwarf chameleons as each of the study species occupy both urban and natural habitats. Given that most urban habitats are highly transformed, the expectation was that microbial assemblages of the gastro-intestinal tracts of all three Bradypodion species would show significant differences between populations (i.e., natural, or urban). It was found, however, that the level of effect was contingent on species: B. melanocephalum populations showed noticeable microbiome differences between urban and natural populations; B. thamnobates showed variations in microbial community dispersions between populations; and B. setaroi showed no significant microbiome differences based on diversity metrics although some frequency differences, in microbiome composition, were observed between populations. We suggest that the magnitude of difference between the habitats occupied by the populations is a factor, given the apparent disparity between the natural and urban habitats for B. melanocephalum as compared to the other two species.}, }
@article {pmid40028829, year = {2025}, author = {Leiva, C and Torda, G and Zhou, C and Pan, Y and Harris, J and Xiang, X and Tan, S and Tian, W and Hume, B and Miller, DJ and Li, Q and Zhang, G and Cooke, I and Rodolfo-Metalpa, R}, title = {Rapid Evolution in Action: Environmental Filtering Supports Coral Adaptation to a Hot, Acidic, and Deoxygenated Extreme Habitat.}, journal = {Global change biology}, volume = {31}, number = {3}, pages = {e70103}, pmid = {40028829}, issn = {1365-2486}, support = {DE200101064//Australian Research Council's Discovery Early Career Award/ ; Adaptationofcoralstoclimatechange//French Government's Ministry of Foreign Affairs' Fonds Pacifique scheme/ ; //Flotte Oc&#xe9;anographique Fran&#xe7;aise/ ; OIA-1946352//National Science Foundation NSF-EPSCoR/ ; //BGI Australia through the BGI Biodiversity Research Grant/ ; //China National GeneBank/ ; }, mesh = {Animals ; *Anthozoa/physiology/genetics/microbiology ; Climate Change ; New Caledonia ; *Adaptation, Physiological ; *Biological Evolution ; Hot Temperature ; Symbiosis ; Extreme Environments ; Ecosystem ; Polymorphism, Single Nucleotide ; Hydrogen-Ion Concentration ; Coral Reefs ; }, abstract = {The semienclosed Bouraké lagoon in New Caledonia is a natural system that enables observation of evolution in action with respect to stress tolerance in marine organisms, a topic directly relevant to understanding the consequences of global climate change. Corals inhabiting the Bouraké lagoon endure extreme conditions of elevated temperature (> 33°C), acidification (7.2 pH units), and deoxygenation (2.28 mg O2 L-1), which fluctuate with the tide due to the lagoon's geomorphology. To investigate the underlying bases of the apparent stress tolerance of these corals, we combined whole genome resequencing of the coral host and ITS2 metabarcoding of the photosymbionts from 90 Acropora tenuis colonies from three localities along the steep environmental gradient from Bouraké to two nearby control reefs. Our results highlight the importance of coral flexibility to associate with different photosymbionts in facilitating stress tolerance of the holobiont; but, perhaps more significantly, strong selective effects were detected at specific loci in the host genome. Fifty-seven genes contained SNPs highly associated with the extreme environment of Bouraké and were enriched in functions related to sphingolipid metabolism. Within these genes, the conserved sensor of noxious stimuli TRPA1 and the ABCC4 transporter stood out due to the high number of environmentally selected SNPs that they contained. Protein 3D structure predictions suggest that a single-point mutation causes the rotation of the main regulatory domain of TRPA1, which may be behind this case of natural selection through environmental filtering. While the corals of the Bouraké lagoon provide a striking example of rapid adaptation to extreme conditions, overall, our results highlight the need to preserve the current standing genetic variation of coral populations to safeguard their adaptive potential to ongoing rapid environmental change.}, }
@article {pmid40015318, year = {2025}, author = {Mudlaff, CM and Weinberger, F and Düsedau, L and Ghotbi, M and Künzel, S and Bonthond, G}, title = {Seasonal Cycles in a Seaweed Holobiont: A Multiyear Time Series Reveals Repetitive Microbial Shifts and Core Taxa.}, journal = {Environmental microbiology}, volume = {27}, number = {3}, pages = {e70062}, pmid = {40015318}, issn = {1462-2920}, support = {WE2700/5-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Seasons ; *Microbiota ; *Gracilaria/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Seaweed/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Seasonality is an important natural feature that drives cyclic environmental changes. Seaweed holobionts, inhabiting shallow waters such as rocky shores and mud flats, are subject to seasonal changes in particular, but little is known about the influence of seasonality on their microbial communities. In this study, we conducted a three-year time series, sampling at two-month intervals, to assess the seasonality of microbial epibiota in the seaweed holobiont Gracilaria vermiculophylla. Our results reveal pronounced seasonal shifts that are both taxonomic and functional, oscillating between late winter and early summer across consecutive years. While epibiota varied taxonomically between populations, they were functionally similar, indicating that seasonal variability drives functional changes, while spatial variability is more redundant. We also identified seasonal core microbiota that consistently (re)associated with the host at specific times, alongside a permanent core that is present year-round, independent of season or geography. These findings highlight the dynamic yet resilient nature of seaweed holobionts and demonstrate that their epibiota undergo predictable changes. Therewith, this research offers important insights into the temporal dynamics of seaweed-associated microbiota and demonstrates that the relationship between seaweed host and its epibiota is not static but naturally subject to an ongoing seasonal succession process.}, }
@article {pmid40005803, year = {2025}, author = {Minerdi, D and Sabbatini, P}, title = {Exploring the Grapevine Microbiome: Insights into the Microbial Ecosystem of Grape Berries.}, journal = {Microorganisms}, volume = {13}, number = {2}, pages = {}, pmid = {40005803}, issn = {2076-2607}, abstract = {Plant growth, health, and resilience to stress are intricately linked to their associated microbiomes. Grapevine, functioning as a holobiont, forms essential relationships with fungi and bacteria across both its belowground (roots) and aboveground (leaves and berries) compartments. The root microbiome exhibits a stable, site-specific structure, whereas the microbiomes of ephemeral tissues such as leaves and berries, which regenerate annually, display more stochastic assembly patterns across growing seasons. Among these, grape berries represent a critical component in viticulture due to their direct influence on wine quality and flavor complexity. Berries provide a unique ecological niche, hosting diverse microbial communities composed of yeasts, bacteria, and fungi that interact with the grapevine and its surrounding environment. These microorganisms are not only pivotal to berry development but also contribute significantly to the synthesis of secondary metabolites and fermentation processes, ultimately shaping the sensory and organoleptic properties of wine. This review consolidates current knowledge on the grapevine microbiome, with a particular emphasis on the microbial dynamics of grape berries.}, }
@article {pmid40003826, year = {2025}, author = {Castañeda-Espinosa, A and Duque-Granda, D and Cadavid-Restrepo, G and Murcia, LM and Junca, H and Moreno-Herrera, CX and Vivero-Gómez, RJ}, title = {Study of Bacterial Communities in Water and Different Developmental Stages of Aedes aegypti from Aquatic Breeding Sites in Leticia City, Colombian Amazon Biome.}, journal = {Insects}, volume = {16}, number = {2}, pages = {}, pmid = {40003826}, issn = {2075-4450}, support = {57545//Universidad Nacional de Colombia/ ; }, abstract = {Aedes aegypti is a key vector in the transmission of arboviral diseases in the Colombian Amazon. This study aimed to characterize microbiota composition using DNA extracted from water in artificial breeding sites, immature stages, and adults of Ae. aegypti in Leticia, Amazonas. Additionally, the physicochemical water variables were correlated with the bacterial communities present. Eight artificial breeding sites were identified, with bucket, plant pot, and tire being the most frequent. The breeding sites exhibited similar physicochemical profiles, with significant temperature and salinity differences (p-value < 0.03). The most representative bacterial genera included Ottowia (82%), Xanthobacter (70.59%), and Rhodocyclaceae (92.78%) in breeding site water; Aquabacterium (61.07%), Dechloromonas (82.85%), and Flectobacillus (58.94%) in immature stages; and Elizabethkingia (70.89%) and Cedecea (39.19%) in males and females of Ae. aegypti. Beta diversity analysis revealed distinct clustering between adults and the water and immature communities (p-value < 0.001). Multivariate analysis showed strong correlations among bacterial communities, breeding sites, and physicochemical variables such as tire and drum cover which exhibited high levels of total dissolved solids, conductivity, and salinity associated with Flectobacillus, Leifsonia, Novosphingobium, Ottowia, and Rhodobacter. Bacterial genera such as Mycobacterium, Escherichia, Salmonella, and Clostridium, present in artificial breeding sites, are associated with public health relevance. This study provides insights into bacterial community dynamics across Ae. aegypti's life cycle and underscores the importance of water physicochemical and biological characteristics for developing new vector control strategies.}, }
@article {pmid39998222, year = {2025}, author = {Williamson, EM and Hammer, TJ and Hogendoorn, K and Eisenhofer, R}, title = {Blanking on blanks: few insect microbiota studies control for contaminants.}, journal = {mBio}, volume = {16}, number = {4}, pages = {e0265824}, pmid = {39998222}, issn = {2150-7511}, mesh = {*Insecta/microbiology ; Animals ; *Microbiota ; Bacteria/genetics/classification ; *DNA Contamination ; }, abstract = {Research on insect-microbe relationships is booming, with DNA sequencing being the most commonly used method to describe insect microbiota. However, sequencing is vulnerable to contamination, especially when the sample has low microbial biomass. Such low-biomass samples are common across insect taxa, developmental stages, and tissue types. Identifying putative contaminants is essential to distinguish between true microbiota and introduced contaminant DNA. It is therefore important that studies control for contamination, but how often this is done is unknown. To investigate the status quo of contamination control, we undertook a systematic literature review to quantify the prevalence of negative control usage and contamination control across the literature on insect microbiota (specifically bacterial communities) over a 10 year period. Two-thirds of the 243 insect microbiota studies evaluated had not included blanks (negative controls), and only 13.6% of the studies sequenced these blanks and controlled for contamination in their samples. Our findings highlight a major lack of contamination control in the field of insect microbiota research. This result suggests that a number of microbes reported in the literature may be contaminants as opposed to insect-associated microbiota and that more rigorous contamination control is needed to improve research reliability, validity, and reproducibility. Based on our findings, we recommend the previously developed guidelines outlined in the RIDE checklist, with the addition of one more guideline. We refer to this as the RIDES checklist, which stands for Report methodology, Include negative controls, Determine the level of contamination, Explore contamination downstream, and State the amount of off-target amplification.IMPORTANCEOur systematic review reveals a major lack of methodological rigor within the field of research on insect-associated microbiota. The small percentage of studies that control for contamination suggests that an unknown but potentially considerable number of bacteria reported in the literature could be contaminants. The implication of this finding is that true microbiota may be masked or misrepresented, especially in insects with low microbial biomass.}, }
@article {pmid39993925, year = {2025}, author = {Sajid, S and Xiao, B and Zhang, G and Zhang, Z and Chen, L and Fang, JK and Lu, Y and Cai, L}, title = {Increased sulfate-reducing bacteria can drive microbial dysbiosis in bleached corals.}, journal = {Journal of applied microbiology}, volume = {136}, number = {3}, pages = {}, doi = {10.1093/jambio/lxaf043}, pmid = {39993925}, issn = {1365-2672}, support = {JCYJ20200109144803833//Natural Science Foundation of Shenzhen/ ; 2019YFE0198500//National Key Research and Development Program of China/ ; MHP/009/19//Mainland-Hong Kong Joint Funding Scheme, Innovation and Technology Fund/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Sulfates/metabolism ; Microbiota ; Phylogeny ; Symbiosis ; *Dinoflagellida/genetics/classification ; Biodiversity ; China ; DNA, Bacterial/genetics ; }, abstract = {AIMS: Coral bleaching occurs when coral colonies lose their Symbiodiniaceae partner and turn pale or white. Although this event is generally temperature-induced, there is also the possibility of holobiont microbial infection and dysbiosis. To address this issue, this study was conducted to investigate the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of Porites lutea collected from eastern Shenzhen.<br><br>METHODS AND RESULTS: Internal transcribed spacer 2 and 16S amplicon sequencing analysis were used to explore the diversity and composition of Symbiodiniaceae and bacteria in healthy and bleached colonies of P. lutea. Bacterial diversity and richness were significantly higher in bleached colonies than in healthy colonies (P&#xa0;<&#xa0;0.05), whereas the diversity and richness of Symbiodiniaceae showed no significant changes. The bleaching event exerted a more significant impact on Symbiodiniaceae composition, which differed between healthy and bleached colonies (PERMANOVA, F&#xa0;=&#xa0;8.246, P&#xa0;<&#xa0;0.05). In terms of composition, Clade C (Cladocopium) was the predominant Symbiodiniaceae, whereas subclade C116 and C2r were significantly less abundant in bleached colonies than in healthy colonies (P&#xa0;<&#xa0;0.05). The phyla Bacteroidetes, Acidobacteria, and Actinobacteria were significantly more abundant in bleached colonies than in healthy colonies (P&#xa0;<&#xa0;0.05). The sulfate-reducing bacteria (SRB) Desulfobulbus and Desulfobacter at the genus level and Desulfobacterales and Desulfuromonadales at the order level were significantly more abundant in bleached colonies than in healthy colonies (P&#xa0;<&#xa0;0.05). The co-occurrence patterns of Symbiodiniaceae and bacteria revealed a negative correlation of Desulfofaba, Desulfovibrio, Desulfarculus, and Desulfobulbus with Endozoicomonas, a very common symbiotic bacterial genus found in corals.<br><br>CONCLUSION: Coral bleaching may be associated with significant shifts in microbial communities, including increased SRB abundance, which may disrupt microbial balance and contribute to bleaching.}, }
@article {pmid39985228, year = {2025}, author = {Song, MJ and Freund, F and Tribble, CM and Toffelmier, E and Miller, C and Bradley Shaffer, H and Li, FW and Rothfels, CJ}, title = {The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal.}, journal = {American journal of botany}, volume = {112}, number = {3}, pages = {e70010}, doi = {10.1002/ajb2.70010}, pmid = {39985228}, issn = {1537-2197}, support = {//California Conservation Genomics Project, with funding provided to the University of California by the State of California, State Budget Act of 2019 [UC Award ID RSI-19-690224]./ ; }, mesh = {*Ferns/microbiology ; *Microbiota ; *Symbiosis ; *Nitrogen Fixation ; }, abstract = {PREMISE: Azolla is a genus of floating ferns that has closely evolved with a vertically transmitted obligate cyanobacterium endosymbiont-Anabaena azollae-that fixes nitrogen. There are also other lesser-known Azolla symbionts whose role and mode of transmission are unknown.<br><br>METHODS: We sequenced 112 Azolla specimens collected across the state of California and characterized their metagenomes to identify the common bacterial endosymbionts and assess their patterns of interaction.<br><br>RESULTS: Four genera were found across all samples, establishing that multiple Azolla endosymbionts were consistently present. We found varying degrees of cophylogenetic signal across these taxa as well as varying degrees of isolation by distance and of pseudogenation, which demonstrates that multiple processes underlie how this endosymbiotic community is constituted. We also characterized the entire Azolla leaf pocket microbiome.<br><br>CONCLUSIONS: These results show that the Azolla symbiotic community is complex and features members at potentially different stages of symbiosis evolution, further supporting the utility of the Azolla microcosm as a system for studying the evolution of symbioses.}, }
@article {pmid39984283, year = {2025}, author = {Adouane, E and Hubas, C and Leblanc, C and Lami, R and Prado, S}, title = {Multi-omics analysis of the correlation between surface microbiome and metabolome in Saccharina latissima (Laminariales, Phaeophyceae).}, journal = {FEMS microbiology ecology}, volume = {101}, number = {3}, pages = {}, pmid = {39984283}, issn = {1574-6941}, support = {//National Museum of Natural History/ ; }, mesh = {*Metabolome ; *Microbiota ; *Fungi/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Phaeophyceae/microbiology/metabolism ; Metabolomics ; Multiomics ; Edible Seaweeds ; Laminaria ; }, abstract = {The microbiome of Saccharina latissima, an important brown macroalgal species in Europe, significantly influences its health, fitness, and pathogen resistance. Yet, comprehensive studies on the diversity and function of microbial communities (bacteria, eukaryotes, and fungi) associated with this species are lacking. Using metabarcoding, we investigated the epimicrobiota of S. latissima and correlated microbial diversity with metabolomic patterns (liquid chromatography coupled to tandem mass spectrometry). Specific epibacterial and eukaryotic communities inhabit the S. latissima surface, alongside a core microbiota, while fungal communities show lower and more heterogeneous diversity. Metabolomic analysis revealed a large diversity of mass features, including putatively annotated fatty acids, amino derivatives, amino acids, and naphthofurans. Multiple-factor analysis linked microbial diversity with surface metabolome variations, driven mainly by fungi and bacteria. Two taxa groups were identified: one associated with bacterial consortia and the other with fungal consortia, each correlated with specific metabolites. This study demonstrated a core bacterial and eukaryotic microbiota associated with a core metabolome and highlighted interindividual variations. Annotating the surface metabolome using Natural Products databases suggested numerous metabolites potentially involved in interspecies chemical interactions. Our findings establish a link between microbial community structure and function, identifying two microbial consortia potentially involved in the chemical defense of S. latissima.}, }
@article {pmid39980208, year = {2025}, author = {Holman, LE and Zampirolo, G and Gyllencreutz, R and Scourse, J and Frøslev, T and Carøe, C and Gopalakrishnan, S and Pedersen, MW and Bohmann, K}, title = {Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e14086}, doi = {10.1111/1755-0998.14086}, pmid = {39980208}, issn = {1755-0998}, support = {856488//H2020 European Research Council/ ; }, abstract = {The condition of ancient marine ecosystems provides context for contemporary biodiversity changes in human-impacted oceans. Sequencing sedimentary ancient DNA (sedaDNA) is an emerging method for generating high-resolution biodiversity time-series data, offering insights into past ecosystems. However, few studies directly compare the two predominant sedaDNA sequencing approaches: metabarcoding and shotgun-metagenomics, and it remains unclear if these methodological differences affect diversity metrics. We compared these methods using sedaDNA from an archived marine sediment record sampled in the Skagerrak, North Sea, spanning almost 8000 years. We performed metabarcoding of a eukaryotic 18S rRNA region (V9) and sequenced 153-229 million metagenomic reads per sample. Our results show limited overlap between metabarcoding and metagenomics, with only three metazoan genera detected by both methods. For overlapping taxa, metabarcoding detections became inconsistent for samples older than 2000 years, while metagenomics detected taxa throughout the time series. We observed divergent patterns of alpha diversity, with metagenomics indicating decreased richness towards the present and metabarcoding showing an increase. However, beta diversity patterns were similar between methods, with discrepancies only in metazoan data comparisons. Our findings demonstrate that the choice of sequencing method significantly impacts detected biodiversity in an ancient marine sediment record. While we stress that studies with limited variation in DNA degradation among samples may not be strongly affected, researchers should exonerate methodological explanations for observed biodiversity changes in marine sediment cores, particularly when considering alpha diversity, before making ecological interpretations.}, }
@article {pmid39974953, year = {2025}, author = {Cansado-Utrilla, C and Saldaña, MA and Golovko, G and Khanipov, K and Wild, AL and Brettell, LE and Weaver, SC and Heinz, E and Hughes, GL}, title = {Mosquito host background influences microbiome-ZIKV interactions in field and laboratory-reared Aedes aegypti.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39974953}, issn = {2692-8205}, support = {R21 AI124452/AI/NIAID NIH HHS/United States ; R21 AI129507/AI/NIAID NIH HHS/United States ; R24 AI120942/AI/NIAID NIH HHS/United States ; }, abstract = {The mosquito microbiota represents an intricate assemblage of microorganisms, comprising bacteria, fungi, viruses, and protozoa. Factors modulating microbiome abundance and composition include host genetic background, environmental parameters, and pathogen exposure. Conversely, the microbiome profoundly influences pathogen infection of the mosquito host and thus harbours considerable potential to impact the transmission of vector-borne diseases. As such, there is a growing interest in using the microbiome in novel vector-control strategies, including exploiting the natural ability of some microbes to interfere with infection of the vectors by pathogens. However, before novel microbiome-based vector control approaches can move towards translation, a more complete understanding of the interactions between mosquitoes, their microbiome, and the pathogens they transmit, is required to better appreciate how variation in the microbiome of field mosquitoes affects these interactions. To examine the impact of the host background and the associated diversity of microbiomes within distinct hosts, but without artificially manipulating the microbiome, we exposed several laboratory-reared and field-collected Aedes aegypti mosquito lines to Zika virus (ZIKV) and correlated their microbial load and composition to pathogen exposure and viral infection success. We observed significant differences in ZIKV exposure outcomes between the different mosquito lines and their associated microbiomes, and found that ZIKV alteration of the microbiomes was distinct in different lines. We also identified microbial taxa correlating with either ZIKV infection or a lack of infection. In summary, our study provides novel insights into the variability of pathogen interactions within the mosquito holobiont. A more complete understanding of which factors influence the tripartite interactions between Aedes mosquitoes, their microbiome, and arboviral pathogens, will be critical for the development of microbial-based interventions aimed at reducing vector-borne disease burden.}, }
@article {pmid39965412, year = {2025}, author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L}, title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {221}, number = {}, pages = {109646}, doi = {10.1016/j.plaphy.2025.109646}, pmid = {39965412}, issn = {1873-2690}, mesh = {*Plant Roots/metabolism/microbiology ; *Rhizosphere ; *Stress, Physiological ; *Metabolome ; *Arabidopsis/metabolism/microbiology ; Metabolomics ; Soil Microbiology ; Water/metabolism ; Multiomics ; }, abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.}, }
@article {pmid39955557, year = {2025}, author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A}, title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {15}, pmid = {39955557}, issn = {2524-4671}, support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.}, }
@article {pmid39955302, year = {2025}, author = {Khogali, R and Bastos, A and Getange, D and Bargul, JL and Kalayou, S and Ongeso, N and Verhoeven, JTP and Kabii, J and Ngiela, J and Masiga, D and Villinger, J}, title = {Exploring the microbiomes of camel ticks to infer vector competence: insights from tissue-level symbiont-pathogen relationships.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {5574}, pmid = {39955302}, issn = {2045-2322}, support = {101000365/ERC_/European Research Council/International ; }, mesh = {Animals ; *Camelus/parasitology/microbiology ; *Symbiosis ; *Microbiota ; Rickettsia/genetics/isolation &amp; purification ; *Ticks/microbiology ; RNA, Ribosomal, 16S/genetics ; Coxiella/genetics ; Female ; Kenya ; Bacteria/genetics/classification ; Male ; Ixodidae/microbiology ; }, abstract = {Ticks are blood-feeding ectoparasites that harbor diverse pathogens and endosymbionts. Their microbial communities vary based on tick species, stage, sex, geographical location, surrounding environment, and tissue type. Understanding tick microbiota at the tissue level is crucial for unraveling how microbiomes are distributed in tick tissues and influence pathogen transmission. We used V1-V2 16 S rRNA gene sequencing to analyze tissue-specific bacterial compositions (hemolymph, saliva, salivary glands, and midgut) of Amblyomma gemma, Rhipicephalus pulchellus, Hyalomma dromedarii, and Hyalomma rufipes ticks collected from camels in Marsabit County, northern Kenya. The V1-V2 region of the 16 S rRNA gene effectively differentiated 43 Rickettsia africae and 16 Rickettsia aeschlimannii tick samples from other rickettsial species, as well as Coxiella endosymbionts from Coxiella burnetii. In contrast, the V3-V4 region sequences of these species could not be clearly distinguished. Coxiella endosymbionts were most common in Am. gemma and Rh. pulchellus, while Francisella endosymbionts predominated in Hyalomma ticks; both were primarily localized in the salivary glands. High abundances of Coxiella endosymbionts, as well as Pseudomonas, were associated with the absence or low abundance of Rickettsia pathogens in both Am. gemma and Rh. pulchellus, suggesting competitive interactions between these microbes. Additionally, Proteus mirabilis, an opportunistic pathogen of the urinary tract in humans, was found predominantly in Hyalomma ticks, except for the salivary glands, which were most abundant with Francisella endosymbionts. Furthermore, we detected the Acinetobacter, Pseudomonas, and Corynebacterium genera in all the tick tissues, supporting the hypothesis that these bacteria might circulate between camel blood and ticks. Saliva and hemolymph generally harbored more extracellular bacteria than the salivary glands and midgut. This study provides a new approach to unravel tick-endosymbiont-pathogen interactions by examining the tissue localization of tick-borne pathogens and symbionts in Am. gemma, Rh. pulchellus, Hy. dromedarii, and Hy. rufipes from camels in northern Kenya. Our findings establish a baseline for developing an understanding of the functional capacities of symbionts and for designing symbiont-based control strategies.}, }
@article {pmid39953749, year = {2025}, author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A}, title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.}, journal = {Molecular ecology}, volume = {34}, number = {6}, pages = {e17695}, pmid = {39953749}, issn = {1365-294X}, support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Cats/microbiology ; Animals, Wild/microbiology ; Metagenomics ; Metagenome ; Male ; Female ; }, abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.}, }
@article {pmid39952679, year = {2025}, author = {Lobo, D and Morales, HE and Van Oosterhout, C and López-Bao, JV and Silva, P and Llaneza, L and Pacheco, C and Castro, D and Hernández-Alonso, G and Pacheco, G and Archer, J and Gilbert, MTP and Ferrand, N and Godinho, R}, title = {Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes.}, journal = {Genome research}, volume = {35}, number = {3}, pages = {432-445}, pmid = {39952679}, issn = {1549-5469}, mesh = {Animals ; *Wolves/genetics ; Dogs/genetics ; *Genetic Introgression ; Humans ; *Genome ; Spain ; Haplotypes ; Hybridization, Genetic ; Portugal ; *Adaptation, Physiological/genetics ; }, abstract = {Understanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive genome-wide analysis of 145 historical and contemporary Iberian wolf samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our estimates place the average timing of introgression between 6100 and 3000 years ago, with low sequence divergence to dogs from the Iberian Peninsula suggesting a single local origin for the hybridization event. Using forward genetic simulations, we show that the introgressed haplotype is most likely being maintained in Iberian wolves by selection. The introgressed dog variants are located within the MAST4 gene, which has been linked to neurological disorders, including cognitive and motor developmental delays, hinting at a potential role in cognitive behavior in Iberian wolves. This study uncovers a case of putative adaptive introgression from domestic dogs into wolves, offering new insights into wild canids' adaptation to human-dominated landscapes.}, }
@article {pmid39947860, year = {2025}, author = {Hu, J and Camerón, H and Rilling, JI and Campos, M and Ruiz-Gil, T and Gonzalez, MA and Gajardo, G and Vergara, K and Guzmán, L and Espinoza-González, O and Fuenzalida, G and Riquelme, C and Ueki, S and Nagai, S and Maruyama, F and Fujiyoshi, S and Yarimizu, K and Perera, IU and Ávila, A and Acuña, JJ and Zhang, Q and Jorquera, MA}, title = {Differentiation of microbial communities in coastal seawater before and during an Akashiwo sanguinea (Dinophyceae) bloom in the urban area of Antofagasta city (northern Chile).}, journal = {Harmful algae}, volume = {142}, number = {}, pages = {102782}, doi = {10.1016/j.hal.2024.102782}, pmid = {39947860}, issn = {1878-1470}, mesh = {Chile ; *Seawater/microbiology ; *Harmful Algal Bloom ; RNA, Ribosomal, 16S/genetics/analysis ; *Microbiota ; *Dinoflagellida/physiology/growth &amp; development ; Biodiversity ; RNA, Ribosomal, 18S/genetics ; Bacteria/classification/genetics ; Cities ; }, abstract = {Harmful algal blooms (HABs) are highly relevant for public health, the economy, the ecosystem, and biodiversity stability in southern Chile (40° to 53°S), where they occur regularly and are frequently monitored. However, HAB events and their associated microbes in northern Chile (17° to 30°S) remain unknown and difficult to track due to a lack of monitoring, particularly in urban areas. We investigated changes in microbial communities in coastal seawater before and during an Akashiwo sanguinea bloom (B) at two sampling points in Antofagasta city (23°38'39S, 70°24'39W). Seawater samples (filtered at 1 and 0.2 μm) were collected during distinct bloom phases (control, prebloom, and in-bloom), and 16S and 18S rDNA gene libraries were constructed and analyzed via the DNA metabarcoding technique. Our findings indicate that species diversity within the 16S rDNA-based community was greater during the prebloom phase than during the control and in-bloom phases. Conversely, species diversity within the 18S rDNA-based community was lower during the in-bloom phase than during the control and prebloom phases. Independent of the sampling points and fractions, principal coordinate analysis (PCoA) revealed distinct differences in both the 16S and 18S rDNA-based communities between the analyzed bloom phases. Our analysis further revealed that the 16S rDNA-based community was dominated by the Flavobacteriaceae and Rhodobacteraceae families, whose abundance decreased and increased, respectively, during the bloom. As anticipated, the structure of the 18S rDNA-based community was predominantly governed by the Gymnodiniaceae family, specifically the Akashiwo genus, during the bloom. The differentiation in microbial communities was more pronounced in taxa with low abundances than in the dominant taxa. Additionally, co-occurrence network analysis revealed predominantly positive relationships within the microbial communities, particularly during the bloom event. Our analysis also identified several bacterial genera as keystone taxa within the microbial communities, notably members of Pseudomonadota and Bacteroidota.}, }
@article {pmid39930064, year = {2025}, author = {Eriksen, AMH and Rodríguez, JA and Seersholm, F and Hollund, HI and Gotfredsen, AB and Collins, MJ and Grønnow, B and Pedersen, MW and Gilbert, MTP and Matthiesen, H}, title = {Exploring DNA degradation in situ and in museum storage through genomics and metagenomics.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {210}, pmid = {39930064}, issn = {2399-3642}, mesh = {*Museums ; *Metagenomics/methods ; *Genomics/methods ; Animals ; *DNA/genetics ; Archaeology ; Microbiota ; Greenland ; DNA, Ancient/analysis ; *Specimen Handling ; Bone and Bones/microbiology ; DNA Damage ; Fossils ; }, abstract = {Understanding the environmental and microbial processes involved in DNA degradation from archaeological remains is a fundamental part of managing bone specimens. We investigated the state of DNA preservation in 33 archaeozoological caribou (Rangifer tarandus) ribs excavated from the same excavation trench at a former Inuit hunting camp in West Greenland, separated by 43 years: 1978 and 2021. Our findings show that DNA is better preserved in the most recently excavated samples, indicating a detrimental effect of museum storage on DNA integrity. Additionally, our data reveals a diverse microbiome in these bones, encoding genes relevant for bone degradation, such as enzymatic families relating to collagenases, peptidases and glycosidases. Microbes associated with bone degradation were present in both new and historical samples, with museum-stored bones showing significantly more DNA damage. Overall, our research sheds light on the nuanced dynamics governing the preservation of genomic material in archaeological contexts, underscoring the vital importance of careful considerations in museum curation practices for the sustainable conservation of invaluable skeletal records in museum repositories and in situ.}, }
@article {pmid39921668, year = {2025}, author = {Duan, S and Jin, Z and Zhang, L and Declerck, S}, title = {Mechanisms of cooperation in the plants-arbuscular mycorrhizal fungi-bacteria continuum.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39921668}, issn = {1751-7370}, support = {202206350052//China Scholarship Council/ ; W2421024//National Natural Science Foundation of China/ ; }, mesh = {*Mycorrhizae/physiology ; *Symbiosis ; *Plants/microbiology ; *Soil Microbiology ; *Bacteria/metabolism ; Plant Roots/microbiology ; Carbon/metabolism ; *Bacterial Physiological Phenomena ; }, abstract = {In nature, cooperation is an essential way for species, whether they belong to the same kingdom or to different kingdoms, to overcome the scarcity of resources and improve their fitness. Arbuscular mycorrhizal fungi are symbiotic microorganisms whose origin date back 400 million years. They form symbiotic associations with the vast majority of terrestrial plants, helping them to obtain nutrients from the soil in exchange for carbon. At the more complex level, soil bacteria participate in the symbiosis between arbuscular mycorrhizal fungi and plants: they obtain carbon from the exudation of hyphae connected to the roots and compensate for the limited saprophytic capacity of arbuscular mycorrhizal fungi by mineralizing organic compounds. Therefore, plants, arbuscular mycorrhizal fungi and soil bacteria constitute a continuum that may be accompanied by multiple forms of cooperation. In this review, we first analyzed the functional complementarities and differences between plants and arbuscular mycorrhizal fungi in arbuscular mycorrhizal symbiosis. Secondly, we discussed the resource exchange relationship between plants and arbuscular mycorrhizal fungi from the perspective of biological market theory and "surplus carbon" hypothesis. Finally, on the basis of mechanisms for maintaining cooperation, direct and indirect reciprocity in the hyphosphere, induced by the availability of external resource and species fitness, were examined. Exploring these reciprocal cooperations will provide a better understanding of the intricate ecological relationships between plants, arbuscular mycorrhizal fungi and soil bacteria as well as their evolutionary implications.}, }
@article {pmid39915510, year = {2025}, author = {Rabbani, G and Afiq-Rosli, L and Lee, JN and Waheed, Z and Wainwright, BJ}, title = {Effects of life history strategy on the diversity and composition of the coral holobiont communities of Sabah, Malaysia.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4459}, pmid = {39915510}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Malaysia ; *Microbiota ; Biodiversity ; Symbiosis ; Coral Reefs ; Bacteria/genetics/classification ; Climate Change ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral-associated microbes have essential roles in promoting and regulating host function and health. As climate change advances and other environmental perturbations increasingly impact corals, it is becoming ever more important that we understand the composition of the microbial communities hosted. Without this baseline it is impossible to assess the magnitude and direction of any future changes in microbial community structure. Here, we characterised both the bacterial and Symbiodiniaceae communities in four coral species (Diploastrea heliopora, Porites lutea, Pachyseris speciosa, and Pocillopora acuta) collected from Sabah, Malaysia. Our findings reveal distinct microbial communities associated with different coral species tending to reflect the varied life history strategies of their hosts. Microbial communities could be differentiated by collection site, with shifts in Symbiodiniaceae communities towards more stress tolerant types seen in samples collected on the shallow Sunda Shelf. Additionally, we identified a core microbiome within species and a more discrete core between all species. We show bacterial and Symbiodiniaceae communities are structured by host species and appear to be influenced by host life history characteristics. Furthermore, we identified a core microbiome for each species finding that several amplicon sequence variants were shared between hosts, this suggests a key role in coral health regardless of species identity. Given the paucity of work performed in megadiverse regions such as the Coral Triangle, this research takes on increased importance in our efforts to understand how the coral holobiont functions and how it could be altered as climate change advances.}, }
@article {pmid39906166, year = {2025}, author = {Shi, WX and Guo, JJ and Yu, XX and Li, ZX and Weng, BY and Wang, DX and Su, SH and Sun, YF and Tan, JF and Xie, RH}, title = {Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances.}, journal = {Horticulture research}, volume = {12}, number = {2}, pages = {uhae290}, pmid = {39906166}, issn = {2662-6810}, abstract = {Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e. multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.}, }
@article {pmid39899343, year = {2025}, author = {Narechania, A and Bobo, D and DeSalle, R and Mathema, B and Kreiswirth, B and Planet, PJ}, title = {What Do We Gain When Tolerating Loss? The Information Bottleneck Wrings Out Recombination.}, journal = {Molecular biology and evolution}, volume = {42}, number = {3}, pages = {}, pmid = {39899343}, issn = {1537-1719}, mesh = {*Recombination, Genetic ; Phylogeny ; Models, Genetic ; }, abstract = {Most microbes have the capacity to acquire genetic material from their environment. Recombination of foreign DNA yields genomes that are, at least in part, incongruent with the vertical history of their species. Dominant approaches for detecting these transfers are phylogenetic, requiring a painstaking series of analyses including alignment and tree reconstruction. But these methods do not scale. Here, we propose an unsupervised, alignment-free, and tree-free technique based on the sequential information bottleneck, an optimization procedure designed to extract some portion of relevant information from 1 random variable conditioned on another. In our case, this joint probability distribution tabulates occurrence counts of k-mers against their genomes of origin with the expectation that recombination will create a strong signal that unifies certain sets of co-occurring k-mers. We conceptualize the technique as a rate-distortion problem, measuring distortion in the relevance information as k-mers are compressed into clusters based on their co-occurrence in the source genomes. The result is fast, model-free, lossy compression of k-mers into learned groups of shared genome sequence, differentiating recombined elements from the vertically inherited core. We show that the technique yields a new recombination measure based purely on information, divorced from any biases and limitations inherent to alignment and phylogeny.}, }
@article {pmid39897778, year = {2025}, author = {Raethong, N and Chamtim, P and Thananusak, R and Whanmek, K and Santivarangkna, C}, title = {Genome-wide transcriptomics revealed carbon source-mediated gamma-aminobutyric acid (GABA) production in a probiotic, Lactiplantibacillus pentosus 9D3.}, journal = {Heliyon}, volume = {11}, number = {2}, pages = {e41879}, pmid = {39897778}, issn = {2405-8440}, abstract = {GABA-producing probiotics present promising opportunities for developing functional foods. Carbon sources have been identified as a critical influence on GABA production. Therefore, this study investigated the holistic metabolic responses and GABA biosynthesis to various carbon sources of Lactiplantibacillus pentosus 9D3, a proficient GABA producer, using a genome-wide transcriptomic approach. The analysis revealed 414 genes with differential expression responses to altering carbon sources, i.e., glucose, sucrose, and lactose, notably sugar phosphotransferase systems (PTS) (11 genes), indicating carbon source-mediated transcriptional change patterns in L. pentosus 9D3. The integration of transcriptome data with a genome-scale metabolic network (GSMN) revealed that L. pentosus 9D3 displays adaptability by synthesizing GABA as an alternative acid-tolerant mechanism when lactose is used as a carbon source rather than depending on the fatty acid synthesis and the arginine catabolic pathway. The findings of this study offer valuable insights into optimal carbon source utilization and gene expression co-regulation, thereby enhancing the GABA-producing capability of a probiotic and broadening its potential applications in the functional food industry.}, }
@article {pmid39891167, year = {2025}, author = {Marangon, E and Rädecker, N and Li, JYQ and Terzin, M and Buerger, P and Webster, NS and Bourne, DG and Laffy, PW}, title = {Destabilization of mutualistic interactions shapes the early heat stress response of the coral holobiont.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {31}, pmid = {39891167}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Symbiosis/physiology ; *Heat-Shock Response ; *Dinoflagellida/physiology/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Coral Reefs ; Hot Temperature ; Microbiota ; Transcriptome ; }, abstract = {BACKGROUND: The stability of the symbiotic relationship between coral and their dinoflagellate algae (Symbiodiniaceae) is disrupted by ocean warming. Although the coral thermal response depends on the complex interactions between host, Symbiodiniaceae and prokaryotes, the mechanisms underlying the initial destabilization of these symbioses are poorly understood.<br><br>RESULTS: In a 2-month manipulative experiment, we exposed the coral Porites lutea to gradually increasing temperatures corresponding to 0-8 degree heating weeks (DHW) and assessed the response of the coral holobiont using coral and Symbiodiniaceae transcriptomics, microbial 16S rRNA gene sequencing and physiological measurements. From early stages of heat stress (<&#x2009;1 DHW), the increase in metabolic turnover shifted the holobiont to a net heterotrophic state in which algal-derived nutrients were insufficient to meet host energy demands, resulting in reduced holobiont performance at 1 DHW. We postulate the altered nutrient cycling also affected the coral-associated microbial community, with the relative abundance of Endozoicomonas bacteria declining under increasing heat stress. Integration of holobiont stress responses correlated this decline to an increase in expression of a host ADP-ribosylation factor, suggesting that Symbiodiniaceae and Endozoicomonas may underlie similar endosymbiotic regulatory processes.<br><br>CONCLUSIONS: The thermotolerance of coral holobionts therefore is influenced by the nutritional status of its members and their interactions, and this identified metabolic interdependency highlights the importance of applying an integrative approach to guide coral reef conservation efforts. Video Abstract.}, }
@article {pmid39884320, year = {2025}, author = {Thanh Phạm, HT and Kuroda, S and Khairina, Y and Morikawa, M}, title = {Creation of a functional duckweed holobiont to reduce nutrient competition with microalgae for high-yield biomass production.}, journal = {Bioresource technology}, volume = {421}, number = {}, pages = {132110}, doi = {10.1016/j.biortech.2025.132110}, pmid = {39884320}, issn = {1873-2976}, mesh = {*Microalgae/growth &amp; development/metabolism ; *Biomass ; *Araceae/growth &amp; development/metabolism ; Coculture Techniques ; *Nutrients/metabolism ; Wastewater/microbiology ; }, abstract = {Duckweed has been highlighted as an appropriate biomass for low-carbon industries because of its significantly high production rate and multiple resource value. However, the outbreak of microalgae is a practical issue that decreases duckweed production yield. This study demonstrated that the growth of the duckweed Lemna aequinoctialis from factory wastewater was enhanced by colonization with indigenous plant growth-promoting bacteria (PGPB), whereas the growth of a duckweed competitor microalga, Coelastrella sp. KC10, from the same wastewater was reduced by indigenous microalgal growth-inhibiting bacteria (MGIB). Finally, a quadruple co-culture of a synthetic duckweed holobiont, L. aequinoctialis colonized by both KLaR20 (PGPB) and KLaR16 (MGIB), and Coelastrella sp. KC10 successfully recovered the duckweed production level by 117.5% in frond number and 84.5% in dry weight compared to those in the absence of microalgae. This case study demonstrates for the first time that duckweed holobionts can be reconstructed and enforced to antagonize growth competitor microalgae.}, }
@article {pmid39879954, year = {2025}, author = {Estrada, CSD and Oliveira, OA and Varasteh, T and Avelino-Alves, D and Lima, M and Barelli, V and Campos, LS and Cavalcanti, G and Dias, GM and Tschoeke, D and Thompson, C and Thompson, F}, title = {Short-term negative effects of seawater acidification on the rhodolith holobionts metatranscriptome.}, journal = {The Science of the total environment}, volume = {965}, number = {}, pages = {178614}, doi = {10.1016/j.scitotenv.2025.178614}, pmid = {39879954}, issn = {1879-1026}, mesh = {*Seawater/chemistry ; *Transcriptome ; Hydrogen-Ion Concentration ; Brazil ; *Microbiota ; *Rhodophyta/physiology ; Ocean Acidification ; }, abstract = {Rhodolith holobionts are formed by calcareous coralline algae (e.g., Corallinales) and associated microbiomes. The largest rhodolith bank in the South Atlantic is located in the Abrolhos Bank, in southwestern Brazil, covering an area of 22,000 km[2]. Rhodoliths serve as nurseries for marine life. However, ocean acidification threatens them with extinction. The acute effects of high pCO2 levels on rhodolith metatranscriptomes remain unknown. This study investigates the transcriptomic profiles of rhodoliths exposed to short-term (96-h) high pCO2 levels (up to 1638 ppm). Metatranscriptomes were generated for both dead and alive rhodoliths (15.48 million Illumina reads in total). Alive rhodoliths showed an enrichment of gene transcripts related to environmental stress responses and photosynthesis (Cyanobacteria). In contrast, the metatranscriptomes of dead rhodoliths were dominated by heterotrophic (Proteobacteria and Bacteroidetes) metabolism and virulence factors. The rhodolith holobiont metatranscriptomes respond rapidly to short-term acidification (within 1 h), suggesting that these holobionts may have some capacity to cope with acute acidification effects. However, the negative impacts of prolonged ocean acidification on rhodolith health cannot be overlooked. Rhodoliths exposed to low pH (7.5) for 96 h exhibited a completely altered transcriptomic profile compared to controls. This study highlights the plasticity of rhodolith transcriptomes in the face of ocean acidification and climate change.}, }
@article {pmid39879552, year = {2025}, author = {Tomarovsky, A and Khan, R and Dudchenko, O and Totikov, A and Serdyukova, NA and Weisz, D and Vorobieva, NV and Bulyonkova, T and Abramov, AV and Nie, W and Wang, J and Romanenko, SA and Proskuryakova, AA and Cherkasov, N and Ferguson-Smith, MA and Yang, F and Balanovskaya, E and Gilbert, MTP and Graphodatsky, AS and Aiden, EL and Powell, R and Koepfli, KP and Perelman, PL and Kliver, S}, title = {Chromosome length genome assembly of the stone marten (Martes foina, Mustelidae): a new view on one of the cornerstones in carnivore cytogenetics.}, journal = {The Journal of heredity}, volume = {}, number = {}, pages = {}, doi = {10.1093/jhered/esaf001}, pmid = {39879552}, issn = {1465-7333}, abstract = {The stone marten (Martes foina) is an important species for cytogenetic studies in the order Carnivora. ZooFISH probes created from its chromosomes provided a strong and clean signal in chromosome painting experiments and were valuable for studying the evolution of carnivoran genome architecture. The research revealed that the stone marten chromosome set is similar to the presumed ancestral karyotype of the Carnivora, which added an additional value for the species. Using linked-read and Hi-C sequencing, we generated a chromosome-length genome assembly of a male stone marten (Gansu province, China) from a primary cell line. The stone marten assembly had a length of 2.42 Gbp, scaffold N50 of 144 Mbp, and a 96.2% BUSCO completeness score. We identified 19 chromosomal scaffolds (2n=38) and assigned them chromosome ids based on chromosome painting data. Annotation identified 20,087 protein-coding gene models, of which 18,283 were assigned common names. Comparison of the stone marten assembly with the cat, dog, and human genomes revealed several small syntenic blocks absent on the published painting maps. Finally, we assessed the heterozygosity and its distribution over the chromosomes. The detected low heterozygosity level (0.4 hetSNPs/kbp) and the presence of long RoHs require further research and a new evaluation of the conservation status of the stone marten in China. Combined with available carnivoran genomes in large scale synteny analysis, the stone marten genome will highlight new features and events in carnivoran evolution, hidden from cytogenetic approaches.}, }
@article {pmid39865026, year = {2024}, author = {Fayoud, H and Belousov, MV and Antonets, KS and Nizhnikov, AA}, title = {Pathogenesis-Associated Bacterial Amyloids: The Network of Interactions.}, journal = {Biochemistry. Biokhimiia}, volume = {89}, number = {12}, pages = {2107-2132}, doi = {10.1134/S0006297924120022}, pmid = {39865026}, issn = {1608-3040}, mesh = {Humans ; *Amyloid/metabolism/chemistry ; *Bacteria/metabolism/pathogenicity ; Animals ; *Bacterial Proteins/metabolism/chemistry ; Microbiota ; }, abstract = {Amyloids are protein fibrils with a characteristic cross-β structure that is responsible for the unusual resistance of amyloids to various physical and chemical factors, as well as numerous pathogenic and functional consequences of amyloidogenesis. The greatest diversity of functional amyloids was identified in bacteria. The majority of bacterial amyloids are involved in virulence and pathogenesis either via facilitating formation of biofilms and adaptation of bacteria to colonization of a host organism or through direct regulation of toxicity. Recent studies have shown that, beside their commonly known activity, amyloids may be involved in the spatial regulation of proteome by modulating aggregation of other amyloidogenic proteins with multiple functional or pathological effects. Although the studies on the role of microbiome-produced amyloids in the development of amyloidoses in humans and animals have only been started, it is clear that humans as holobionts contain amyloids encoded not only by the host genome, but also by microorganisms that constitute the microbiome. Amyloids acquired from external sources (e.g., food) can interact with holobiont amyloids and modulate the effects of bacterial and host amyloids, thus adding another level of complexity to the holobiont-associated amyloid network. In this review, we described bacterial amyloids directly or indirectly involved in disease pathogenesis in humans and discussed the significance of bacterial amyloids in the three-component network of holobiont-associated amyloids.}, }
@article {pmid39864304, year = {2025}, author = {Labarga, D and Mairata, A and Puelles, M and Wallner, A and Aziz, A and Alícia, P}, title = {Rootstocks and drought stress impact the composition and functionality of grapevine rhizosphere bacterial microbiota.}, journal = {Microbiological research}, volume = {293}, number = {}, pages = {128073}, doi = {10.1016/j.micres.2025.128073}, pmid = {39864304}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Droughts ; *Vitis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Microbiota ; Soil Microbiology ; *Plant Roots/microbiology ; *Stress, Physiological ; Metagenomics ; Biodiversity ; }, abstract = {The microbiota, a component of the plant holobiont, plays an active role in the response to biotic and abiotic stresses. Nowadays, with recurrent drought and global warming, a growing challenge in viticulture is being addressed by different practices, including the use of adapted rootstocks. However, the relationships between these practices, abiotic stress and the composition and functions of the rhizosphere microbiota remain to be deciphered. This study aimed to unravel the impact of five rootstocks, water management and the combination of both on the rhizosphere bacterial microbiota in grapevines using shotgun metagenomics approach. The results showed that drought impacted the diversity, composition and functionality of the rhizosphere bacterial community. The genera Mycolicibacterium, Mycobacterium and Rhodococcus, and the bacterial functions, including DNA damage repair, fatty acid synthesis, sugar and amino acid transport, oxidative stress reduction, toxin synthesis and detoxification of exogenous compounds were significantly enriched under drought conditions. Rootstocks also significantly affected the rhizosphere bacterial richness but its influence on diversity and functionality compared to water management was weaker. Some taxa and function could be linked to water managements applied. The interaction between rootstocks and water management further influenced the rhizosphere composition, especially under drought conditions, where distinct clustering was observed for specific rootstocks. The results highlight the importance of conducting multifactorial studies to better understand their impact on shaping functional rhizosphere bacterial communities. This study paves the way for future research on beneficial bacterial inoculation and genetic engineering of rootstock to cope with drought stress.}, }
@article {pmid39858777, year = {2024}, author = {Apostolou, K and Radea, C and Meziti, A and Kormas, KA}, title = {Bacterial Diversity Associated with Terrestrial and Aquatic Snails.}, journal = {Microorganisms}, volume = {13}, number = {1}, pages = {}, pmid = {39858777}, issn = {2076-2607}, abstract = {The introduction of the holobiont concept has triggered scientific interest in depicting the structural and functional diversity of animal microbial symbionts, which has resulted in an unprecedented wealth of such cross-domain biological associations. The steadfast technological progress in nucleic acid-based approaches would cause one to expect that scientific works on the microbial symbionts of animals would be balanced at least for the farmed animals of human interest. For some animals, such as ruminants and a few farmed fish species of financial significance, the scientific wealth of the microbial worlds they host is immense and ever growing. The opposite happens for other animals, such as snails, in both the wild and farmed species. Snails are evolutionary old animals, with complex ecophysiological roles, living in rich microbial habitats such as soil and sediments or water. In order to create a stepping stone for future snail microbiome studies, in this literature review, we combined all the available knowledge to date, as documented in scientific papers, on any microbes associated with healthy and diseased terrestrial and aquatic snail species from natural and farmed populations. We conducted a Boolean search in Scopus, Web of Science, and ScienceDirect until June 2024, identifying 137 papers, of which 60 were used for original data on snail bacterial communities in the gastrointestinal tract, hepatopancreas, and feces. We provide a synthesis on how representative this knowledge is towards depicting the possible snail core microbiota, as well as the steps that need to be taken in the immediate future to increase the in-depth and targeted knowledge of the bacterial component in snail holobionts.}, }
@article {pmid39852521, year = {2025}, author = {De Domenico, S and Toso, A and De Rinaldis, G and Mammone, M and Fumarola, LM and Piraino, S and Leone, A}, title = {Wild or Reared? Cassiopea andromeda Jellyfish as a Potential Biofactory.}, journal = {Marine drugs}, volume = {23}, number = {1}, pages = {}, pmid = {39852521}, issn = {1660-3397}, support = {No. 774499 - GoJelly_ Research and Innovation Program project//European Union/ ; Practice code AFD9B120, project idea UNISAL119//Apulian Region program "REFIN-Research for Innovation"/ ; n.3138-"National Biodiversity Future Center-NBFC", Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022,NextGenerationEU, Italian National Recovery and Resilience Plan (NRRP)//European Union/ ; }, mesh = {Animals ; *Scyphozoa/chemistry ; *Antioxidants/pharmacology/chemistry/isolation &amp; purification ; Mediterranean Sea ; Dinoflagellida ; Sicily ; Fatty Acids ; }, abstract = {The zooxanthellate jellyfish Cassiopea andromeda (Forsskål, 1775), a Lessepsian species increasingly common in the western and central Mediterranean Sea, was investigated here to assess its potential as a source of bioactive compounds from medusa specimens both collected in the wild (the harbor of Palermo, NW Sicily) and reared under laboratory-controlled conditions. A standardized extraction protocol was used to analyze the biochemical composition of the two sampled populations in terms of protein, lipid, and pigment contents, as well as for their relative concentrations of dinoflagellate symbionts. The total extracts and their fractions were also biochemically characterized and analyzed for their in vitro antioxidant activity to quantify differences in functional compounds between wild and reared jellyfish. The two populations were similar in terms of extract yield, but with substantial differences in biomass, the number of zooxanthellae, protein and lipid contents, and fatty acid composition. The hydroalcoholic extracts obtained from jellyfish grown under controlled conditions showed greater antioxidant activity due to the presence of a higher content of bioactive compounds compared to wild jellyfish. This study could be the basis for considering the sustainable breeding of this holobiont or other similar organisms as a source of valuable compounds that can be used in the food, nutraceutical, or pharmaceutical sectors.}, }
@article {pmid39844957, year = {2025}, author = {Martins, V and Abdallah, C and Teixeira, A and Moreira, C and Nóbrega, M and Lanoue, A and Gerós, H}, title = {Subregional pedoclimatic conditions with contrasted UV-radiation shape host-microbiome and metabolome phenotypes in the grape berry.}, journal = {Food chemistry: X}, volume = {25}, number = {}, pages = {102139}, pmid = {39844957}, issn = {2590-1575}, abstract = {This study used integrative omics to address the response of key elements of the grapevine holobiont to contrasted pedoclimatic conditions found in distinct subregions of Douro Valley (Portugal). A metabolic OPLS-DA model predicted with 100 % accuracy the geographic origin of berries; higher UV radiation, higher temperature and lower precipitation stimulated the accumulation of phenolic acids, flavonols and malvidin conjugates, in detriment of amino acids, organic acids, flavan-3-ols, proanthocyanidins and non-malvidin anthocyanins. Metabarcoding showed a trade-off between bacteria and fungal diversity among subregions, with Pseudomonas, Lactobacillus, Aspergillus and Penicillium acting as intraregional microbial markers. The high phenotypic plasticity of berries and the role of microbes in this process are relevant upon current projections for increased UV radiation and temperature in Southern European viticulture, in a climate change scenario, with predicted impacts on regional wine quality and on the development of adaptation strategies for resilient viticulture.}, }
@article {pmid39844274, year = {2025}, author = {Camper, BT and Kanes, AS and Laughlin, ZT and Manuel, RT and Bewick, SA}, title = {Transgressive hybrids as hopeful holobionts.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {19}, pmid = {39844274}, issn = {2049-2618}, mesh = {*Hybridization, Genetic ; *Symbiosis ; Biological Evolution ; Animals ; *Microbiota ; }, abstract = {BACKGROUND: Hybridization between evolutionary lineages has profound impacts on the fitness and ecology of hybrid progeny. In extreme cases, the effects of hybridization can transcend ecological timescales by introducing trait novelty upon which evolution can act. Indeed, hybridization can even have macroevolutionary consequences, for example, as a driver of adaptive radiations and evolutionary innovations. Accordingly, hybridization is now recognized as a motor for macrobial evolution. By contrast, there has been substantially less progress made towards understanding the positive eco-evolutionary consequences of hybridization on holobionts. Rather, the emerging paradigm in holobiont literature is that hybridization disrupts symbiosis between a host lineage and its microbiome, leaving hybrids at a fitness deficit. These conclusions, however, have been drawn based on results from predominantly low-fitness hybrid organisms. Studying "dead-end" hybrids all but guarantees finding that hybridization is detrimental. This is the pitfall that Dobzhansky fell into over 80 years ago when he used hybrid sterility and inviability to conclude that hybridization hinders evolution. Goldschmidt, however, argued that rare saltational successes-so-called hopeful monsters-disproportionately drive positive evolutionary outcomes. Goldschmidt's view is now becoming a widely accepted explanation for the prevalence of historical hybridization in extant macrobial lineages. Aligning holobiont research with this broader evolutionary perspective requires recognizing the importance of similar patterns in host-microbiome systems. That is, rare and successful "hopeful holobionts" (i.e., hopeful monsters at the holobiont scale) might be disproportionately responsible for holobiont evolution. If true, then it is these successful systems that we should be studying to assess impacts of hybridization on the macroevolutionary trajectories of host-microbiome symbioses.<br><br>RESULTS: In this paper, we explore the effects of hybridization on the gut (cloacal) and skin microbiota in an ecologically successful hybrid lizard, Aspidoscelis neomexicanus. Specifically, we test the hypothesis that hybrid lizards have host-associated (HA) microbiota traits strongly differentiated from their progenitor species. Across numerous hybrid microbiota phenotypes, we find widespread evidence of transgressive segregation. Further, microbiota restructuring broadly correlates with niche restructuring during hybridization. This suggests a relationship between HA microbiota traits and ecological success.<br><br>CONCLUSION: Transgressive segregation of HA microbiota traits is&#xa0;not only limited to hybrids at a fitness deficit but also occurs in ecologically successful hybrids. This suggests that hybridization may be a mechanism for generating novel and potentially beneficial holobiont phenotypes. Supporting such a conclusion, the correlations that we find between hybrid microbiota and the hybrid niche indicate that hybridization might change host microbiota in ways that promote a shift or an expansion in host niche space. If true, hybrid microbiota restructuring may underly ecological release from progenitors. This, in turn, could drive evolutionary diversification. Using our system as an example, we elaborate on the evolutionary implications of host hybridization within the context of holobiont theory and then outline the next steps for understanding the role of hybridization in holobiont research. Video Abstract.}, }
@article {pmid39838803, year = {2025}, author = {Chan, WY and Sakamoto, R and Doering, T and Narayana, VK and De Souza, DP and McConville, MJ and van Oppen, MJH}, title = {Heat-Evolved Microalgae (Symbiodiniaceae) Are Stable Symbionts and Influence Thermal Tolerance of the Sea Anemone Exaiptasia diaphana.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70011}, pmid = {39838803}, issn = {1462-2920}, support = {DE240100317//Australian Research Council/ ; FL180100036//Australian Research Council/ ; APP1154540//National Health and Medical Research Council/ ; //Westpac Research Fellowship/ ; }, mesh = {*Symbiosis ; Animals ; *Sea Anemones/physiology ; Hot Temperature ; *Thermotolerance ; *Microalgae/physiology ; }, abstract = {Symbiotic cnidarians, such as sea anemones and corals, rely on their mutualistic microalgal partners (Symbiodiniaceae) for survival. Marine heatwaves can disrupt this partnership, and it has been proposed that introducing experimentally evolved, heat-tolerant algal symbionts could enhance host thermotolerance. To test this hypothesis, the sea anemone Exaiptasia diaphana (a coral model) was inoculated with either the heterologous wild type or heat-evolved algal symbiont, Cladocopium proliferum, and homologous wild-type Breviolum minutum. The novel symbioses persisted for 1.5 years and determined holobiont thermotolerance during a simulated summer heatwave. Anemones hosting SS8, one of the six heat-evolved strains tested, exhibited the highest thermotolerance. Notably, anemones hosting the wild-type C. proliferum (WT10) were the second most thermally tolerant group, whereas anemones hosting the heat-evolved SS5 or SS9 strains were among the most thermosensitive. Elevated temperatures led to an increase in the levels of many amino acids and a decrease in tricarboxylic acid (TCA) metabolites in all anemone hosts, potentially indicating an increase in autophagy and a reduction in energy and storage production. Some consistent differences were observed in changes in metabolite levels between anemone groups in response to elevated temperature, suggesting that the algal symbiont influenced host metabolome and nutritional budget.}, }
@article {pmid39832281, year = {2025}, author = {Middelboe, M and Traving, SJ and Castillo, D and Kalatzis, PG and Glud, RN}, title = {Prophage-encoded chitinase gene supports growth of its bacterial host isolated from deep-sea sediments.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, pmid = {39832281}, issn = {1751-7370}, support = {//Coasts &amp; Oceans Centre of New Zealand's National Institute of Water &amp; Atmospheric Research/ ; 669947//HADES-ERC/ ; DNRF145//Danish National Research Foundation/ ; //Independent Research Fund Denmark/ ; }, mesh = {*Chitinases/genetics/metabolism ; *Geologic Sediments/microbiology ; *Prophages/genetics/enzymology ; Chitin/metabolism ; *Pseudomonas/virology/growth &amp; development/genetics/isolation &amp; purification ; *Viral Proteins/genetics/metabolism ; Seawater/microbiology ; Lysogeny ; Bacteriophages/genetics ; }, abstract = {Auxiliary metabolic genes encoded by bacteriophages can influence host metabolic function during infection. In temperate phages, auxiliary metabolic genes (AMGs) may increase host fitness when integrated as prophages into the host genome. However, little is known about the contribution of prophage-encoded AMGs to host metabolic properties. In this study, we examined a temperate bacteriophage, and its piezotolerant Pseudomonas sp. host obtained from sediment samples collected from the Kermadec Trench at ~10 000 m water depth. Both the phage and host were present throughout the sediment profiles from the surface to 30 cm into the sediment, covering large gradients of environmental conditions. The host and phage each carried one chitinase gene, which differed from each other, suggesting that chitin degradation plays a role in their substrate supply. We demonstrated that prophage-encoded chitinase supported host chitin degradation and growth in the presence of chitin. Furthermore, prophage induction dynamics were strongly substrate-dependent, suggesting that the host controls the lysis-lysogeny switch in response to the presence of chitin, thus optimizing the trade-off between the loss of cells from prophage induction and prophage enhancement of host performance. Overall, the results demonstrate prophage-encoded AMGs as collaborative goods for their hosts and emphasize the potential role of phage-host interactions in benthic biogeochemical cycling, as well as for the capability of deep-sea bacteria to efficiently adapt and thrive at a wide range of environmental conditions.}, }
@article {pmid39827902, year = {2025}, author = {Brown, TM and Dunn, AM and Quinnell, RJ and Clarke, E and Cunningham, AA and Goodman, SJ}, title = {An interdisciplinary approach to improving conservation outcomes for parasites.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {39}, number = {1}, pages = {e14431}, pmid = {39827902}, issn = {1523-1739}, support = {//The Leverhulme Trust/ ; }, mesh = {*Conservation of Natural Resources/methods ; *Parasites/physiology ; *Biodiversity ; Animals ; Ecosystem ; }, abstract = {Parasites represent a significant proportion of Earth's biodiversity and play important roles in the ecology and biology of ecosystems and hosts, making them an important target for conservation. Despite increasing calls to prioritize protection for parasites in the academic literature, they remain undervalued and underrepresented in global biodiversity conservation efforts, not least due to the perception that the interests of parasite and host conservation are opposing and the common misconception that parasites are a threat, rather than a benefit, to conservation. We considered whether taking an interdisciplinary approach to parasite conservation research will generate novel insights and solutions concerning why and how parasite conservation should be practiced for the benefit of parasites, their hosts, ecosystems, and people. We argue that 2 of the main barriers to more widespread parasite conservation are the knowledge gap concerning the role of sociocultural factors affecting the willingness to enact parasite conservation and the lack of a consistent and cohesive philosophical basis for parasite conservation. Possible sociocultural barriers to parasite conservation include misconceptions of the risks posed by parasites, taxonomic bias, differences in conservation values, economic constraints, and technical challenges. The use of social science can generate insights into levels of awareness and support for parasite conservation and improve understanding of how human values and attitudes mediate conservation practices concerning parasites. Such knowledge will have a critical role in addressing sociocultural barriers and improving support for parasite conservation. Issues with the current philosophical basis for parasite conservation include contradictory accounts of which parasites merit conservation, insufficient explanation of how different conservation values apply to parasite biodiversity, and the existence of a false antagonism between host and parasite conservation. Greater engagement with philosophical work on environmental ethics and biological unitization will strengthen existing arguments for parasite conservation and will support conservation decision-making processes.}, }
@article {pmid39827366, year = {2025}, author = {Liu, HJ and Liu, J and Zhai, Z and Dai, M and Tian, F and Wu, Y and Tang, J and Lu, Y and Wang, H and Jackson, D and Yang, X and Qin, F and Xu, M and Fernie, AR and Zhang, Z and Yan, J}, title = {Maize2035: A decadal vision for intelligent maize breeding.}, journal = {Molecular plant}, volume = {18}, number = {2}, pages = {313-332}, doi = {10.1016/j.molp.2025.01.012}, pmid = {39827366}, issn = {1752-9867}, mesh = {*Zea mays/genetics ; *Plant Breeding/methods ; Agriculture ; }, abstract = {Maize, a cornerstone of global food security, has undergone remarkable transformations through breeding, yet further increase in global maize production faces mounting challenges in a changing world. In this Perspective paper, we overview the historical successes of maize breeding that laid the foundation for present opportunities. We examine both the specific and shared breeding goals related to diverse geographies and end-use demands. Achieving these coordinated breeding objectives requires a holistic approach to trait improvement for sustainable agriculture. We discuss cutting-edge solutions, including multi-omics approaches from single-cell analysis to holobionts, smart breeding with advanced technologies and algorithms, and the transformative potential of rational design with synthetic biology approaches. A transition toward a data-driven future is currently underway, with large-scale precision agriculture and autonomous systems poised to revolutionize farming practice. Realizing these futuristic opportunities hinges on collaborative efforts spanning scientific discoveries, technology translations, and socioeconomic considerations in maximizing human and environmental well-being.}, }
@article {pmid39823339, year = {2025}, author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O}, title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadr6070}, pmid = {39823339}, issn = {2375-2548}, mesh = {*Ulva/microbiology ; *Salinity ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; }, abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.}, }
@article {pmid39823335, year = {2025}, author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS}, title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadq2583}, pmid = {39823335}, issn = {2375-2548}, mesh = {*Anthozoa/microbiology/physiology ; Animals ; Phenotype ; *Microbiota ; Temperature ; Metagenomics/methods ; Symbiosis ; Bacteria/genetics/classification ; }, abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.}, }
@article {pmid39822124, year = {2025}, author = {Doonan, JM and Budde, KB and Kosawang, C and Lobo, A and Verbylaite, R and Brealey, JC and Martin, MD and Pliura, A and Thomas, K and Konrad, H and Seegmüller, S and Liziniewicz, M and Cleary, M and Nemesio-Gorriz, M and Fussi, B and Kirisits, T and Gilbert, MTP and Heuertz, M and Kjær, ED and Nielsen, LR}, title = {Multiple, Single Trait GWAS and Supervised Machine Learning Reveal the Genetic Architecture of Fraxinus excelsior Tolerance to Ash Dieback in Europe.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {5}, pages = {3793-3809}, pmid = {39822124}, issn = {1365-3040}, support = {//This research was supported by the Independent Research Fund Denmark (DFF|Technology and Production Sciences) under the grant no. 8022-00355B. Field work in Austria was supported by BML DaFNE grant no. 101476 ("Esche in Not-Phase II") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management, the Austrian Chamber of Agriculture, the governments of all Austrian provinces, the Forest Office and Urban Agriculture (MA 49) of the Vienna City Administration and "&#xd6;sterreichischer Forstverein"; as well as by BML DaFNE grant no. 101684 ("Waldfonds" project "AshBack") funded by the Austrian Federal Ministry of Agriculture, Forestry, Regions and Water Management. The establishment of the German trial site "Chiemsee" was supported by the Bavarian Ministry under the projects KLIP1 and ST272. J.C.B. was funded by the European Union's Horizon 2020 Action grant 8177291009 "HoloFood"./ ; }, mesh = {*Fraxinus/genetics/microbiology ; *Genome-Wide Association Study ; *Machine Learning ; Polymorphism, Single Nucleotide/genetics ; *Plant Diseases/microbiology/genetics ; Europe ; *Ascomycota/physiology ; Genotype ; Phenotype ; Disease Resistance/genetics ; }, abstract = {Common ash (Fraxinus excelsior) is under intensive attack from the invasive alien pathogenic fungus Hymenoscyphus fraxineus, causing ash dieback at epidemic levels throughout Europe. Previous studies have found significant genetic variation among genotypes in ash dieback susceptibility and that host phenology, such as autumn yellowing, is correlated with susceptibility of ash trees to H. fraxineus; however, the genomic basis of ash dieback tolerance in F. excelsior requires further investigation. Here, we integrate quantitative genetics based on multiple replicates and genome-wide association analyses with machine learning to reveal the genetic architecture of ash dieback tolerance and of phenological traits in F. excelsior populations in six European countries (Austria, Denmark, Germany, Ireland, Lithuania, Sweden). Based on phenotypic data of 486 F. excelsior replicated genotypes we observed negative genotypic correlations between crown damage caused by ash dieback and intensity of autumn leaf yellowing within multiple sampling sites. Our results suggest that the examined traits are polygenic and using genomic prediction models, with ranked single nucleotide polymorphisms (SNPs) based on GWAS associations as input, a large proportion of the variation was predicted by unlinked SNPs. Based on 100 unlinked SNPs, we can predict 55% of the variation in disease tolerance among genotypes (as phenotyped in genetic trials), increasing to a maximum of 63% when predicted from 9155 SNPs. In autumn leaf yellowing, 52% of variation is predicted by 100 unlinked SNPs, reaching a peak of 72% using 3740 SNPs. Based on feature permutations within genomic prediction models, a total of eight nonsynonymous SNPs linked to ash dieback crown damage and autumn leaf yellowing (three and five SNPs, respectively) were identified, these were located within genes related to plant defence (pattern triggered immunity, pathogen detection) and phenology (regulation of flowering and seed maturation, auxin transport). We did not find an overlap between genes associated with crown damage level and autumn leaf yellowing. Hence, our results shed light on the difference in the genomic basis of ADB tolerance and autumn leaf yellowing despite these two traits being correlated in quantitative genetic analysis. Overall, our methods show the applicability of genomic prediction models when combined with GWAS to reveal the genomic architecture of polygenic disease tolerance enabling the identification of ash dieback tolerant trees for breeding or conservation purposes.}, }
@article {pmid39816161, year = {2025}, author = {Parreira, BR and Gopalakrishnan, S and Chikhi, L}, title = {Effects of Social Structure on Effective Population Size Change Estimates.}, journal = {Evolutionary applications}, volume = {18}, number = {1}, pages = {e70063}, pmid = {39816161}, issn = {1752-4571}, abstract = {Most methods currently used to infer the "demographic history of species" interpret this expression as a history of population size changes. The detection, quantification, and dating of demographic changes often rely on the assumption that population structure can be neglected. However, most vertebrates are typically organized in populations subdivided into social groups that are usually ignored in the interpretation of genetic data. This could be problematic since an increasing number of studies have shown that population structure can generate spurious signatures of population size change. Here, we simulate microsatellite data from a species subdivided into social groups where reproduction occurs according to different mating systems (monogamy, polygynandry, and polygyny). We estimate the effective population size (N e) and quantify the effect of social structure on estimates of changes in N e. We analyze the simulated data with two widely used methods for demographic inference. The first approach, BOTTLENECK, tests whether the samples are at mutation-drift equilibrium and thus whether a single N e can be estimated. The second approach, msvar, aims at quantifying and dating changes in N e. We find that social structure may lead to signals of departure from mutation-drift equilibrium including signals of expansion and bottlenecks. We also find that expansion signals may be observed under simple stationary Wright-Fisher models with low diversity. Since small populations tend to characterize many endangered species, we stress that methods trying to infer N e should be interpreted with care and validated with simulated data incorporating information about structure. Spurious expansion signals due to social structure can mask critical population size changes. These can obscure true bottleneck events and be particularly problematic in endangered species.}, }
@article {pmid39813343, year = {2025}, author = {Aichelman, HE and Benson, BE and Gomez-Campo, K and Martinez-Rugerio, MI and Fifer, JE and Tsang, L and Hughes, AM and Bove, CB and Nieves, OC and Pereslete, AM and Stanizzi, D and Kriefall, NG and Baumann, JH and Rippe, JP and Gondola, P and Castillo, KD and Davies, SW}, title = {Cryptic coral diversity is associated with symbioses, physiology, and response to thermal challenge.}, journal = {Science advances}, volume = {11}, number = {3}, pages = {eadr5237}, pmid = {39813343}, issn = {2375-2548}, mesh = {*Anthozoa/physiology/classification/microbiology/genetics ; *Symbiosis ; Animals ; Coral Reefs ; *Biodiversity ; Temperature ; Climate Change ; Phylogeny ; Panama ; }, abstract = {Coral persistence in the Anthropocene depends on interactions among holobiont partners (coral animals and microbial symbionts) and their environment. Cryptic coral lineages-genetically distinct yet morphologically similar groups-are critically important as they often exhibit functional diversity relevant to thermal tolerance. In addition, environmental parameters such as thermal variability may promote tolerance, but how variability interacts with holobiont partners to shape responses to thermal challenge remains unclear. Here, we identified three cryptic lineages of Siderastrea siderea in Bocas del Toro, Panamá that differ in distributions across inshore and offshore reefs, microbial associations, phenotypic traits of holobiont partners (i.e., phenomes), and skeleton morphologies. A thermal variability experiment failed to increase thermal tolerance, but subsequent thermal challenge and recovery revealed that one lineage maintained elevated energetic reserves, photochemical efficiency, and growth. Last, coral cores highlighted that this lineage also exhibited greater growth historically. Functional variation among cryptic lineages highlights their importance in predicting coral reef responses to climate change.}, }
@article {pmid39812892, year = {2025}, author = {Kerlin, JR and Barnas, DM and Silbiger, NJ}, title = {Conspecific interactions between corals mediate the effect of submarine groundwater discharge on coral physiology.}, journal = {Oecologia}, volume = {207}, number = {1}, pages = {21}, pmid = {39812892}, issn = {1432-1939}, support = {1924281//Division of Ocean Sciences/ ; 1637396//Division of Ocean Sciences/ ; }, mesh = {Animals ; *Anthozoa/physiology ; *Groundwater ; Coral Reefs ; Symbiosis ; Ecosystem ; }, abstract = {Land-based inputs, such as runoff, rivers, and submarine groundwater, can alter biologic processes on coral reefs. While the abiotic factors associated with land-based inputs have strong effects on corals, corals are also affected by biotic interactions, including other neighboring corals. The biologic responses of corals to changing environmental conditions and their neighbors are likely interactive; however, few studies address both biotic and abiotic interactions in concert. In a manipulative field experiment, we tested how the natural environmental gradient created by submarine groundwater discharge (SGD) affected holobiont and symbiont metabolic rates and endosymbiont physiology of Porites rus. We further tested how the effect of SGD on the coral was mediated by intra and interspecific interactions. SGD is a natural land-sea connection that delivers nutrients, inorganic carbon, and other solutes to coastal ecosystems worldwide. Our results show that a natural gradient of nutrient enrichment and pH variability as a result of acute SGD exposure generally benefited P. rus, increasing gross photosynthesis, respiration, endosymbiont densities, and chlorophyll a content. Conspecifics in direct contact with the a neighboring coral, however, altered the relationship between coral physiology and SGD, lowering the photosynthetic and respiration rates from expected values when the coral had no neighbor. We show that the response of corals to environmental change is dependent on the types of nearby neighbor corals and how neighbors alter the chemical or physical environment around the coral. Our study underscores the importance of considering biotic interactions when predicting the physiologic responses of corals to the environment.}, }
@article {pmid39810029, year = {2025}, author = {de Freitas Neto, LL and Santos, RFB and da Silva, MA and de Souza Bezerra, R and Saldanha-Corrêa, F and Espósito, BP}, title = {Zinc speciation promotes distinct effects on dinoflagellate growth and coral trypsin-like enzyme activity.}, journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine}, volume = {38}, number = {2}, pages = {573-586}, pmid = {39810029}, issn = {1572-8773}, support = {2021/07153-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2021/10894-5//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 372742/2022-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {*Dinoflagellida/growth &amp; development/drug effects/enzymology ; *Zinc/chemistry/pharmacology ; Animals ; *Anthozoa/enzymology/drug effects ; *Trypsin/metabolism ; Histidine/chemistry/pharmacology ; }, abstract = {Zinc is an essential metal to living organisms, including corals and their symbiotic microalgae (Symbiodiniaceae). Both Zn(II) deprivation and overload are capable of leading to dysfunctional metabolism, coral bleaching, and even organism death. The present work investigated the effects of chemically defined Zn species (free Zn, ZnO nanoparticles, and the complexes Zn-histidinate and Zn-EDTA) over the growth of the dinoflagellates Symbiodinium microadriaticum, Breviolum minutum, and Effrenium voratum, and on the trypsin-like proteolytic activity of the hydrocoral Millepora alcicornis. B. minutum was the most sensitive strain to any form of added Zn. For the other strains, the complex [Zn(His)2] better translated metal load into growth. This complex was the only tested compound that did not interfere with the trypsin-like activity of Millepora alcicornis extracts. Also, histidine was able to recover the activity of the enzyme inhibited by zinc. [Zn(His)2] is a potential biocarrier of zinc for microalgae or coral cultivation. These findings suggest that the control of chemical speciation of an essential metal could lead to useful compounds that assist autotrophy, while not affecting heterotrophy, in the coral holobiont.}, }
@article {pmid39799372, year = {2025}, author = {Perez, V and Boulo, V and De Lorgeril, J and Pham, D and Ansquer, D and Plougoulen, G and Ballan, V and Lam, JS and Romatif, O and Le Luyer, J and Falchetto, C and Basset, C and Flohr, S and Maamaatuaiahutapu, M and Lafille, MA and Lau, C and Saulnier, D and Wabete, N and Callac, N}, title = {Hemolymph microbiota and immune effectors' expressions driven by geographical rearing acclimation of the aquacultured Penaeus stylirostris.}, journal = {Animal microbiome}, volume = {7}, number = {1}, pages = {5}, pmid = {39799372}, issn = {2524-4671}, abstract = {BACKGROUND: In holobiont, microbiota is known to play a central role on the health and immunity of its host. Then, understanding the microbiota, its dynamic according to the environmental conditions and its link to the immunity would help to react to potential dysbiosis of aquacultured species. While the gut microbiota is highly studied, in marine invertebrates the hemolymph microbiota is often set aside even if it remains an important actor of the hemolymph homeostasis. Indeed, the hemolymph harbors the factors involved in the animal homeostasis that interacts with the microbiota, the immunity. In the Southwest Pacific, the high economical valued shrimp Penaeus stylirostris is reared in two contrasted sites, in New Caledonia (NC) and in French Polynesia (FP).<br><br>RESULTS: We characterized the active microbiota inhabiting the hemolymph of shrimps while considering its stability during two seasons and at a one-month interval and evidenced an important microbial variability between the shrimps according to the rearing conditions and the sites. We highlighted specific biomarkers along with a common core microbiota composed of 6 ASVs. Putative microbial functions were mostly associated with bacterial competition, infections and metabolism in NC, while they were highly associated with the cell metabolism in FP suggesting a rearing site discrimination. Differential relative expression of immune effectors measured in the hemolymph of two shrimp populations from NC and FP, exhibited higher level of expression in NC compared to FP. In addition, differential relative expression of immune effectors was correlated to bacterial biomarkers based on their geographical location.<br><br>CONCLUSIONS: Our data suggest that, in Pacific shrimps, both the microbiota and the expression of the immune effectors could have undergone differential immunostimulation according to the rearing site as well as a geographical adaptative divergence of the shrimps as an holobiont, to their rearing sites. Further, the identification of proxies such as the core microbiota and site biomarkers, could be used to guide future actions to monitor the bacterial microbiota and thus preserve the productions.}, }
@article {pmid39797569, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, pmid = {39797569}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; *Microbiota ; *Salmon/microbiology ; *Databases, Genetic ; *Host Microbial Interactions ; Metadata ; *Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, }
@article {pmid39769364, year = {2024}, author = {Grzyb, T and Szulc, J}, title = {Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, pmid = {39769364}, issn = {1422-0067}, mesh = {*Microbiota ; *Bacteria/genetics/classification/metabolism ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Phosphorus/metabolism ; Nitrogen/metabolism ; Symbiosis ; Nutrients/metabolism ; }, abstract = {While gaining increasing attention, plant-microbiome-environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron-elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology.}, }
@article {pmid39762949, year = {2025}, author = {Ferreira, C and Burgsdorf, I and Perez, T and Ramírez, G and Lalzar, M and Huchon, D and Steindler, L}, title = {Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {4}, pmid = {39762949}, issn = {2049-2618}, support = {GBMF9352//Gordon and Betty Moore Foundation/ ; 933/23//Israel Science Foundation/ ; }, mesh = {*Symbiosis ; *Porifera/microbiology ; *Phylogeny ; Animals ; *Genomics ; Bacterial Proteins/genetics/metabolism ; Phosphoproteins/genetics ; Multigene Family ; Genome, Bacterial ; Actinobacteria/genetics/classification ; }, abstract = {BACKGROUND: Sponges harbor microbial communities that play crucial roles in host health and ecology. However, the genetic adaptations that enable these symbiotic microorganisms to thrive within the sponge environment are still being elucidated. To understand these genetic adaptations, we conducted a comparative genomics analysis on 350 genomes of Actinobacteriota, a phylum commonly associated with sponges.<br><br>RESULTS: Our analysis uncovered several differences between symbiotic and free-living bacteria, including an increased abundance of genes encoding prokaryotic defense systems (PDSs) and eukaryotic-like proteins (ELPs) in symbionts. Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. Analyses of a broader set of microbes showed that members of the GPP34 family are also found in sponge symbionts across 16 additional bacterial phyla. While GPP34 proteins were thought to be restricted to eukaryotes, our phylogenetic analysis shows that the GPP34 domain is found in all three domains of life, suggesting its ancient origin. We also show that the GPP34 family includes genes with two main structures: a short form that includes only the GPP34 domain and a long form that encompasses a GPP34 domain coupled with a cytochrome P450 domain, which is exclusive to sponge symbiotic bacteria.<br><br>CONCLUSIONS: Given previous studies showing that GPP34 is a phosphatidylinositol-4-phosphate (PI4P)-binding protein in eukaryotes and that other PI4P-binding proteins from bacterial pathogens can interfere with phagolysosome maturation, we propose that symbionts employ GPP34 to modulate phagocytosis to colonize and persist within sponge hosts. Video Abstract.}, }
@article {pmid39750118, year = {2025}, author = {Butdee, W and Saimee, Y and Suriyachadkun, C and Duangmal, K}, title = {Pseudonocardia spirodelae sp. nov., isolated from duckweed and formal proposal to reclassify Pseudonocardia antarctica as a later heterotypic synonym of Pseudonocardia alni and reclassify Pseudonocardia carboxydivorans as Pseudonocardia alni subsp. carboxydivorans.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {75}, number = {1}, pages = {}, doi = {10.1099/ijsem.0.006608}, pmid = {39750118}, issn = {1466-5034}, mesh = {*RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Nucleic Acid Hybridization ; *Vitamin K 2/analogs &amp; derivatives/analysis ; *Fatty Acids/chemistry ; *Sequence Analysis, DNA ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *Araceae/microbiology ; Base Composition ; Phospholipids ; }, abstract = {A novel Pseudonocardia strain DW16-2[T], isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8[T] (98.8%), followed by Pseudonocardia tropica YIM 61452[T] (98.7%), Pseudonocardia antarctica DVS 5a1[T] (98.7%) and Pseudonocardia alni DSM 44104[T] (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2[T] and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2[T] were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2[T] contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H4). The cellular fatty acids (>5 %) were iso-C16 : 0, iso-C16 : 1 H, summed feature 3: C16 : 1 ω7c/C16 : 1 ω6c; C16 : 1 ω6c/C16 : 1 ω7c, C17 : 1 ω8c and anteiso-C17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2[T] represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2[T] = TBRC 16418[T] = NBRC 115857[T]) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.}, }
@article {pmid39748821, year = {2024}, author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L}, title = {A multi-omics approach to unravel the interaction between heat and drought stress in the Arabidopsis thaliana holobiont.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1484251}, pmid = {39748821}, issn = {1664-462X}, abstract = {The impact of combined heat and drought stress was investigated in Arabidopsis thaliana and compared to individual stresses to reveal additive effects and interactions. A combination of plant metabolomics and root and rhizosphere bacterial metabarcoding were used to unravel effects at the plant holobiont level. Hierarchical cluster analysis of metabolomics signatures pointed out two main clusters, one including heat and combined heat and drought, and the second cluster that included the control and drought treatments. Overall, phenylpropanoids and nitrogen-containing compounds, hormones and amino acids showed the highest discriminant potential. A decrease in alpha-diversity of Bacteria was observed upon stress, with stress-dependent differences in bacterial microbiota composition. The shift in beta-diversity highlighted the pivotal enrichment of Proteobacteria, including Rhizobiales, Enterobacteriales and Azospirillales. The results corroborate the concept of stress interaction, where the combined heat and drought stress is not the mere combination of the single stresses. Intriguingly, multi-omics interpretations evidenced a good correlation between root metabolomics and root bacterial microbiota, indicating an orchestrated modulation of the whole holobiont.}, }
@article {pmid39738126, year = {2024}, author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T}, title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10858}, pmid = {39738126}, issn = {2041-1723}, mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; }, abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.}, }
@article {pmid39735181, year = {2024}, author = {Trefault, N}, title = {Editorial: Impact of anthropogenic stressors on marine sponge holobiomes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1533416}, pmid = {39735181}, issn = {1664-302X}, }
@article {pmid39731136, year = {2024}, author = {Balamurugan, BS and Marimuthu, MMC and Sundaram, VA and Saravanan, B and Chandrababu, P and Chopra, H and Malik, T}, title = {Micro nutrients as immunomodulators in the ageing population: a focus on inflammation and autoimmunity.}, journal = {Immunity &amp; ageing : I &amp; A}, volume = {21}, number = {1}, pages = {88}, pmid = {39731136}, issn = {1742-4933}, abstract = {Immunosenescence, the slow degradation of immune function over time that is a hallmark and driver of aging, makes older people much more likely to be killed by common infections (such as flu) than young adults, but it also contributes greatly to rates of chronic inflammation in later life. Such micro nutrients are crucial for modulating effective immune responses and their deficiencies have been associated with dysfunctional immunity in the elderly. In this review, we specifically focused on the contribution of major micro nutrients (Vitamins A, D and E, Vitamin C; Zinc and Selenium) as immunomodulators in ageing population especially related to inflame-ageing process including autoimmunity. This review will cover these hologenomic interactions, including how micro nutrients can modulate immune cell function and/or cytokine production to benefit their hosts with healthy mucous-associated immunity along with a sustainable immunologic homeostasis. For example, it points out the modulatory effects of vitamin D on both innate and adaptive immunity, with a specific focus on its ability to suppress pro-inflammatory cytokines synthesis while enhancing regulatory T-cell function. In the same context, also zinc is described as important nutrient for thymic function and T-cell differentiation but exhibits immunomodulatory functions by decreasing inflammation. In addition, the review will go over how micro nutrient deficiencies increase systemic chronic low-grade inflammation and, inflammaging as well as actually enhance autoimmune pathologies in old age. It assesses the potential role of additional targeted nutritional supplementation with micro nutrients to counteract these effects, promoting wider immune resilience in older adults. This review collates the current evidence and highlights the role of adequate micro nutrient intake on inflammation and autoimmunity during ageing, providing plausible origins for nutritional interventions to promote healthy immune aging.}, }
@article {pmid39730835, year = {2025}, author = {Orkin, JD and Kuderna, LFK and Hermosilla-Albala, N and Fontsere, C and Aylward, ML and Janiak, MC and Andriaholinirina, N and Balaresque, P and Blair, ME and Fausser, JL and Gut, IG and Gut, M and Hahn, MW and Harris, RA and Horvath, JE and Keyser, C and Kitchener, AC and Le, MD and Lizano, E and Merker, S and Nadler, T and Perry, GH and Rabarivola, CJ and Rasmussen, L and Raveendran, M and Roos, C and Wu, DD and Zaramody, A and Zhang, G and Zinner, D and Pozzi, L and Rogers, J and Farh, KK and Marques Bonet, T}, title = {Ecological and anthropogenic effects on the genomic diversity of lemurs in Madagascar.}, journal = {Nature ecology &amp; evolution}, volume = {9}, number = {1}, pages = {42-56}, pmid = {39730835}, issn = {2397-334X}, support = {LCF/BQ/PI20/11760004//"la Caixa" Foundation (Caixa Foundation)/ ; DGECR-2023-00272//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en G&#xe9;nie du Canada)/ ; STF 8286//European Molecular Biology Organization (EMBO)/ ; NE/T000341/1//RCUK | Natural Environment Research Council (NERC)/ ; BCS 1926215//National Science Foundation (NSF)/ ; BCS 1926105//National Science Foundation (NSF)/ ; 864203//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; }, mesh = {Animals ; Madagascar ; *Genetic Variation ; *Lemur/genetics ; *Anthropogenic Effects ; *Genome ; *Lemuridae/genetics ; }, abstract = {Ecological variation and anthropogenic landscape modification have had key roles in the diversification and extinction of mammals in Madagascar. Lemurs represent a radiation with more than 100 species, constituting roughly one-fifth of the primate order. Almost all species of lemurs are threatened with extinction, but little is known about their genetic diversity and demographic history. Here, we analyse high-coverage genome-wide resequencing data from 162 unique individuals comprising 50 species of Lemuriformes, including multiple individuals from most species. Genomic diversity varies widely across the infraorder and yet is broadly consistent among individuals within species. We show widespread introgression in multiple genera and generally high levels of genomic diversity likely resulting from allele sharing that occurred during periods of connectivity and fragmentation during climatic shifts. We find distinct patterns of demographic history in lemurs across the ecogeographic regions of Madagascar within the last million years. Within the past 2,000 years, lemurs underwent major declines in effective population size that corresponded to the timing of human population expansion in Madagascar. In multiple regions of the island, we identified chronological trajectories of inbreeding that are consistent across genera and species, suggesting localized effects of human activity. Our results show how the extraordinary diversity of these long-neglected, endangered primates has been influenced by ecological and anthropogenic factors.}, }
@article {pmid39729906, year = {2025}, author = {Abdelghany, S and Simancas-Giraldo, SM and Zayed, A and Farag, MA}, title = {How does the coral microbiome mediate its natural host fitness under climate stress conditions? Physiological, molecular, and biochemical mechanisms.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106920}, doi = {10.1016/j.marenvres.2024.106920}, pmid = {39729906}, issn = {1879-0291}, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Microbiota/physiology ; *Climate Change ; Symbiosis ; Stress, Physiological ; Coral Reefs ; Heat-Shock Response ; }, abstract = {Although the symbiotic partnership between corals and algal endosymbionts has been extensively explored, interactions between corals, their algal endosymbionts and microbial associates are still less understood. Screening the response of natural microbial consortiums inside corals can aid in exploiting them as markers for dysbiosis interactions inside the coral holobiont. The coral microbiome includes archaea, bacteria, fungi, and viruses hypothesized to play a pivotal vital role in coral health and tolerance to heat stress condition via different physiological, biochemical, and molecular mechanisms. The dynamic behaviour of microbial associates could denote their potential role in coral adaptation to future climate change, with microbiome shifts occurring independently as a response to thermal stress or as a response to host stress response. Associated adaptations include regulation of coral-algal-microbial interactions, expression of heat shock proteins, microbial composition changes, and accumulation of secondary metabolites to aid in sustaining the coral's overall homeostasis under ocean warming scenarios.}, }
@article {pmid39715180, year = {2024}, author = {Bjørnsen, MB and Valerón, NR and Vásquez, DP and Velasco, EM and Hansen, AJ and Hauptmann, AL}, title = {Microbiota in the ptarmigan intestine-An Inuit delicacy and its potential in popular cuisine.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0305317}, pmid = {39715180}, issn = {1932-6203}, mesh = {Animals ; *Inuit ; *Intestines/microbiology ; *Gastrointestinal Microbiome ; *RNA, Ribosomal, 16S/genetics ; Humans ; Galliformes/microbiology ; Greenland ; }, abstract = {The consumption of prey intestines and their content, known as gastrophagy, is well-documented among Arctic Indigenous peoples, particularly Inuit. In Greenland, Inuit consume intestines from various animals, including the ptarmigan, a small herbivorous grouse bird. While gastrophagy provides the potential to transfer a large number of intestinal microorganisms from prey to predator, including to the human gut, its microbial implications remain to be investigated. This study addresses this gap by investigating the microbial composition of the Greenlandic rock ptarmigan's gastrointestinal tract by analyzing the crop, stomach, and intestines while also comparing it with the microbiota found in garum, a fermented sauce made from ptarmigan meat and intestines. Through 16S rRNA gene sequencing, we assessed whether garum made from ptarmigan intestines provides access to microbial diversity otherwise only accessible through gastrophagy. Our findings reveal that garum made from ptarmigan intestines displayed distinct flavors and microbial composition similar to that found in the ptarmigan gut and intestines, highlighting the potential role of fermented products in mediating food microbial diversity associated with Indigenous food practices. Furthermore, our study underscores the broader importance of understanding microbial diversity in different food systems, particularly in the context of shifting dietary patterns and concerns about diminishing food microbial diversity. By elucidating the microbial richness gained through gastrophagy this research contributes to a deeper understanding of traditional and Indigenous foodways and their implications for human gut health.}, }
@article {pmid39710259, year = {2024}, author = {Callaway, T and Perez, HG and Corcionivoschi, N and Bu, D and Fluharty, FL}, title = {The Holobiont concept in ruminant physiology - more of the same, or something new and meaningful to food quality, food security, and animal health?.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-25847}, pmid = {39710259}, issn = {1525-3198}, abstract = {The holobiont concept has emerged as an attempt to recognize and describe the myriad interactions and physiological signatures inherent to a host organism, as impacted by the microbial communities that colonize and/or co-inhabit the environment within which the host resides. The field acknowledges and draws upon principles from evolution, ecology, genetics, and biology, and in many respects has been "pushed" by the advent of high throughput DNA sequencing and, to a lesser extent, other "omics"-based technologies. Despite the explosion in data generation and analyses, much of our current understanding of the human and ruminant "holobiont" is based on compositional forms of data and thereby, restricted to describing host phenotypes via associative or correlative studies. So, where to from here? We will discuss some past findings arising from ruminant and human gut microbiota research and seek to evaluate the rationale, progress, and opportunities that might arise from the "holobiont" approach to the ruminant and human host. In particular, we will consider what is a "good" or "bad" host gastrointestinalmicrobiome in different scenarios, as well as potential avenues to sustain or alter the holobiont. While the holobiont approach might improve food quality, food security and animal health, these benefits will be most likely achieved via a judicious and pragmatic compromise in data generation, both in terms of its scale, as well as its generation in context with the "forgotten" knowledge of ruminant and human physiology.}, }
@article {pmid39709663, year = {2025}, author = {Augusto, AM and Pereira, S and Rodrigues, S and Marques, F and Aizpurua, O and Alberdi, A and Jones, G and Razgour, O and Marques, TA and Russo, D and Rebelo, H}, title = {Landscape influences bat suppression of pine processionary moth: Implications for pest management.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123803}, doi = {10.1016/j.jenvman.2024.123803}, pmid = {39709663}, issn = {1095-8630}, mesh = {Animals ; *Moths/physiology ; *Chiroptera ; Ecosystem ; Pest Control ; Portugal ; Conservation of Natural Resources ; Predatory Behavior ; }, abstract = {Bats provide important ecosystem services, particularly in agriculture, yet integrating bat management into conservation plans remains challenging. Some landscape features considerably influence bat presence, diversity, and ecosystem service provision. Understanding the relationship between landscape structure, composition, pest suppression, and ecosystem services is crucial. We modelled areas where bats most effectively suppress pine processionary moths (Thaumetopoea pityocampa), considering landscape characteristics to predict ecosystem services and optimise pest suppression in Serra da Estrela, Portugal. Faecal samples collected during fieldwork were analysed for pine processionary moth presence in bat diets. Lasso regression assessed spatial landscape variables to create an "optimal landscape" for predation. Landscape structure and composition influenced pest suppression differently, with the greatest impact within a 5000-m buffer. "Riparian edge" and "tree cover density" were key habitat structure variables supporting bat navigation and access to hunting areas, while "other forest" and "vineyard/orchard" areas were important composition variables. Optimising landscape composition involves incorporating diverse forest within agroforestry systems to enhance pest suppression by creating habitats reflecting bats' foraging preferences. We recommend strategies focusing on riparian edge conservation, selective canopy reduction, and promoting diverse forest compositions. These strategies aim to create mosaic landscapes balancing land uses, fostering optimal conditions for bat foraging. Our study shows edges provide the highest rates of bats-pine processionary moth interactions. However, caution is needed to avoid excessive fragmentation, which may reduce habitat suitability and increase pest presence before effective bat predation. A balanced approach, focusing on edge creation without over-fragmenting the landscape, is key to promoting sustainable pest management.}, }
@article {pmid39702455, year = {2024}, author = {García, FC and Osman, EO and Garcias-Bonet, N and Delgadillo-Ordoñez, N and Santoro, EP and Raimundo, I and Villela, HDM and Voolstra, CR and Peixoto, RS}, title = {Seasonal changes in coral thermal threshold suggest species-specific strategies for coping with temperature variations.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1680}, pmid = {39702455}, issn = {2399-3642}, support = {BAS/1/1095-01-01//King Abdullah University of Science and Technology (KAUST)/ ; FCC/1/1973-51-01//King Abdullah University of Science and Technology (KAUST)/ ; URF/1/4723-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Anthozoa/physiology ; Animals ; *Seasons ; *Temperature ; *Species Specificity ; Acclimatization ; Thermotolerance ; Photosynthesis ; Indian Ocean ; }, abstract = {Coral thermotolerance research has focused on the ability of coral holobionts to maximize withstanding thermal stress exposure. Yet, it's unclear whether thermal thresholds adjust across seasons or remain constant for a given species and location. Here, we assessed the thermal tolerance thresholds over time spanning the annual temperature variation in the Red Sea for Pocillopora verrucosa and Acropora spp. colonies. Utilizing the Coral Bleaching Automated Stress System (CBASS), we conducted standardized acute thermal assays by exposing corals to a range of temperatures (30 to 39 °C) and measuring their photosynthetic efficiency (Fv/Fm). Our results reveal species-specific thermal tolerance patterns. P. verrucosa exhibited significant seasonal changes in their thermal thresholds of around 3 °C, while Acropora spp. remained rather stable, showing changes of around 1 °C between seasons. Our work shows that thermal thresholds can vary with seasonal temperature fluctuations, suggesting that coral species may acclimate to these natural temperature hanges over short periods in a species-specific manner.}, }
@article {pmid39701859, year = {2025}, author = {Barnes, CJ and Bahram, M and Nicolaisen, M and Gilbert, MTP and Vestergård, M}, title = {Microbiome selection and evolution within wild and domesticated plants.}, journal = {Trends in microbiology}, volume = {33}, number = {4}, pages = {447-458}, doi = {10.1016/j.tim.2024.11.011}, pmid = {39701859}, issn = {1878-4380}, mesh = {*Microbiota/genetics ; *Plants/microbiology/genetics ; *Biological Evolution ; Bacteria/genetics/classification ; Domestication ; Host Microbial Interactions ; Selection, Genetic ; }, abstract = {Microbes are ubiquitously found across plant surfaces and even within their cells, forming the plant microbiome. Many of these microbes contribute to the functioning of the host and consequently affect its fitness. Therefore, in many contexts, including microbiome effects enables a better understanding of the phenotype of the plant rather than considering the genome alone. Changes in the microbiome composition are also associated with changes in the functioning of the host, and there has been considerable focus on how environmental variables regulate plant microbiomes. More recently, studies suggest that the host genome also preconditions the microbiome to the environment of the plant, and the microbiome is therefore subject to evolutionary forces. Here, we outline how plant microbiomes are governed by both environmental variables and evolutionary processes and how they can regulate plant health together.}, }
@article {pmid39691438, year = {2024}, author = {Armstrong, KC and Lippert, M and Hanson, E and Nestor, V and Cornwell, B and Walker, NS and Golbuu, Y and Palumbi, SR}, title = {Fine-Scale Geographic Variation of Cladocopium in Acropora hyacinthus Across the Palauan Archipelago.}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70650}, pmid = {39691438}, issn = {2045-7758}, abstract = {Symbiont genotype plays a vital role in the ability of a coral host to tolerate rising ocean temperatures, with some members of the family Symbiodiniaceae possessing more thermal tolerance than others. While existing studies on genetic structure in symbiont populations have focused on broader scales of 10-100 s of km, there is a noticeable gap in understanding the seascape genetics of coral symbionts at finer-yet ecologically and evolutionarily relevant-scales. Here, we mapped short reads from 271 holobiont genome libraries of individual Acropora hyacinthus colonies to protein coding genes from the chloroplast genome to identify patterns of symbiont population genetic structure. Utilizing this low-pass method, we assayed over 13,000 bases from every individual, enabling us to discern genetic variation at a finer geographic scale than previously reported at the population level. We identified five common Cladocopium chloroplast SNP profiles present across Palau, with symbiont structure varying between Northern, mid-lagoon, and Southern regions, and inshore-offshore gradients. Although symbiont populations within reefs typically contained significant genetic diversity, we also observed genetic structure between some nearby reefs. To explore whether coral hosts retain their symbionts post-transplantation, we experimentally moved 79 corals from their native reefs to transplant sites with both different and similar chloroplast SNP profiles. Over 12 months, we observed 12 instances where transplanted corals changed profiles, often transitioning to a profile present in adjacent corals. Symbiont genetic structure between reefs suggests either low dispersal of symbionts or environmental selection against dispersers, both resulting in the potential for significant adaptive differentiation across reef environments. The extent to which local corals and their symbionts are co-adapted to environments on a reef-by-reef scale is currently poorly known. Chloroplast sequences offer an additional tool for monitoring symbiont genetics and coral-symbiont interactions when assisted migration is used in restoration.}, }
@article {pmid39681619, year = {2024}, author = {Niedzwiedz, S and Schmidt, C and Yang, Y and Burgunter-Delamare, B and Andersen, S and Hildebrandt, L and Pröfrock, D and Thomas, H and Zhang, R and Damsgård, B and Bischof, K}, title = {Run-off impacts on Arctic kelp holobionts have strong implications on ecosystem functioning and bioeconomy.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30506}, pmid = {39681619}, issn = {2045-2322}, support = {869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869383//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 869154//European Union's Horizon 2020 research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 101136480//European Union's Horizon research and innovation programme/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; 2021YFE0193000//National Key Research and Development Program of China/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2023SP218//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, mesh = {*Kelp ; Arctic Regions ; *Ecosystem ; *Climate Change ; Food Chain ; }, abstract = {Kelps (Laminariales, Phaeophyceae) are foundation species along Arctic rocky shores, providing the basis for complex ecosystems and supporting a high secondary production. Due to ongoing climate change glacial and terrestrial run-off are currently accelerating, drastically changing physical and chemical water column parameters, e.g., water transparency for photosynthetically active radiation or dissolved concentrations of (harmful) elements. We investigated the performance and functioning of Arctic kelp holobionts in response to run-off gradients, with a focus on the effect of altered element concentrations in the water column. We found that the kelp Saccharina latissima accumulates harmful elements (e.g., cadmium, mercury) originating from coastal run-off. As kelps are at the basis of the food web, this might lead to biomagnification, with potential consequences for high-latitude kelp maricultures. In contrast, the high biosorption potential of kelps might be advantageous in monitoring environmental pollution or potentially extracting dissolved rare earth elements. Further, we found that the relative abundances of several kelp-associated microbial taxa significantly responded to increasing run-off influence, changing the kelps functioning in the ecosystem, e.g., the holobionts nutritional value and elemental cycling. The responses of kelp holobionts to environmental changes imply cascading ecological and economic consequences for Arctic kelp ecosystems in future climate change scenarios.}, }
@article {pmid39680902, year = {2024}, author = {Lipowska, MM and Sadowska, ET and Kohl, KD and Koteja, P}, title = {Experimental Evolution of a Mammalian Holobiont? Genetic and Maternal Effects on the Cecal Microbiome in Bank Voles Selectively Bred for Herbivorous Capability.}, journal = {Ecological and evolutionary physiology}, volume = {97}, number = {5}, pages = {274-291}, doi = {10.1086/732781}, pmid = {39680902}, issn = {2993-7973}, mesh = {Animals ; *Arvicolinae/microbiology/genetics ; *Herbivory ; *Gastrointestinal Microbiome/genetics ; Female ; Cecum/microbiology ; Biological Evolution ; Maternal Inheritance/genetics ; Selective Breeding/genetics ; Male ; Diet/veterinary ; }, abstract = {AbstractMammalian herbivory represents a complex adaptation requiring evolutionary changes across all levels of biological organization, from molecules to morphology to behavior. Explaining the evolution of such complex traits represents a major challenge in biology, as it is simultaneously muddled and enlightened by a growing awareness of the crucial role of symbiotic associations in shaping organismal adaptations. The concept of hologenomic evolution includes the partnered unit of the holobiont, the host with its microbiome, as a selection unit that may undergo adaptation. Here, we test some of the assumptions underlying the concept of hologenomic evolution using a unique experimental evolution model: lines of the bank vole (Myodes [=Clethrionomys] glareolus) selected for increased ability to cope with a low-quality herbivorous diet and unselected control lines. Results from a complex nature-nurture design, in which we combined cross-fostering between the selected and control lines with dietary treatment, showed that the herbivorous voles harbored a cecal microbiome with altered membership and structure and changed abundances of several phyla and genera regardless of the origin of their foster mothers. Although the differences were small, they were statistically significant and partially robust to changes in diet and housing conditions. Microbial characteristics also correlated with selection-related traits at the level of individual variation. Thus, the results support the hypothesis that selection on a host performance trait leads to genetic changes in the host that promote the maintenance of a beneficial microbiome. Such a result is consistent with some of the assumptions underlying the concept of hologenomic evolution.}, }
@article {pmid39670091, year = {2024}, author = {Garzon-Machado, M and Luna-Fontalvo, J and García-Urueña, R}, title = {Disease prevalence and bacterial isolates associated with Acropora palmata in the Colombian Caribbean.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16886}, pmid = {39670091}, issn = {2167-8359}, mesh = {*Anthozoa/microbiology ; Animals ; Colombia/epidemiology ; Caribbean Region/epidemiology ; Prevalence ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; Vibrio/isolation &amp; purification/genetics/pathogenicity ; }, abstract = {The decline in Acropora palmata populations in Colombian reefs has been mainly attributed to diseases outbreaks. The population size structure and prevalence of white pox and white band disease were evaluated in six localities of the Colombian Caribbean. Here, we aimed to isolate enteric bacteria and Vibrios from healthy and diseased coral mucus to relate its presence to the health status of Acropora palmata. The isolated bacteria were identified using molecular analyses with the 16S rRNA gene. Larger colonies had the highest percentage of the prevalence of both diseases. The strains that were identified as Vibrio sp. and Bacillus sp. were common in the healthy and diseased mucus of the holobiont. The Exiguobacterium sp. and Cobetia sp. strains isolated from diseased mucus may indicate maintenance and resilience mechanisms in the coral. Enterococcus sp. and other bacteria of the Enterobacteriaceae family were isolated from some localities, suggesting that probably contamination due to poor treatment of domestic wastewater and contributions from river discharges can affect coral health. The spatial heterogeneity of Colombian coral reefs exhibited variability in the bacteria, wherein environmental alterations can trigger signs of disease.}, }
@article {pmid39658219, year = {2024}, author = {Juéry, C and Auladell, A and Füssy, Z and Chevalier, F and Yee, DP and Pelletier, E and Corre, E and Allen, AE and Richter, DJ and Decelle, J}, title = {Transportome remodeling of a symbiotic microalga inside a planktonic host.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39658219}, issn = {1751-7370}, support = {ANR-11-INBS-0013//Institut Fran&#xe7;ais de Bioinformatique/ ; DE-AC02-05CH11231//Office of Science of the US Department of Energy/ ; 970820//Principles of Microbial Ecosystems/ ; NSF-OCE-1756884//National Science Foundation/ ; NA19NOS4780181//National Oceanic and Atmospheric Administration/ ; 949745-GROWCEAN-ERC-2020-STG/ERC_/European Research Council/International ; 824110//European Union's Horizon 2020/ ; ERC-SymbiOCEAN-101088661)//CNRS and ATIP-Avenir program funding, and by the European Union/ ; }, mesh = {*Symbiosis ; *Microalgae/metabolism ; Plankton/metabolism/genetics ; Haptophyta/metabolism/genetics ; Photosynthesis ; Transcriptome ; }, abstract = {Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange remain largely unknown, especially in unicellular photosymbioses that are widespread in the open ocean. Combining genomics, single-holobiont transcriptomics, and environmental metatranscriptomics, we revealed the transportome of the marine microalga Phaeocystis in symbiosis within acantharia, with a focus on sugar transporters. At the genomic level, the sugar transportome of Phaeocystis is comparable to non-symbiotic haptophytes. By contrast, we found significant remodeling of the expression of the transportome in symbiotic microalgae compared to the free-living stage. More particularly, 36% of sugar transporter genes were differentially expressed. Several of them, such as GLUTs, TPTs, and aquaporins, with glucose, triose-phosphate sugars, and glycerol as potential substrates, were upregulated at the holobiont and community level. We also showed that algal sugar transporter genes exhibit distinct temporal expression patterns during the day. This reprogramed transportome indicates that symbiosis has a major impact on sugar fluxes within and outside the algal cell, and highlights the complexity and the dynamics of metabolic exchanges between partners. This study improves our understanding of the molecular players of the metabolic connectivity underlying the ecological success of planktonic photosymbiosis and paves the way for more studies on transporters across photosymbiotic models.}, }
@article {pmid39653763, year = {2025}, author = {Forrester, JV and McMenamin, PG}, title = {Evolution of the ocular immune system.}, journal = {Eye (London, England)}, volume = {39}, number = {3}, pages = {468-477}, pmid = {39653763}, issn = {1476-5454}, mesh = {Humans ; Animals ; *Eye/immunology ; *Biological Evolution ; *Immune System/physiology ; Immunity, Innate ; Adaptive Immunity ; }, abstract = {The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).}, }
@article {pmid39651872, year = {2025}, author = {Marques, M and da Silva, DM and Santos, E and Baylina, N and Peixoto, R and Kyrpides, NC and Woyke, T and Whitman, WB and Keller-Costa, T and Costa, R}, title = {Genome sequences of four novel Endozoicomonas strains associated with a tropical octocoral in a long-term aquarium facility.}, journal = {Microbiology resource announcements}, volume = {14}, number = {1}, pages = {e0083324}, pmid = {39651872}, issn = {2576-098X}, support = {C644915664-00000026//Next Generation EU European Fund/ ; UIDB/04565/2020//MEC | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; UIDP/04565/2020//MEC | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; LA/P/0140/2020//MEC | Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia (FCT)/ ; 10.46936/10.25585/60001079//U.S. Department of Energy (DOE)/ ; }, abstract = {We report the genome sequences of four Endozoicomonas sp. strains isolated from the octocoral Litophyton maintained long term at an aquarium facility. Our analysis reveals the coding potential for versatile polysaccharide metabolism; Type II, III, IV, and VI secretion systems; and the biosynthesis of novel ribosomally synthesized and post-translationally modified peptides.}, }
@article {pmid39637852, year = {2025}, author = {Ramos-Madrigal, J and Fritz, GJ and Schroeder, B and Smith, B and Sánchez-Barreiro, F and Carøe, C and Runge, AKW and Boer, S and McGrath, K and Vieira, FG and Liu, S and da Fonseca, RR and Guo, C and Zhang, G and Petersen, B and Sicheritz-Pontén, T and Gopalakrishnan, S and Gilbert, MTP and Wales, N}, title = {The genomic origin of early maize in eastern North America.}, journal = {Cell}, volume = {188}, number = {1}, pages = {33-43.e16}, doi = {10.1016/j.cell.2024.11.003}, pmid = {39637852}, issn = {1097-4172}, mesh = {*Zea mays/genetics/metabolism ; *Genome, Plant ; North America ; Plant Proteins/genetics/metabolism ; Phylogeny ; Domestication ; Amylose/metabolism ; Plant Breeding ; }, abstract = {Indigenous maize varieties from eastern North America have played an outsized role in breeding programs, yet their early origins are not fully understood. We generated paleogenomic data to reconstruct how maize first reached this region and how it was selected during the process. Genomic ancestry analyses reveal recurrent movements northward from different parts of Mexico, likely culminating in at least two dispersals from the US Southwest across the Great Plains to the Ozarks and beyond. We find that 1,000-year-old Ozark specimens carry a highly differentiated wx1 gene, which is involved in the synthesis of amylose, highlighting repeated selective pressures on the starch metabolic pathway throughout maize's domestication. This population shows a close affinity with the lineage that ultimately became the Northern Flints, a major contributor to modern commercial maize.}, }
@article {pmid39633476, year = {2024}, author = {Manrique-de-la-Cuba, MF and Parada-Pozo, G and Rodríguez-Marconi, S and López-Rodríguez, MR and Abades, S and Trefault, N}, title = {Evidence of habitat specificity in sponge microbiomes from Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {100}, pmid = {39633476}, issn = {2524-6372}, support = {Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; DG_02-22//Instituo Antartico Chileno- INACH/ ; Doctoral fellowship N&#xb0; 21211164//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, abstract = {BACKGROUND: Marine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.<br><br>RESULTS: Our study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.<br><br>CONCLUSIONS: This study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.}, }
@article {pmid39631125, year = {2024}, author = {Zhang, JY and Li, XY and Li, DX and Zhang, ZH and Hu, LQ and Sun, CX and Zhang, XN and Wu, M and Liu, LT}, title = {Endoplasmic reticulum stress in intestinal microecology: A controller of antineoplastic drug-related cardiovascular toxicity.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {181}, number = {}, pages = {117720}, doi = {10.1016/j.biopha.2024.117720}, pmid = {39631125}, issn = {1950-6007}, mesh = {Animals ; Humans ; *Antineoplastic Agents/adverse effects ; Cardiotoxicity/etiology ; Dysbiosis/chemically induced ; *Endoplasmic Reticulum Stress/drug effects ; *Gastrointestinal Microbiome/drug effects ; Intestines/drug effects/microbiology ; *Cardiovascular Diseases/chemically induced/microbiology ; }, abstract = {Endoplasmic reticulum (ER) stress is extensively studied as a pivotal role in the pathological processes associated with intestinal microecology. In antineoplastic drug treatments, ER stress is implicated in altering the permeability of the mechanical barrier, depleting the chemical barrier, causing dysbiosis, exacerbating immune responses and inflammation in the immune barrier. Enteric dysbiosis and intestinal dysfunction significantly affect the circulatory system in various heart disorders. In antineoplastic drug-related cardiovascular (CV) toxicity, ER stress constitutes a web of relationships in the host-microbiome symbiotic regulatory loop. Therefore, understanding the holobiont perspective will help de-escalate spatial and temporal restrictions. This review investigates the role of ER stress-mediated gut microecological alterations in antineoplastic treatment-induced CV toxicity.}, }
@article {pmid39620136, year = {2024}, author = {Ellegaard, MR and Ebenesersdóttir, SS and Moore, KHS and Petersén, A and Vågene, &#xc5;J and Bieker, VC and Denham, SD and Cavalleri, GL and Gilbert, E and Werge, T and Hansen, TF and Kockum, I and Alfredsson, L and Olsson, T and Hovig, E and Gilbert, MTP and Stefánsson, K and Stenøien, HK and Helgason, A and Martin, MD}, title = {Corroborating written history with ancient DNA: The case of the Well-man described in an Old Norse saga.}, journal = {iScience}, volume = {27}, number = {11}, pages = {111076}, pmid = {39620136}, issn = {2589-0042}, abstract = {The potential of ancient DNA analyses to provide independent sources of information about events in the historical record remains to be demonstrated. Here we apply palaeogenomic analysis to human remains excavated from a medieval well at the ruins of Sverresborg Castle in central Norway. In Sverris Saga, the Old Norse saga of King Sverre Sigurdsson, one passage details a 1197-CE raid on the castle and mentions a dead man thrown into the well. Radiocarbon dating supports that these are that individual's remains. We sequenced the Well-man's nuclear genome to 3.4× and compared it to Scandinavian populations, revealing he was closely related to inhabitants of southern Norway. This was surprising because King Sverre's defeated army was assumed to be recruited from parts of central Norway, whereas the raiders were from the south. The findings also indicate that the unique genetic drift seen in present-day southern Norwegians already existed 800 years ago.}, }
@article {pmid39620087, year = {2024}, author = {Zhang, X and Xi, T and Wang, Y and Fan, X and Xu, D and Zhang, P and Sun, K and Zhang, Y and Ma, J and Ye, N}, title = {Chemical interactions between kelp Macrocystis pyrifera and symbiotic bacteria under elevated CO2 condition.}, journal = {Marine life science &amp; technology}, volume = {6}, number = {4}, pages = {700-712}, pmid = {39620087}, issn = {2662-1746}, abstract = {UNLABELLED: Kelps are pivotal to temperate coastal ecosystems, providing essential habitat and nutrients for diverse marine life, and significantly enhancing local biodiversity. The impacts of elevated CO2 levels on kelps may induce far-reaching effects throughout the marine food web, with potential consequences for biodiversity and ecosystem functions. This study considers the kelp Macrocystis pyrifera and its symbiotic microorganisms as a holistic functional unit (holobiont) to examine their collective response to heightened CO2 levels. Over a 4 month cultivation from the fertilization of M. pyrifera gametes to the development of juvenile sporophytes, our findings reveal that elevated CO2 levels influence the structure of the M. pyrifera symbiotic microbiome, alter metabolic profiles, and reshape microbe-metabolite interactions using 16S rRNA amplicon sequencing and liquid chromatography coupled to mass spectrometry analysis. Notably, Dinoroseobacter, Sulfitobacter, Methylotenera, Hyphomonas, Milano-WF1B-44 and Methylophaga were selected as microbiome biomarkers, which showed significant increases in comparative abundance with elevated CO2 levels. Stress-response molecules including fatty-acid metabolites, oxylipins, and hormone-like compounds such as methyl jasmonate and prostaglandin F2a emerged as critical metabolomic indicators. We propose that elevated CO2 puts certain stress on the M. pyrifera holobiont, prompting the release of these stress-response molecules. Moreover, these molecules may aid the kelp's adaptation by modulating the microbial community structure, particularly influencing potential pathogenic bacteria, to cope with environmental change. These results will enrich the baseline data related to the chemical interactions between the microbiota and M. pyrifera and provide clues for predicting the resilience of kelps to future climate change.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00259-5.}, }
@article {pmid39615101, year = {2025}, author = {Huang, W and Huang, Z and Yang, E and Meng, L and Chen, J and Tan, R and Xiao, Z and Zhou, Y and Xu, M and Yu, K}, title = {High- and low-temperature stress responses of Porites lutea from the relatively high-latitude region of the South China Sea.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106858}, doi = {10.1016/j.marenvres.2024.106858}, pmid = {39615101}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/physiology ; China ; Climate Change ; *Stress, Physiological ; Coral Reefs ; *Cold Temperature ; *Hot Temperature ; Symbiosis ; Temperature ; Dinoflagellida/physiology ; }, abstract = {Global climate change has led to more frequent extreme temperature (extreme heat and cold) events, posing a serious threat to coral reef ecosystems. Higher latitudes are considered potential refuges for reef-building corals, but their response to extreme temperature stress in these regions remain unclear. This study, indoor simulated stress experiments ranging on Porites lutea from Weizhou Island in the northern part of the South China Sea, simulating suitable (26 °C) to extreme high (34 °C) and extreme low (12 °C) temperatures. Physiological, biochemical, and transcriptional responses, were analysed. Results showed P. lutea's tentacles contracted, and symbiotic relationships broke down at both high and low temperatures; leading to oxidative stress, and a higher risk of disease. The coral host's response to temperature stress was positively regulated, mainly through apoptosis and metabolic inhibition pathways, whereas Symbiodiniaceae C15 showed no significant response to either high- or low-temperature stress. The coral host played a dominant role in the holobiont's stress response, using similar mechanisms for both high- and low-temperatures with some differences in the details. This study enhances understanding the temperature response mechanisms of the dominant coral species, P. lutea in the relatively high-latitude regions of the South China Sea.}, }
@article {pmid39603001, year = {2025}, author = {Gao, X and Chen, J and Ma, Y and Zheng, Y and Bu, Y and Yu, X and Yu, K}, title = {Differential physiological and microbial responses of the octocoral Junceella squamata to high-temperature and cadmium stress.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106865}, doi = {10.1016/j.marenvres.2024.106865}, pmid = {39603001}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/physiology/microbiology/drug effects ; *Cadmium/toxicity ; Stress, Physiological ; *Hot Temperature/adverse effects ; Symbiosis ; *Water Pollutants, Chemical/toxicity ; Transcriptome ; Microbiota ; }, abstract = {Global warming and heavy metals have become the major threat to the growth and reproduction of corals. However, unlike scleractinian corals, in the context of widespread coral degradation worldwide, there are few reports on the response of octocorallia corals to high-temperature stress and heavy metals. In the present study, we conducted indoor simulation experiments using Junceella squamata. We evaluated the physiological response of these corals under high-temperature stress at 33 °C and cadmium (Cd) stress by comparing the composition and diversity of their symbiotic bacteria and analyzing differences in their transcriptome. The results show that high-temperature stress has more severe adverse effects than cadmium stress. High-temperature stress disrupts coral symbiotic relationships, leading to an increase in alpha diversity associated with disease-causing bacteria, which may increase the risk of infection and potentially contribute to coral mortality. Meanwhile, cadmium stress increases the instability of the coral holobiont, potentially disrupting DNA stability and RNA transcriptional regulation. However, an increase in Cd-tolerant bacteria may help corals respond to cadmium stress. This study reveals the effects of harmful substances on coral and highlights the urgent need for action to protect octocorals in the face of environmental stress.}, }
@article {pmid39602985, year = {2025}, author = {Gao, X and Chen, J and Yu, K and Bu, Y and Wang, L and Yu, X}, title = {Exposure to polypropylene microplastics induces the upregulation of protein digestion-associated genes and microbiome reorganization in the octocoral Junceella squamata.}, journal = {Marine pollution bulletin}, volume = {210}, number = {}, pages = {117331}, doi = {10.1016/j.marpolbul.2024.117331}, pmid = {39602985}, issn = {1879-3363}, mesh = {*Anthozoa/drug effects ; Animals ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects ; *Coral Reefs ; *Polypropylenes ; Symbiosis ; Up-Regulation ; }, abstract = {Microplastics, a new type of pollutants found in coral reefs, have attracted increasing attention. However, most of the current research focuses on the scleractinian corals and few reports on Octocorallia. To reveal the impact of microplastic exposure on Octocorallia, we analyzed the transcriptional response of the coral hosts Junceella squamata along with changes to the diversity and community structure of its symbiotic bacteria following exposure to polystyrene microplastics. These results suggest that the microplastics have adverse impacts on nutrient metabolism and absorption in J. squamata. The symbiotic bacteria of J. squamata exhibited a clear response after exposure to microplastics, which may also reflect an adaptation mechanism of corals, and help to maintain the physiological function of coral symbiotic function under the exposure of microplastics. This study has revealed the impact of microplastic exposure on J. squamata, providing new insights for coral protection against the background of increased microplastics pollution.}, }
@article {pmid39600252, year = {2024}, author = {Grupstra, CGB and Meyer-Kaiser, KS and Bennett, MJ and Andres, MO and Juszkiewicz, DJ and Fifer, JE and Da-Anoy, JP and Gomez-Campo, K and Martinez-Rugerio, I and Aichelman, HE and Huzar, AK and Hughes, AM and Rivera, HE and Davies, SW}, title = {Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17578}, doi = {10.1111/gcb.17578}, pmid = {39600252}, issn = {1365-2486}, support = {2048589//The National Science Foundation's Division of Ocean Sciences/ ; 2048678//The National Science Foundation's Division of Ocean Sciences/ ; }, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Climate Change ; *Coral Reefs ; *Symbiosis ; Microbiota ; Dinoflagellida/physiology ; }, abstract = {As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e. cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic ("typical" conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages are widespread. All corals harbored Cladocopium C15 photobionts; L1 and L2 shared a photobiont pool that differed in composition between reef types, yet L3 mostly harbored unique photobiont strains not found in the other lineages. Assemblages of bacterial partners differed among reef types in lineage-specific ways, suggesting that lineages employ distinct microbiome regulation strategies. Analysis of light-harvesting capacity and thermal tolerance revealed adaptive variation underpinning survival in distinct habitats: L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting that it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, suggesting that is a generalist lineage. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations, can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.}, }
@article {pmid39593141, year = {2024}, author = {Steiner, LX and Schmittmann, L and Rahn, T and Lachnit, T and Jahn, MT and Hentschel, U}, title = {Phage-induced disturbance of a marine sponge microbiome.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {97}, pmid = {39593141}, issn = {2524-6372}, support = {CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; CRC1182-TP C04//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Bacteriophages are known modulators of community composition and activity in environmental and host-associated microbiomes. However, the impact single phages have on bacterial community dynamics under viral predation, the extent and duration of their effect, are not completely understood. In this study, we combine morphological and genomic characterization of a novel marine phage, isolated from the Baltic sponge Halichondria panicea, and report on first attempts of controlled phage-manipulation of natural sponge-associated microbiomes.<br><br>RESULTS: We used culture-based and culture-independent (16S rRNA gene amplicon sequencing) methods to investigate bacterial community composition and dynamics in sponge microbiomes with and without the addition of phages. Upon application of a novel Maribacter specialist phage Panino under controlled conditions, we were able to detect community-wide shifts in the microbiome composition and load after 72&#xa0;h. While bacterial community composition became more dissimilar over time in the presence of phages, species evenness and richness were maintained. Upon phage exposure, we observed the loss of several low-abundance constituent taxa of the resident microbiota, while other originally underrepresented taxa increased. Virulent phages likely induce community-wide disturbances, evident in changes in the total sponge microbial profile by specific elimination of constituent taxa, which leads to an increase in bacterial abundance of opportunistic taxa, such as the genera Vibrio, Pseudoalteromonas, and Photobacterium.<br><br>CONCLUSIONS: Our findings suggest that sponge microbiome diversity and, by extension, its resilience depend on the maintenance of resident bacterial community members, irrespective of their abundance. Phage-induced disturbances can significantly alter community structure by promoting the growth of opportunistic bacteria like Vibrio and shifting the microbiome to a dysbiotic state. These insights highlight the role of bacteriophages in shaping microbiome dynamics and underscore the potential for phage application in managing bacterial community composition in marine host-associated environments.}, }
@article {pmid39590502, year = {2024}, author = {Schapheer, C and González, LM and Villagra, C}, title = {Microorganism Diversity Found in Blatta orientalis L. (Blattodea: Blattidae) Cuticle and Gut Collected in Urban Environments.}, journal = {Insects}, volume = {15}, number = {11}, pages = {}, pmid = {39590502}, issn = {2075-4450}, abstract = {Pest cockroaches share urban habitats with us; their prevalence in urban areas prompts concerns regarding their effect on human health, as synanthropic cockroaches often host pathogenic microorganisms. Nonetheless, microbial associates in these insects can also be related to their biology, contributing to their physiological homeostasis and reproductive success. In this article, we present in detail, for the first time, the bacterial community associated with the oriental cockroach Blatta orientalis, one of the world's five most prominent pest cockroaches. We report the composition of the communities of bacteria found over the exoskeleton and inside the gut of this global pest. We collected B. orientalis in Santiago, Chile's capital city, and the urban nucleus in this country. We conducted DNA extractions and metabarcoding analysis. We found diverse bacterial lineages, including mutualist symbiotic strains, and microorganisms considered pathogenic to humans. We also analyzed the metabolic functions of the bacterial communities identified and discussed the role of B. orientalis as a reservoir and vector of pathogens in urban areas. We discuss to what extent the diversity of functions of the microbial community associated with cockroaches may contribute to emergent properties enabling these insects to inhabit human-modified habitats.}, }
@article {pmid39589622, year = {2024}, author = {Wong, JM and Liu, AC and Lin, HT and Shinzato, C and Yang, SY and Yang, SH}, title = {An Improved RNA Extraction Method for Octocorals and Its Application in Transcriptome Analysis of Dark-Induced Bleaching Octocoral.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {8}, pmid = {39589622}, issn = {1436-2236}, support = {NSTC 112-2311-B-002 -017//National Science and Technology Council/ ; NTU 112L2033-05//National Taiwan University/ ; }, mesh = {*Anthozoa/genetics/metabolism ; Animals ; *Gene Expression Profiling ; *RNA/isolation &amp; purification/genetics ; *Dinoflagellida/genetics ; *Transcriptome ; Symbiosis ; Coral Reefs ; }, abstract = {Octocorals, vital components of reef ecosystems, inhabit various marine environments across diverse climate zones, spanning from tropical shallows to frigid deep-sea regions. Certain octocoral species, notably Lobophytum and Sinularia, are particularly intriguing due to their production of diverse metabolites, warranting continuous investigation. Although octocorals played the roles in coral ecosystems, the studies are rare in comparison to scleractinian corals, especially in transcriptomic and genomic data. However, RNA extraction was massively interfered by the polysaccharides and secondary metabolites produced from octocoral holobiont. For this purpose, five lysis buffer systems and two extraction processes were examined for the RNA extraction efficiency in octocorals. We found CTAB/10%SDS as a new method for RNA extraction from six different octocoral genera. Furthermore, our new method is enable to extract RNA with good quality for downstream application such as quantitative PCR and RNA sequencing. Finally, comparative transcriptomic analysis between healthy octocorals and those dark-induced bleaching corals in Lobophytum hsiehi revealed extracellular matrix and immunity-related genes may play the important roles in coral-symbiodinium symbiosis. We believe that this study's findings and the developed RNA extraction method will serve as valuable references for future research, particularly in octocorals.}, }
@article {pmid39589125, year = {2024}, author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J}, title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0081624}, pmid = {39589125}, issn = {2379-5042}, mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation &amp; purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; }, abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.<br><br>IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.}, }
@article {pmid39580487, year = {2024}, author = {Rosenberg, E}, title = {Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {134}, pmid = {39580487}, issn = {2055-5008}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Biodiversity ; Colon/microbiology ; }, abstract = {The composition of bacteria in the human colon has been a subject of interest since the beginning of microbiology. With the development of methods for culturing strict anaerobic bacteria under multiple culture conditions, it was shown the gut contained more than 400 bacterial species and different people harbor different abundant species. The term "gut microbiome" in this review refers to bacteria studied in stool samples. Molecular methods for determining the bacterial composition of human gut has revealed more than 3000 species and less than 130 genera, indicating that the diversity of human colonic bacteria is concentrated at the species and strain levels. This review concludes with a discussion of how diversity can lead to unity of individual holobionts, between holobionts, and between populations. One of the reasons for the unity is that different bacterial species can have similar functional genes.}, }
@article {pmid39575186, year = {2024}, author = {Verma, T and Hendiani, S and Carbajo, C and Andersen, SB and Hammarlund, EU and Burmølle, M and Sand, KK}, title = {Recurrence and propagation of past functions through mineral facilitated horizontal gene transfer.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1449094}, pmid = {39575186}, issn = {1664-302X}, abstract = {Horizontal gene transfer is one of the most important drivers of bacterial evolution. Transformation by uptake of extracellular DNA is traditionally not considered to be an effective mode of gene acquisition, simply because extracellular DNA is degraded in a matter of days when it is suspended in e.g. seawater. Recently the age span of stored DNA was increased to at least 2 Ma. Here, we show that Acinetobacter baylyi can incorporate 60 bp DNA fragments adsorbed to common sedimentary minerals and that the transformation frequencies scale with mineral surface properties. Our work highlights that ancient environmental DNA can fuel the evolution of contemporary bacteria. In contrast to heritable stochastic mutations, the processes by which bacteria acquire new genomic material during times of increased stress and needs, indicate a non-random mechanism that may propel evolution in a non-stochastic manner.}, }
@article {pmid39574203, year = {2024}, author = {Rhimi, S and Jablaoui, A and Hernandez, J and Mariaule, V and Akermi, N and Méric, T and Mkaouar, H and Wysocka, M and Lesner, A and Borgi, MA and Maguin, E and Rhimi, M}, title = {Industrial diet intervention modulates the interplay between gut microbiota and host in semi-stray dogs.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {69}, pmid = {39574203}, issn = {2524-4671}, support = {twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; twinning European project: 952583-MICAfrica//European Commission/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; RestorPro no ANR-23-CE14-0073-01//Agence Nationale de la Recherche/ ; }, abstract = {BACKGROUND: The gut microbiota and derived metabolites play a key role in regulating host physiology. Diet is identified as a key regulatory factor of the microbiota composition and, potentially, of subsequent functionalities. Demonstrating the role of diet may be complex as most human studies are cross-sectional and dietary intervention is often accompanied by hygienic changes. The objective of the present study was to investigate the impact of an industrial diet on the modulation of the microbiota and targeted functionalities using a canine "natural" model.<br><br>RESULTS: We carried out a controlled dietary trial in a cohort of Tunisian semi-stray dogs. We made a transition from a natural diet to an industrial kibble diet and monitored the composition of the fecal microbiota, the concentration of short-chain fatty acids (SCFA) and bile acids (BAs), and protease activities. We demonstrated that dietary change significantly decreased fecal primary bile acids levels and protease activities. Interestingly, correlation analyses demonstrated that variation of specific microbial genera were associated with modulated physiological parameters.<br><br>CONCLUSIONS: Our study reveals that an industrial diet induces beneficial changes in microbial composition and functions characterised by increased diversity, synthesis of SCFA and secondary bile acids production, stressing the key role of the diet-microbiota-dog crosstalk.}, }
@article {pmid39574002, year = {2024}, author = {Pereira, H and Chakarov, N and Caspers, BA and Gilles, M and Jones, W and Mijoro, T and Zefania, S and Székely, T and Krüger, O and Hoffman, JI}, title = {The gut microbiota of three avian species living in sympatry.}, journal = {BMC ecology and evolution}, volume = {24}, number = {1}, pages = {144}, pmid = {39574002}, issn = {2730-7182}, support = {316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 316099922//Deutsche Forschungsgemeinschaft/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; 396780709//Deutsche Forschungsgemeinschaft,/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Sympatry ; Species Specificity ; Madagascar ; }, abstract = {BACKGROUND: Evolutionary divergence and genetic variation are often linked to differences in microbial community structure and diversity. While environmental factors and diet heavily influence gut microbial communities, host species contributions are harder to quantify. Closely related species living in sympatry provide a unique opportunity to investigate species differences without the confounding effects of habitat and dietary variation. We therefore compared and contrasted the gut microbiota of three sympatric plover species: the widespread Kittlitz's and white-fronted plovers (Anarhynchus pecuarius and A. marginatus) and the endemic and vulnerable Madagascar plover (A. thoracicus).<br><br>RESULTS: We found no significant differences in the beta diversity (composition) of the gut microbiota of the three species. However, A. thoracicus exhibited higher intraspecific compositional similarity (i.e. lower pairwise distances) than the other two species; this pattern was especially pronounced among juveniles. By contrast, microbial alpha diversity varied significantly among the species, being highest in A. pecuarius, intermediate in A. marginatus and lowest in A. thoracicus. This pattern was again stronger among juveniles. Geographical distance did not significantly affect the composition of the gut microbiota, but genetic relatedness did.<br><br>CONCLUSION: While patterns of microbial diversity varied across species, the lack of compositional differences suggests that habitat and diet likely exert a strong influence on the gut microbiota of plovers. This may be enhanced by their precocial, ground-dwelling nature, which could facilitate the horizontal transmission of microbes from the environment. We hypothesise that gut microbiota diversity in plovers primarily reflects the ecological pool of microbiota, which is subsequently modified by host-specific factors including genetics. The reduced microbial and genetic diversity of the endemic A. thoracicus may hinder its ability to adapt to environmental changes, highlighting the need for increased conservation efforts for this vulnerable species.}, }
@article {pmid39570654, year = {2024}, author = {Yan, C and Zhang, K and Shi, S and Jian, L and Chen, B and Quadri, SR and Tian, X}, title = {Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {11}, pages = {}, doi = {10.1099/ijsem.0.006577}, pmid = {39570654}, issn = {1466-5034}, mesh = {*Phylogeny ; *Anthozoa/microbiology ; Animals ; *Fatty Acids ; *DNA, Bacterial/genetics ; *Bacterial Typing Techniques ; *RNA, Ribosomal, 16S/genetics ; *Sequence Analysis, DNA ; *Ubiquinone ; *Coral Reefs ; Base Composition ; Sphingomonadaceae/genetics/isolation &amp; purification/classification ; Nucleic Acid Hybridization ; Phototrophic Processes ; }, abstract = {The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989[T], was isolated from the reef-building coral Favia sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with Parasphingorhabdus litoris DSM 22379[T] (95.9%) and Altererythrobacter ishigakiensis ATCC BAA-2084[T] (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family Sphingomonadaceae. The predominant fatty acids were C18 : 1 ω7c and/or C18 : 1 ω6c and C16 : 0. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between SCSIO 66989[T] and the type strains of P. litoris DSM 22379[T] and A. ishigakiensis ATCC BAA-2084[T] were 69.2-70.0%, 58.6-61.2% and 19.2-19.7%, respectively. These results indicate that strain SCSIO 66989[T] represents a new species of a novel genus in the family Sphingomonadaceae, for which the name Alterisphingorhabdus coralli gen. nov. sp. nov. is proposed.}, }
@article {pmid39570026, year = {2024}, author = {Waterworth, SC and Solomons, GM and Kalinski, J-CJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA}, title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0084524}, pmid = {39570026}, issn = {2379-5042}, support = {87583//National Research Foundation (NRF)/ ; 110612//National Research Foundation (NRF)/ ; 96185//South African Medical Research Council (SAMRC)/ ; 101038//National Research Foundation (NRF)/ ; }, mesh = {*Symbiosis ; Animals ; *Porifera/microbiology ; *Phylogeny ; Metagenome ; Spirochaetales/genetics/classification/physiology ; }, abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, sponge-associated unclassified lineage (SAUL), and Tethybacterales, appear to have broad-host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, having thus far been observed only in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.IMPORTANCESouth African latrunculid sponges are host to co-dominant Tethybacterales and Spirochete symbionts. While the Tethybacterales are broad-host range symbionts, the spirochetes have not been reported as abundant in any other marine sponge except Clathrina clathrus. However, spirochetes are regularly the most dominant populations in marine corals and terrestrial invertebrates where they are predicted to serve as beneficial symbionts. Here, we interrogated eight metagenome-assembled genomes of the latrunculid-associated spirochetes and found that these symbionts are phylogenetically distinct from all invertebrate-associated spirochetes. The symbiosis between the spirochetes and their sponge host appears to have been established relatively recently.}, }
@article {pmid39568770, year = {2024}, author = {Guéganton, M and Methou, P and Aubé, J and Noël, C and Rouxel, O and Cueff-Gauchard, V and Gayet, N and Durand, L and Pradillon, F and Cambon-Bonavita, MA}, title = {Symbiont Acquisition Strategies in Post-Settlement Stages of Two Co-Occurring Deep-Sea Rimicaris Shrimp.}, journal = {Ecology and evolution}, volume = {14}, number = {11}, pages = {e70369}, pmid = {39568770}, issn = {2045-7758}, abstract = {At deep-sea hydrothermal vents, deprived of light, most living communities are fueled by chemosynthetic microorganisms. These can form symbiotic associations with metazoan hosts, which are then called holobionts. Among these, two endemic co-occurring shrimp of the Mid-Atlantic Ridge (MAR), Rimicaris exoculata and Rimicaris chacei are colonized by dense and diversified chemosynthetic symbiotic communities in their cephalothoracic cavity and their digestive system. Although both shrimp harbor similar communities, they exhibit widely different population densities, distribution patterns at small scale and diet, as well as differences in post-settlement morphological modifications leading to the adult stage. These contrasting biological traits may be linked to their symbiotic development success. Consequently, key questions related to the acquisition of the symbiotic communities and the development of the three symbiotic organs are still open. Here we examined symbiotic development in juveniles of R. exoculata and R. chacei from TAG and Snake Pit using 16S metabarcoding to identify which symbiotic lineages are present at each juvenile stage. In addition, we highlighted the abundance and distribution of microorganisms at each stage using Fluorescence in situ Hybridization (FISH) and Scanning Electron Microscopy (SEM). For the first time, Candidatus Microvillispirillaceae family with Candidatus Rimicarispirillum spp. (midgut tube), Candidatus Foregutplasma rimicarensis and Candidatus BG2-rimicarensis (foregut) were identified in late juvenile stages. However, these lineages were absent in early juvenile stages, which coincides for the midgut tube with our observations of an immature tissue, devoid of microvilli. Conversely, symbiotic lineages from the cephalothoracic cavity were present from the earliest juvenile stages of both species and their overall diversities were similar to those of adults. These results suggest different symbiont acquisition dynamics between the cephalothoracic cavity and the digestive system, which may also involve distinct transmission mechanisms.}, }
@article {pmid39565113, year = {2024}, author = {Nowak, VV and Hou, P and Owen, JG}, title = {Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {12}, pages = {e0072624}, pmid = {39565113}, issn = {1098-5336}, support = {Doctoral Scholarship//Victoria University of Wellington (WGTN)/ ; Contract 16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; RDF-VUW1601//Royal Society Te Ap&#x101;rangi (Royal Society of New Zealand)/ ; RTVU1908 and UOAX2010//Ministry for Business Innovation and Employment (MBIE)/ ; }, mesh = {*Porifera/microbiology ; Animals ; New Zealand ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Metagenome ; *Microbiota ; Mediterranean Sea ; Multigene Family ; Metagenomics ; Phylogeny ; }, abstract = {Marine sponges are a prolific source of biologically active small molecules, many of which originate from sponge-associated bacteria. Identifying the producing bacteria is a key step in developing sustainable routes for the production of these metabolites. To facilitate the required computational analyses, we developed MetaSing, a reproducible singularity-based pipeline for assembly, identification of high-quality metagenome-assembled genomes (MAGs), and analysis of biosynthetic gene clusters (BGCs) from metagenomic short-read data. We applied this pipeline to metagenomic sequencing data from 16 marine sponges collected from New Zealand, Tonga, and the Mediterranean Sea. This analysis yielded 643 MAGs representing 510 species. Of the 2,670 BGCs identified across all samples, 70.8% were linked to a MAG. Comparison of BGCs to those identified from previously sequenced bacteria revealed high biosynthetic novelty in variety of underexplored phyla, including Poribacteria, Acidobacteriota, and Dadabacteria. Alongside the observation that each sample contains unique biosynthetic potential, this holds great promise for natural product discovery and for furthering the understanding of different sponge holobionts.IMPORTANCEDiscovery of new chemical compounds such as natural products is a crucial endeavor to combat the increasing resistance to antibiotics and other drugs. This manuscript demonstrates that microbial communities associated with marine sponges investigated in this work encode the potential to produce novel chemistry. Lesser studied bacterial taxa that are often difficult to cultivate are particularly rich in potential.}, }
@article {pmid39558079, year = {2024}, author = {Sun, Y and Sheng, H and Rädecker, N and Lan, Y and Tong, H and Huang, L and Jiang, L and Diaz-Pulido, G and Zou, B and Zhang, Y and Kao, SJ and Qian, PY and Huang, H}, title = {Symbiodiniaceae algal symbionts of Pocillopora damicornis larvae provide more carbon to their coral host under elevated levels of acidification and temperature.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1528}, pmid = {39558079}, issn = {2399-3642}, support = {42206153//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; 41906040//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; *Anthozoa/physiology/metabolism/microbiology ; *Symbiosis ; *Carbon/metabolism ; *Larva/metabolism/growth &amp; development/physiology ; Photosynthesis ; Hydrogen-Ion Concentration ; Temperature ; Dinoflagellida/physiology/metabolism ; Climate Change ; Nitrogen/metabolism ; Seawater/microbiology/chemistry ; }, abstract = {Climate change destabilizes the symbiosis between corals and Symbiodiniaceae. The effects of ocean acidification and warming on critical aspects of coral survical such as symbiotic interactions (i.e., carbon and nitrogen assimilation and exchange) during the planula larval stage remain understudied. By combining physiological and stable isotope techniques, here we show that photosynthesis and carbon and nitrogen assimilation (H[13]CO3[-] and [15]NH4[+]) in Pocillopora damicornis coral larvae is enhanced under acidification (1000 µatm) and elevated temperature (32 °C). Larvae maintain high survival and settlement rates under these treatment conditions with no observed decline in symbiont densities or signs of bleaching. Acidification and elevated temperature both enhance the net and gross photosynthesis of Symbiodiniaceae. This enhances light respiration and elevates C:N ratios within the holobiont. The increased carbon availability is primarily reflected in the [13]C enrichment of the host, indicating a greater contribution of the algal symbionts to the host metabolism. We propose that this enhanced mutualistic symbiotic nutrient cycling may bolster coral larvae's resistance to future ocean conditions. This research broadens our understanding of the early life stages of corals by emphasizing the significance of symbiotic interactions beyond those of adult corals.}, }
@article {pmid39553893, year = {2024}, author = {Pfab, F and Detmer, AR and Moeller, HV and Nisbet, RM and Putnam, HM and Cunning, R}, title = {Heat stress and bleaching in corals: a bioenergetic model.}, journal = {Coral reefs (Online)}, volume = {43}, number = {6}, pages = {1627-1645}, pmid = {39553893}, issn = {1432-0975}, abstract = {UNLABELLED: The coral-dinoflagellate endosymbiosis is based on nutrient exchanges that impact holobiont energetics. Of particular concern is the breakdown or dysbiosis of this partnership that is seen in response to elevated temperatures, where loss of symbionts through coral bleaching can lead to starvation and mortality. Here we extend a dynamic bioenergetic model of coral symbioses to explore the mechanisms by which temperature impacts various processes in the symbiosis and to enable simulational analysis of thermal bleaching. Our model tests the effects of two distinct mechanisms for how increased temperature impacts the symbiosis: 1) accelerated metabolic rates due to thermodynamics and 2) damage to the photosynthetic machinery of the symbiont caused by heat stress. Model simulations show that the model can capture key biological responses to different levels of increased temperatures. Moderately increased temperatures increase metabolic rates and slightly decrease photosynthesis. The slightly decreased photosynthesis rates cause the host to receive less carbon and share more nitrogen with the symbiont. This results in temporarily increased symbiont growth and a higher symbiont/host ratio. In contrast, higher temperatures cause a breakdown of the symbiosis due to escalating feedback that involves further reduction in photosynthesis and insufficient energy supply for CO 2 concentration by the host. This leads to the accumulation of excess light energy and the generation of reactive oxygen species, eventually triggering symbiont expulsion and coral bleaching. Importantly, bleaching does not result from accelerated metabolic rates alone; it only occurs as a result of the photodamage mechanism due to its effect on nutrient cycling. Both higher light intensities and higher levels of DIN render corals more susceptible to heat stress. Conversely, heterotrophic feeding can increase the maximal temperature that can be tolerated by the coral. Collectively these results show that a bioenergetics model can capture many observed patterns of heat stress in corals, such as higher metabolic rates and higher symbiont/host ratios at moderately increased temperatures and symbiont expulsion at strongly increased temperatures.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-024-02561-1.}, }
@article {pmid39543733, year = {2024}, author = {Köster, PC and Figueiredo, AM and Maloney, JG and Dashti, A and Bailo, B and Torres, RT and Fonseca, C and Mysterud, A and Habela, M&#xc1; and Rivero-Juarez, A and Vicente, J and Serrano, E and Arnal, MC and de Luco, DF and Armenteros, JA and Balseiro, A and Cardona, GA and Carvalho, J and Hipólito, D and Fernandes, J and Palmeira, JD and Calero-Bernal, R and González-Barrio, D and Santin, M and Carmena, D}, title = {Correction: Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula.}, journal = {Veterinary research}, volume = {55}, number = {1}, pages = {152}, pmid = {39543733}, issn = {1297-9716}, }
@article {pmid39541453, year = {2024}, author = {Bordenstein, SR and The Holobiont Biology Network,  and , }, title = {The disciplinary matrix of holobiont biology.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6723}, pages = {731-732}, doi = {10.1126/science.ado2152}, pmid = {39541453}, issn = {1095-9203}, mesh = {*Symbiosis/genetics ; Genomics ; Animals ; }, abstract = {Uniting life's seen and unseen realms guides a conceptual advance in research.}, }
@article {pmid39539714, year = {2024}, author = {Hauptmann, AL and Johansen, J and Stæger, FF and Nielsen, DS and Mulvad, G and Hanghøj, K and Rasmussen, S and Hansen, T and Albrechtsen, A}, title = {Gut heavy metal and antibiotic resistome of humans living in the high Arctic.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1493803}, pmid = {39539714}, issn = {1664-302X}, abstract = {Contaminants, such as heavy metals (HMs), accumulate in the Arctic environment and the food web. The diet of the Indigenous Peoples of North Greenland includes locally sourced foods that are central to their nutritional, cultural, and societal health but these foods also contain high concentrations of heavy metals. While bacteria play an essential role in the metabolism of xenobiotics, there are limited studies on the impact of heavy metals on the human gut microbiome, and it is so far unknown if and how Arctic environmental contaminants impact the gut microbes of humans living in and off the Arctic environment. Using a multiomics approach including amplicon, metagenome, and metatranscriptome sequencing, we identified and assembled a near-complete (NC) genome of a mercury-resistant bacterial strain from the human gut microbiome, which expressed genes known to reduce mercury toxicity. At the overall ecological level studied through α- and β-diversity, there was no significant effect of heavy metals on the gut microbiota. Through the assembly of a high number of NC metagenome-assembled genomes (MAGs) of human gut microbes, we observed an almost complete overlap between heavy metal-resistant strains and antibiotic-resistant strains in which resistance genes were all located on the same genetic elements.}, }
@article {pmid39536868, year = {2024}, author = {Koll, R and Hauten, E and Theilen, J and Bang, C and Bouchard, M and Thiel, R and Möllmann, C and Woodhouse, JN and Fabrizius, A}, title = {Spatio-temporal plasticity of gill microbiota in estuarine fish.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177505}, doi = {10.1016/j.scitotenv.2024.177505}, pmid = {39536868}, issn = {1879-1026}, mesh = {Animals ; *Microbiota ; *Estuaries ; *Gills/microbiology ; Fishes/microbiology/physiology ; Environmental Monitoring ; }, abstract = {Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that increasing environmental pressures impact host resilience and favor the raise of opportunistic bacterial taxa. The microbial composition of the gill mucus reflects environmental conditions and represents an entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by increased prevalence of facultatively aerobic (Acinetobacter) and anaerobic heterotrophs (Shewanella, Aeromonas). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify potential biomarkers for fish health monitoring and reconstruct movement patterns of the fish. Our results can help to shape future minimal-invasive and cost-effective monitoring programs, and identify factors that need to be controlled in the estuary to promote fish and stock health.}, }
@article {pmid39536370, year = {2024}, author = {Anthony, CJ and Lock, C and Pérez-Rosales, G and Rouzé, H and Paulino, L and Raymundo, LJ and Bentlage, B}, title = {Symbiodiniaceae phenotypic traits as bioindicators of acclimatization after coral transplantation.}, journal = {Marine pollution bulletin}, volume = {209}, number = {Pt B}, pages = {117250}, doi = {10.1016/j.marpolbul.2024.117250}, pmid = {39536370}, issn = {1879-3363}, mesh = {*Anthozoa/physiology ; *Dinoflagellida/physiology ; Animals ; *Coral Reefs ; *Symbiosis ; *Acclimatization ; *Phenotype ; }, abstract = {Coral-dinoflagellate symbiosis underpins coral reef resilience and influences conservation success, given the relationship's role in coral bleaching. Here, we transplanted Guam's dominant staghorn coral, Acropora pulchra, across four coral gardens and monitored their endosymbiotic dinoflagellates (family Symbiodiniaceae) for ∼15 months (May 2021-August 2022). Transplantation and predation resulted in temporary symbiotic destabilization, as signaled by increased cell roughness and decreased cell density. Eventually, the Symbiodiniaceae phenotypic profile mostly converged with the wild population, although cell density and red fluorescing photopigments remained modified. In March, corals paled, which allowed us to evaluate the Symbiodiniaceae assemblage's relationship with host color. Interestingly, cell density was not the most informative when predicting host color. Instead, fluorescence from antioxidant-associated pigments were most informative. We conclude that Symbiodiniaceae phenotypic traits respond differently depending on the condition, supporting their development as acclimatization bioindicators.}, }
@article {pmid39529628, year = {2024}, author = {López-Rodríguez, MR and Gérikas Ribeiro, C and Rodríguez-Marconi, S and Parada-Pozo, G and Manrique-de-la-Cuba, M and Trefault, N}, title = {Stable dominance of parasitic dinoflagellates in Antarctic sponges.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18365}, pmid = {39529628}, issn = {2167-8359}, mesh = {Antarctic Regions ; *Dinoflagellida/genetics/physiology ; Animals ; *Porifera/parasitology ; Symbiosis ; Seawater/parasitology/microbiology ; Biodiversity ; }, abstract = {BACKGROUND: Marine sponges are dominant components of Antarctic benthos and representative of the high endemism that characterizes this environment. All microbial groups are part of the Antarctic sponge holobionts, but microbial eukaryotes have been studied less, and their symbiotic role still needs to be better understood. Here, we characterize the dynamics of microbial eukaryotes associated with Antarctic sponges, focusing on dinoflagellates over three summer periods to better understand the members, interannual variations, and trophic and lifestyle strategies.<br><br>RESULTS: The analysis revealed that dinoflagellates dominate microeukaryotic communities in Antarctic sponges. The results also showed significant differences in the diversity and composition of dinoflagellate communities associated with sponges compared to those in seawater. Antarctic sponges were dominated by a single dinoflagellate family, Syndiniales Dino-Group-I-Clade 1, which was present in high abundance in Antarctic sponges compared to seawater communities. Despite minor differences, the top microeukaryotic amplicon sequence variants (ASVs) showed no significant interannual abundance changes, indicating general temporal stability within the studied sponge species. Our findings highlight the abundance and importance of parasitic groups, particularly the classes Coccidiomorphea, Gregarinomorphea, and Ichthyosporea, with the exclusive dominance of Syndiniales Dino-Group-I-Clade 1 within sponges.<br><br>CONCLUSIONS: The present study comprehensively characterizes the microbial eukaryotes associated with Antarctic sponges, showing a remarkable stability of parasitic dinoflagellates in Antarctic sponges. These findings underscore the significant role of parasites in these marine hosts, with implications for population dynamics of the microeukaryome and the holobiont response to a changing ocean.}, }
@article {pmid39524434, year = {2024}, author = {Hong, L and Wang, Q and Zhang, J and Chen, X and Liu, Y and Asiegbu, FO and Wu, P and Ma, X and Wang, K}, title = {Advances in the beneficial endophytic fungi for the growth and health of woody plants.}, journal = {Forestry research}, volume = {4}, number = {}, pages = {e028}, pmid = {39524434}, issn = {2767-3812}, abstract = {In recent years, the importance of microorganisms for plant survival has been increasingly recognized. Endophytic fungi, as part of holobiont, can confer growth advantages to plants. Most studies have shown that the endophytic fungi of forest trees can promote host plant growth, increase adversity resistance, and thus improve the survival competitiveness of forest trees. However, the beneficial examples of endophytic fungi on the growth and development of woody plants have not been systematically summarized. This review is focused on various aspects of beneficial endophytic fungi in forest trees (definition, classification, colonization mechanisms, etc.), with an emphasis on their beneficial roles in woody plant growth, protection against biotic and abiotic stresses, as well as the response of forest trees to endophytic fungi. In addition, this review lists a series of experiments on screening beneficial endophytic fungi from Chinese fir (Cunninghamia lanceolata) and verifying their beneficial functions, to explore the mutualistic relationships between them. This review not only provides a theoretical basis for the study of beneficial endophytic fungi in forest trees in the future but also sheds light on the molecular perspectives for a mechanistic understanding of their potential future significance for the sustainable utilization of forest resources and ecological environment protection.}, }
@article {pmid39517101, year = {2024}, author = {Gantt, SE and Kemp, KM and Colin, PL and Hoadley, KD and LaJeunesse, TC and Warner, ME and Kemp, DW}, title = {Influence of reef habitat on coral microbial associations.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70051}, pmid = {39517101}, issn = {1758-2229}, support = {//University of Alabama at Birmingham/ ; IOS-1258058//National Science Foundation/ ; IOS-1258065//National Science Foundation/ ; IOS-1719675//National Science Foundation/ ; OCE-1635695//National Science Foundation/ ; OCE-1636022//National Science Foundation/ ; OCE-1719684//National Science Foundation/ ; }, mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Symbiosis ; *Dinoflagellida/physiology/classification ; *Microbiota ; Bacteria/classification/isolation &amp; purification/genetics ; Ecosystem ; Palau ; }, abstract = {Corals have complex symbiotic associations that can be influenced by the environment. We compare symbiotic dinoflagellate (family: Symbiodiniaceae) associations and the microbiome of five scleractinian coral species from three different reef habitats in Palau, Micronesia. Although pH and temperature corresponded with specific host-Symbiodiniaceae associations common to the nearshore and offshore habitats, bacterial community dissimilarity analyses indicated minimal influence of these factors on microbial community membership for the corals Coelastrea aspera, Psammocora digitata, and Pachyseris rugosa. However, coral colonies sampled close to human development exhibited greater differences in microbial community diversity compared to the nearshore habitat for the coral species Coelastrea aspera, Montipora foliosa, and Pocillopora acuta, and the offshore habitat for Coelastrea aspera, while also showing less consistency in Symbiodiniaceae associations. These findings indicate the influence that habitat location has on the bacterial and Symbiodiniaceae communities comprising the coral holobiont and provide important considerations for the conservation of coral reef communities, especially for island nations with increasing human populations and development.}, }
@article {pmid39513573, year = {2025}, author = {Brown, AL and Koskella, B and Boots, M}, title = {How host-microbiome/holobiont evolution depends on whether the microbiome affects host lifespan or fecundity.}, journal = {Journal of evolutionary biology}, volume = {38}, number = {1}, pages = {41-49}, doi = {10.1093/jeb/voae127}, pmid = {39513573}, issn = {1420-9101}, support = {GBMF10578//Gordon and Betty Moore Foundation/ ; }, mesh = {*Microbiota ; *Biological Evolution ; *Symbiosis ; *Fertility ; Longevity ; Animals ; Host Microbial Interactions ; Models, Biological ; }, abstract = {There is overwhelming evidence that the microbiome can be important to host physiology and fitness. As such, there is interest in and some theoretical work on understanding when hosts and microbiomes (co)evolve so that microbes benefit hosts and hosts favour beneficial microbes. However, the outcome of evolution likely depends on how microbes benefit hosts. Here, we use adaptive dynamics to investigate how host and symbiont evolution depend on whether symbionts increase host lifespan or host reproduction in a simple model of host and symbiont dynamics. In addition, we investigate 2 ways hosts release (and transmit) symbionts: by releasing symbionts steadily during their lifetime or by releasing them at reproduction, potentially increasing symbionts' chances of infecting the host's offspring. The former is strict horizontal transmission, whereas the latter is also a form of indirect or "pseudovertical" transmission. Our first key result is that the evolution of symbionts that benefit host fecundity requires pseudovertical transmission, while the evolution of symbionts that benefit host lifespan does not. Furthermore, our second key result is that when investing in host benefits is costly to the free-living symbiont stage, intermediate levels of pseudovertical transmission are needed for selection to favour beneficial symbionts. This is true regardless of fitness effects because release at reproduction increases the free-living symbiont population, which increases competition for hosts. Consequently, hosts could evolve away from traits that favour beneficial symbionts. Generally, our work emphasizes the importance of different forms of vertical transmission and fitness benefits in host, microbiome, and holobiont evolution as highlighted by our prediction that the evolution of fecundity-increasing symbionts requires parent-to-offspring transmission.}, }
@article {pmid39511978, year = {2025}, author = {Hecht, K and Kowalchuk, GA and Ford Denison, R and Kahmen, A and Xiong, W and Jousset, A and Ravanbakhsh, M}, title = {Deletion of ACC Deaminase in Symbionts Converts the Host Plant From Water Waster to Water Saver.}, journal = {Plant, cell &amp; environment}, volume = {48}, number = {3}, pages = {1919-1931}, pmid = {39511978}, issn = {1365-3040}, mesh = {*Arabidopsis/microbiology/physiology/enzymology/metabolism/genetics ; *Water/metabolism ; *Carbon-Carbon Lyases/genetics/metabolism ; *Pseudomonas putida/enzymology/genetics ; *Symbiosis ; Droughts ; Plant Roots/microbiology ; Ethylenes/metabolism ; }, abstract = {Increasing drought events coupled with dwindling water reserves threaten global food production and security. This issue is exacerbated by the use of crops that overconsume water, undermining yield. We show here that microorganisms naturally associated with plant roots can undermine efficient water use, whereas modified bacteria can enhance it. We demonstrate that microbe-encoded genes shape drought tolerance, likely by modulating plant hormonal balance. Specifically, we built a minimal holobiont out of Arabidopsis thaliana and either the bacterium Pseudomonas putida UW4 or its isogenic AcdS[-] mutant, lacking the enzyme ACC deaminase. This enzyme breaks down the precursor of ethylene, a key regulator in plant response to drought. This single mutation profoundly affected plant physiology and shifted the plant from a 'water-spender' (with more growth under well-watered conditions) to a 'water-spender' phenotype. Under drought, plants associated with wild-type bacteria consumed soil water faster, leading to a shorter period of growth followed by death. In contrast, plants associated with the AcdS[-] mutant managed to maintain growth by reducing water consumption via stomatal closure, thus conserving soil water. This allowed plants to survive severe water deficiency. We conclude that plant-associated bacteria can modulate plant water use strategies, opening possibilities to engineer water-savvy crop-production systems.}, }
@article {pmid39509495, year = {2024}, author = {Arafeh-Dalmau, N and Olguín-Jacobson, C and Earle, S and Bello, M and Lagger, C and Mora-Soto, A and Pantano, C and Palacios, M and Barbosa, RV and Fica-Rojas, E and Guajardo, E and Aburto-Oropeza, O and Eger, A and Dayton, P and Giraldo-Ospina, A and Cavanaugh, K and García-Pantoja, J and Montaño-Moctezuma, G and Possingham, H and Sala, E and Schoeman, D and Torres-Moye, G and Micheli, F}, title = {Protect kelp forests.}, journal = {Science (New York, N.Y.)}, volume = {386}, number = {6722}, pages = {629}, doi = {10.1126/science.adr4814}, pmid = {39509495}, issn = {1095-9203}, }
@article {pmid39508584, year = {2024}, author = {Thomas, F and Asselin, K and MacDonald, N and Brazier, L and Meliani, J and Ujvari, B and Dujon, AM}, title = {Oncogenic processes: a neglected parameter in the evolutionary ecology of animals.}, journal = {Comptes rendus biologies}, volume = {347}, number = {}, pages = {137-157}, doi = {10.5802/crbiol.159}, pmid = {39508584}, issn = {1768-3238}, mesh = {Animals ; *Biological Evolution ; *Neoplasms/genetics/veterinary ; *Carcinogenesis/genetics ; Humans ; Ecosystem ; Ecology ; *Oncogenes/physiology ; }, abstract = {Cancer is a biological process that emerged at the end of the Precambrian era with the rise of multicellular organisms. Traditionally, cancer has been viewed primarily as a disease relevant to human and domesticated animal health, attracting attention mainly from oncologists. In recent years, however, the community of ecologists and evolutionary biologists has recognized the pivotal role of cancer-related issues in the evolutionary paths of various species, influencing multiple facets of their biology. It has become evident that overlooking these issues is untenable for a comprehensive understanding of species evolution and ecosystem functioning. In this article, we highlight some significant advancements in this field, also underscoring the pressing need to consider reciprocal interactions not only between cancer cells and their hosts but also with all entities comprising the holobiont. This reflection gains particular relevance as ecosystems face increasing pollution from mutagenic substances, resulting in a resurgence of cancer cases in wildlife.}, }
@article {pmid39505929, year = {2024}, author = {Dantan, L and Carcassonne, P and Degrémont, L and Morga, B and Travers, MA and Petton, B and Mege, M and Maurouard, E and Allienne, JF and Courtay, G and Romatif, O and Pouzadoux, J and Lami, R and Intertaglia, L and Gueguen, Y and Vidal-Dupiol, J and Toulza, E and Cosseau, C}, title = {Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection in Crassostrea gigas.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {26914}, pmid = {39505929}, issn = {2045-2322}, support = {n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; n&#xb0;PFEA470020FA1000007//Fond Europ&#xe9;en pour les Affaires Maritimes et la P&#xea;che (FEAMP, GESTINNOV)/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-19-CE20-0004//ANR DECICOMP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-41//Laboratoires d'Excellences (LABEX): TULIP/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; ANR-10-LABX-04-01//Laboratoires d'Excellences (LABEX): CEMEB/ ; }, mesh = {Animals ; *Crassostrea/microbiology/immunology ; *Microbiota ; *Vibrio/immunology/pathogenicity ; Larva/microbiology/immunology ; Vibrio Infections/prevention &amp; control/immunology/veterinary/microbiology ; Aquaculture/methods ; }, abstract = {The increase in marine diseases, particularly in economically important mollusks, is a growing concern. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases, such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. The microbial education, which consists of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS and Vibrio aestuarianus infections, highlighting potential applications in oyster production. We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. Furthermore, the added bacteria were not maintained into the oyster microbiota, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression. Our study reveals successful immune system education of oysters by introducing beneficial microorganisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease and Vibrio aestuarianus infections) highlighting the potential of microbial education in aquaculture.}, }
@article {pmid39499397, year = {2024}, author = {Hashemi, TS and Soltani, J and Samsampour, D and Seyahooei, MA and Ghasemi, M}, title = {Spatiotemporal diversity of bacterial endophyte microbiome of mandarin (Citrus reticulata) in the northern Persian Gulf and its HCN production and N2 fixation.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39499397}, issn = {1874-9356}, abstract = {Endophytes are symbionts that live in healthy plants and potentially improve the health of plant holobionts. Here, we investigated the bacterial endophyte community of Citrus reticulata grown in the northern Persian Gulf. Bacteria were isolated seasonally from healthy trees (root, stem, bark, trunk, leaf, and crown tissues) in four regions of Hormozgan province (i.e., Ahmadi, Siyahoo, Sikhoran, Roudan), a subtropical hot region in Iran. A total of 742 strains from 17 taxa, 3 phyla, and 5 orders were found, most of which belonged to Actinobacteria (Actinobacteriales) as the dominant group, followed by Firmicutes (Bacillales), Proteobacteria (Sphingomonadales, Rhizobiales), and Cyanobacteria (Synechoccales). The genera included Altererythrobacter, Arthrobacter, Bacillus, Cellulosimicrobium, Curtobacterium, Kocuria, Kytococcus, Methylopila, Mycobacterium, Nocardioides, Okiabacterium, Paracraurococcus, and Psychrobacillus. The most frequently occurring species included Psychrobacillus psychrodurans, Kytococcus schroetri, and Bacillus cereus. In addition, the overall colonization frequency and variability of endophytes were higher on the trunks. The leaves showed the lowest species variability in all sampling periods. The frequency of endophyte colonization was also higher in summer. The Shannon-Wiener (H') and Simpson indices varied with all factors, i.e., region, season, and tissue type, with the maximum in Roudan. Furthermore, 52.9% of the strains were capable of nitrogen fixation, and 70% produced antagonistic hydrogen cyanide (HCN). Thus, C. reticulata harbors a variety of bioactive bacterial endophytes that could be beneficial for host fitness in such harsh environments.}, }
@article {pmid39498138, year = {2024}, author = {Jain, S and Vaishnav, A and Choudhary, DK}, title = {Editorial: Climate impact on plant holobiont: mitigation strategies and sustainability, volume II.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1503816}, pmid = {39498138}, issn = {1664-302X}, }
@article {pmid39497183, year = {2024}, author = {Prioux, C and Ferrier-Pages, C and Deter, J and Tignat-Perrier, R and Guilbert, A and Ballesta, L and Allemand, D and van de Water, JAJM}, title = {Insights into the occurrence of phylosymbiosis and co-phylogeny in the holobionts of octocorals from the Mediterranean Sea and Red Sea.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {62}, pmid = {39497183}, issn = {2524-4671}, abstract = {BACKGROUND: Corals are the foundational species of coral reefs and coralligenous ecosystems. Their success has been linked to symbioses with microorganisms, and a coral host and its symbionts are therefore considered a single entity, called the holobiont. This suggests that there may be evolutionary links between corals and their microbiomes. While there is evidence of phylosymbiosis in scleractinian hexacorals, little is known about the holobionts of Alcyonacean octocorals.<br><br>RESULTS: 16S rRNA gene amplicon sequencing revealed differences in the diversity and composition of bacterial communities associated with octocorals collected from the mesophotic zones of the Mediterranean and Red Seas. The low diversity and consistent dominance of Endozoicomonadaceae and/or Spirochaetaceae in the bacterial communities of Mediterranean octocorals suggest that these corals may have a shared evolutionary history with their microbiota. Phylosymbiotic signals were indeed detected and cophylogeny in associations between several bacterial strains, particularly those belonging to Endozoicomonadaceae or Spirochaetaceae, and coral species were identified. Conversely, phylosymbiotic patterns were not evident in Red Sea octocorals, likely due to the high bacterial taxonomic diversity in their microbiota, but cophylogeny in associations between certain coral and bacterial species was observed. Noteworthy were the associations with Endozoicomonadaceae, suggesting a plausible evolutionary link that warrants further investigations to uncover potential underlying patterns.<br><br>CONCLUSIONS: Overall, our findings emphasize the importance of Endozoicomonadaceae and Spirochaetaceae in coral symbiosis and the significance of exploring host-microbiome interactions in mesophotic ecosystems for a comprehensive understanding of coral-microbiome evolutionary history.}, }
@article {pmid39489036, year = {2024}, author = {Hussain, M and Aizpurua, O and Pérez de Rozas, A and París, N and Guivernau, M and Jofré, A and Tous, N and Ng'ang'a, ZW and Alberdi, A and Rodríguez-Gallego, E and Kogut, MH and Tarradas, J}, title = {Positive impact of early-probiotic administration on performance parameters, intestinal health and microbiota populations in broiler chickens.}, journal = {Poultry science}, volume = {103}, number = {12}, pages = {104401}, pmid = {39489036}, issn = {1525-3171}, mesh = {Animals ; *Probiotics/administration &amp; dosage/pharmacology ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Diet/veterinary ; *Animal Feed/analysis ; Male ; Intestines/drug effects/microbiology ; Random Allocation ; Animal Nutritional Physiological Phenomena/drug effects ; }, abstract = {Minimizing the utilization of antibiotics in animal production is crucial to prevent the emergence of antimicrobial resistances. Thus, research on alternatives is needed to maintain productivity, sustainability, and animal health. To gain a comprehensive understanding of probiotics' modes of action on performance, intestinal microbiota, and gut health in poultry, 3 probiotic strains (Enterococcus faecalis CV1028 [EntF], Bacteroides fragilis GP1764 [BacF], and Ligilactobacillus salivarius CTC2197 [LacS]) were tested in 2 in vivo trials. Trial 1 comprised of a negative control group fed basal diet (BD) and 3 treatment groups that received BD with EntF, BacF and LacS. Trial 2 included a negative control group, a positive control group with Zinc-Bacitracin as antibiotic growth promoter (AGP), and 2 groups treated with a blend of probiotics (EntF+BacF+LacS) during 0 to 10 or 0 to 35 d, respectively. Wheat-soybean-rye based diets without exogenous enzymes were used as a challenge model to induce intestinal mild- or moderate-inflammatory process in the gut. In Trial 1, individually administered probiotics improved FCR at 8 d compared to Control, but these positive effects were lost in the following growing periods probably due to the high grade of challenging diet and a too low dose of probiotics. In Trial 2, both Probiotic treatments, administered only 10 or 35 d, significantly improved FCR to the same extent as of the Antibiotic group at the end of the trial. Although the performance between antibiotic and probiotic mixture showed similar values, microbiota analysis revealed different microbial composition at 7 d, but not at 21 d. This suggests that modes of action of the AGP and the tested probiotic blend differ on their effects on microbiome, and that the changes observed during the first days' posthatch are relevant on performance at the end of the study. Therefore, the probiotics administration only during the first 10 d posthatch was proven sufficient to induce similar performance improvements to those observed in birds fed antibiotic growth promoters throughout the whole experimental trial.}, }
@article {pmid39474739, year = {2024}, author = {Sun, X and Cavill, EL and Margaryan, A and Lin, J and Thingaard, S and Said, TA and Gopalakrishnan, S and Gilbert, MTP}, title = {A Genomic Exploration of the Possible De-Extirpation of the Zanzibar Leopard.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17566}, doi = {10.1111/mec.17566}, pmid = {39474739}, issn = {1365-294X}, support = {681396//ERC Consolidator Award/ ; }, abstract = {The recently extirpated Zanzibar leopard was the only known African leopard (Panthera pardus spp.) population restricted exclusively to a major island habitat. Although its demise was driven through habitat change and conflict with humans, given its role as a keystone species for the Zanzibar Archipelago, its successful potential reintroduction might offer a means for helping preserve the natural biodiversity of its former habitat. Whether this is feasible, however, would be contingent on both whether closely related source populations can be identified on mainland Africa, and whether the Zanzibar form exhibited any special adaptations that might need to be considered when choosing such a source. In light of these questions, we genomically profiled two of the six known historic specimens, to explore whether they represent a realistic candidate for de-extirpation through reintroduction. Our analyses indicate that despite its geographical separation, the Zanzibar leopard shared a close genetic relationship with mainland East African individuals. Furthermore, although its uniqueness as an island population was emphasised by genomic signatures of high inbreeding and increased mutation load, the latter similar to the level of the critically endangered Amur leopard (P. p. orientalis), we find no evidence of functionally significant genetic diversity unique to Zanzibar. We therefore conclude that should attempts to restore leopards to Zanzibar be considered, then mainland East African leopards would provide a suitable gene pool.}, }
@article {pmid39472959, year = {2024}, author = {Martin-Cuadrado, AB and Rubio-Portillo, E and Rosselló, F and Antón, J}, title = {The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {222}, pmid = {39472959}, issn = {2049-2618}, mesh = {*Anthozoa/microbiology ; Animals ; *Coral Reefs ; *Microbiota ; *Vibrio/genetics/classification/physiology/isolation &amp; purification ; Symbiosis ; Temperature ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Rhodobacteraceae/genetics/classification/isolation &amp; purification/physiology ; Fungi/classification/genetics/isolation &amp; purification ; Vibrionaceae/genetics/classification/isolation &amp; purification ; Vibrio Infections/microbiology ; Climate Change ; }, abstract = {BACKGROUND: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.<br><br>RESULTS: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.<br><br>CONCLUSION: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.}, }
@article {pmid39455736, year = {2024}, author = {Gupta, S and Vera-Ponce de León, A and Kodama, M and Hoetzinger, M and Clausen, CG and Pless, L and Verissimo, ARA and Stengel, B and Calabuig, V and Kvingedal, R and Skugor, S and Westereng, B and Harvey, TN and Nordborg, A and Bertilsson, S and Limborg, MT and Mørkøre, T and Sandve, SR and Pope, PB and Hvidsten, TR and La Rosa, SL}, title = {The need for high-resolution gut microbiome characterization to design efficient strategies for sustainable aquaculture production.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1391}, pmid = {39455736}, issn = {2399-3642}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Aquaculture/methods ; *Salmo salar/microbiology ; *Animal Feed ; Mannans/metabolism ; Dietary Supplements ; Bacteria/genetics/classification/metabolism ; Dietary Fiber/metabolism ; Diet/veterinary ; }, abstract = {Microbiome-directed dietary interventions such as microbiota-directed fibers (MDFs) have a proven track record in eliciting responses in beneficial gut microbes and are increasingly being promoted as an effective strategy to improve animal production systems. Here we used initial metataxonomic data on fish gut microbiomes as well as a wealth of a priori mammalian microbiome knowledge on α-mannooligosaccharides (MOS) and β-mannan-derived MDFs to study effects of such feed supplements in Atlantic salmon (Salmo salar) and their impact on its gut microbiome composition and functionalities. Our multi-omic analysis revealed that the investigated MDFs (two α-mannans and an acetylated β-galactoglucomannan), at a dose of 0.2% in the diet, had negligible effects on both host gene expression, and gut microbiome structure and function under the studied conditions. While a subsequent trial using a higher (4%) dietary inclusion of β-mannan significantly shifted the gut microbiome composition, there were still no biologically relevant effects on salmon metabolism and physiology. Only a single Burkholderia-Caballeronia-Paraburkholderia (BCP) population demonstrated consistent and significant abundance shifts across both feeding trials, although with no evidence of β-mannan utilization capabilities or changes in gene transcripts for producing metabolites beneficial to the host. In light of these findings, we revisited our omics data to predict and outline previously unreported and potentially beneficial endogenous lactic acid bacteria that should be targeted with future, conceivably more suitable, MDF strategies for salmon.}, }
@article {pmid39453088, year = {2024}, author = {Donneschi, A and Recchia, M and Romeo, C and Pozzi, P and Salogni, C and Maisano, AM and Santucci, G and Scali, F and Faccini, S and Boniotti, MB and D'Incau, M and Maes, D and Alborali, GL}, title = {Infectious Agents Associated with Abortion Outbreaks in Italian Pig Farms from 2011 to 2021.}, journal = {Veterinary sciences}, volume = {11}, number = {10}, pages = {}, pmid = {39453088}, issn = {2306-7381}, support = {PRC2017007//Ministero della Salute/ ; }, abstract = {The present study retrospectively analyzed the infectious agents associated with 829 abortion outbreaks occurring from 2011 to 2021 in northern Italy. Foetuses were subjected to necropsies, and organ samples were analyzed by direct PCR to screen for six swine pathogens. In 42.0% of the examined outbreaks, at least one infectious agent was found. Porcine reproductive and respiratory syndrome virus (PRRSV) (24.9%) and porcine circovirus-2 (PCV2) (11.5%) were the most frequently detected among the known abortion-inducing pathogens. Chlamydia spp. (5.6%), porcine parvovirus (PPV) (4.0%), and Leptospira spp. (2.6%) were less common. Although its role in swine reproductive disorders is still unclear, PCV3 was detected in 19.6% of the cases. Coinfections were detected in 25.0% of positive outbreaks, and the most frequent coinfection was represented by PRRSV and PCV2 (32.2%), followed by PRRSV and PCV3 (23%). PCV2 prevalence showed a slight but consistent reduction during the study period, while PCV3 increased in frequency. Our data suggest an overall reduction in abortion outbreaks during the study period. PRRSV was confirmed as the main abortion agent detected in the examined area, while PCV2 prevalence showed a decline. Conversely, PCV3 detection has been increasing, supporting its potential role as an abortion agent. Our results highlight the importance of implementing a consistent and standardized sampling procedure, as well as a thorough diagnostic protocol, to reduce the incidence of inconclusive diagnoses.}, }
@article {pmid39452359, year = {2024}, author = {González-Román, P and Hernández-Oaxaca, D and Bustamante-Brito, R and Rogel, MA and Martínez-Romero, E}, title = {On the Origins of Symbiotic Fungi in Carmine Cochineals and Their Function in the Digestion of Plant Polysaccharides.}, journal = {Insects}, volume = {15}, number = {10}, pages = {}, pmid = {39452359}, issn = {2075-4450}, abstract = {The cochineal insect Dactylopius coccus Costa (Hemiptera) has cultural and economic value because it produces carminic acid that is used commercially. In this study, distinct fungi were cultured from dissected tissue and identified as Penicillium, Coniochaeta, Arthrinium, Cladosporium, Microascus, Aspergillus, and Periconia. Fungi were microscopically observed inside cochineals in the gut, fat body, and ovaries. Since cochineals spend their lives attached to cactus leaves and use the sap as feed, they can obtain fungi from cacti plants. Indeed, we obtained Penicillium, Aspergillus, and Cladosporium fungi from cacti that were identical to those inside cochineals, supporting their plant origin. Fungi could be responsible for the degrading activities in the insect guts, since cellulase, pectinase, and amylase enzymatic activities in insect guts decreased in fungicide-treated cochineals. Our findings set the basis for the further study of the interactions between insects, fungi, and their host plants.}, }
@article {pmid39444680, year = {2024}, author = {Khara, A and Chakraborty, A and Modlinger, R and Synek, J and Roy, A}, title = {Comparative metagenomic study unveils new insights on bacterial communities in two pine-feeding Ips beetles (Coleoptera: Curculionidae: Scolytinae).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1400894}, pmid = {39444680}, issn = {1664-302X}, abstract = {BACKGROUND: Climate change has recently boosted the severity and frequency of pine bark beetle attacks. The bacterial community associated with these beetles acts as "hidden players," enhancing their ability to infest and thrive on defense-rich pine trees. There is limited understanding of the environmental acquisition of these hidden players and their life stage-specific association with different pine-feeding bark beetles. There is inadequate knowledge on novel bacterial introduction to pine trees after the beetle infestation. Hence, we conducted the first comparative bacterial metabarcoding study revealing the bacterial communities in the pine trees before and after beetle feeding and in different life stages of two dominant pine-feeding bark beetles, namely Ips sexdentatus and Ips acuminatus. We also evaluated the bacterial association between wild and lab-bred beetles to measure the deviation due to inhabiting a controlled environment.<br><br>RESULTS: Significant differences in bacterial amplicon sequence variance (ASVs) abundance existed among different life stages within and between the pine beetles. However, Pseudomonas, Serratia, Pseudoxanthomonas, Taibaiella, and Acinetobacter served as core bacteria. Interestingly, I. sexdentatus larvae correspond to significantly higher bacterial diversity and community richness and evenness compared to other developmental stages, while I. acuminatus adults displayed higher bacterial richness with no significant variation in the diversity and evenness between the life stages. Both wild and lab-bred I. sexdentatus beetles showed a prevalence of the bacterial family Pseudomonadaceae. In addition, wild I. sexdentatus showed dominance of Yersiniaceae, whereas Erwiniaceae was abundant in lab-bred beetles. Alternatively, Acidobacteriaceae, Corynebacteriaceae, and Microbacteriaceae were highly abundant bacterial families in lab-bred, whereas Chitinophagaceae and Microbacteriaceae were highly abundant in wild I. accuminatus. We validated the relative abundances of selected bacterial taxa estimated by metagenomic sequencing with quantitative PCR.<br><br>CONCLUSION: Our study sheds new insights into bacterial associations in pine beetles under the influence of various drivers such as environment, host, and life stages. We documented that lab-breeding considerably influences beetle bacterial community assembly. Furthermore, beetle feeding alters bacteriome at the microhabitat level. Nevertheless, our study revisited pine-feeding bark beetle symbiosis under the influence of different drivers and revealed intriguing insight into bacterial community assembly, facilitating future functional studies.}, }
@article {pmid39418324, year = {2024}, author = {Freudenthal, J and Dumack, K and Schaffer, S and Schlegel, M and Bonkowski, M}, title = {Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39418324}, issn = {1751-7370}, mesh = {*Plant Bark/microbiology ; *Microbiota ; *Symbiosis ; *Quercus/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/physiology/isolation &amp; purification ; *Acer/microbiology ; Tilia/microbiology ; Trees/microbiology ; Forests ; Species Specificity ; }, abstract = {With over 3 trillion trees, forest ecosystems comprise nearly one-third of the terrestrial surface of the Earth. Very little attention has been given to the exploration of the above-ground plant microbiome of trees, its complex trophic interactions, and variations among tree species. To address this knowledge gap, we applied a primer-independent shotgun metatranscriptomic approach to assess the entire living canopy bark microbiome comprising prokaryotic and eukaryotic primary producers, decomposers, and various groups of consumers. With almost 1500 genera, we found a high microbial diversity on three tree species with distinct bark textures: oak (Quercus robur), linden (Tilia cordata), both with rough bark, and maple (Acer pseudoplatanus) with smooth bark. Core co-occurrence network analysis revealed a rich food web dominated by algal primary producers, and bacterial and fungal decomposers, sustaining a diverse community of consumers, including protists, microscopic metazoans, and predatory bacteria. Whereas maple accommodated a depauperate microbiome, oak and linden accommodated a richer microbiome mainly differing in their relative community composition: Bacteria exhibited an increased dominance on linden, whereas co-occurring algae and fungi dominated on oak, highlighting the importance of algal-fungal lichen symbioses even at the microscopic scale. Further, due to bacteria-fungi co-exclusion, bacteria on bark are not the main beneficiaries of algae-derived carbon compounds as it is known from aquatic systems.}, }
@article {pmid39414857, year = {2024}, author = {Villela, LB and da Silva-Lima, AW and Moreira, APB and Aiube, YRA and Ribeiro, FV and Villela, HDM and Majzoub, ME and Amario, M and de Moura, RL and Thomas, T and Peixoto, RS and Salomon, PS}, title = {Bacterial and Symbiodiniaceae communities' variation in corals with distinct traits and geographical distribution.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {24319}, pmid = {39414857}, issn = {2045-2322}, support = {310057/2022-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; *Microbiota ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Brazil ; Symbiosis ; Phylogeny ; Dinoflagellida/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Ecosystem ; }, abstract = {Coral microbiomes play crucial roles in holobiont homeostasis and adaptation. The host's ability to populate broad ecological niches and to cope with environmental changes seems to be related to the flexibility of the coral microbiome. By means of high-throughput DNA sequencing we characterized simultaneously both bacterial (16S rRNA) and Symbiodiniaceae (ITS2) communities of four reef-building coral species (Mussismilia braziliensis, Mussismilia harttii, Montastraea cavernosa, and Favia gravida) that differ in geographic distribution and niche specificity. Samples were collected in a marginal reef system (Abrolhos, Brazil) in four sites of contrasting irradiance and turbidity. Biological filters governed by the host are important in shaping corals' microbiome structure. More structured associated microbial communities by reef site tend to occur in coral species with broader geographic and depth ranges, especially for Symbiodiniaceae, whereas the endemic and habitat-specialist host, M. braziliensis, has relatively more homogenous bacterial communities with more exclusive members. Our findings lend credence to the hypothesis that higher microbiome flexibility renders corals more adaptable to diverse environments, a trend that should be investigated in more hosts and reef areas.}, }
@article {pmid39407340, year = {2024}, author = {Chemel, M and Peru, E and Binsarhan, M and Logares, R and Lartaud, F and Galand, PE}, title = {Cold-water coral mortality under ocean warming is associated with pathogenic bacteria.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {76}, pmid = {39407340}, issn = {2524-6372}, support = {ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; ANR-20-CE02-0006//Agence Nationale de la Recherche/ ; }, abstract = {Cold-water corals form vast reefs that are highly valuable habitats for diverse deep-sea communities. However, as the deep ocean is warming, it is essential to assess the resilience of cold-water corals to future conditions. The effects of elevated temperatures on the cold-water coral Lophelia pertusa (now named Desmophyllum pertusum) from the north-east Atlantic Ocean were experimentally investigated at the holobiont level, the coral host, and its microbiome. We show that at temperature increases of + 3 and + 5 °C, L. pertusa exhibits significant mortality concomitant with changes in its microbiome composition. In addition, a metagenomic approach revealed the presence of gene markers for bacterial virulence factors suggesting that coral death was due to infection by pathogenic bacteria. Interestingly, different coral colonies had different survival rates and, colony-specific microbiome signatures, indicating strong colony-specific variability in their response to warming waters. These results suggest that L. pertusa can only survive a long-term temperature increase of < 3 °C. Therefore, regional variations in deep-sea temperature increase should be considered in future estimates of the global distribution of cold-water corals.}, }
@article {pmid39402236, year = {2024}, author = {Vera-Ponce de León, A and Hensen, T and Hoetzinger, M and Gupta, S and Weston, B and Johnsen, SM and Rasmussen, JA and Clausen, CG and Pless, L and Veríssimo, ARA and Rudi, K and Snipen, L and Karlsen, CR and Limborg, MT and Bertilsson, S and Thiele, I and Hvidsten, TR and Sandve, SR and Pope, PB and La Rosa, SL}, title = {Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.}, journal = {Nature microbiology}, volume = {9}, number = {11}, pages = {3059-3074}, pmid = {39402236}, issn = {2058-5276}, support = {300846//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; 757922//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 12/RC/2273-P2//Science Foundation Ireland (SFI)/ ; }, mesh = {Animals ; *Salmo salar/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Aquaculture ; *Genome, Bacterial/genetics ; Seawater/microbiology ; Fresh Water/microbiology ; Phylogeny ; Genomics/methods ; }, abstract = {To ensure sustainable aquaculture, it is essential to understand the path 'from feed to fish', whereby the gut microbiome plays an important role in digestion and metabolism, ultimately influencing host health and growth. Previous work has reported the taxonomic composition of the Atlantic salmon (Salmo salar) gut microbiome; however, functional insights are lacking. Here we present the Salmon Microbial Genome Atlas consisting of 211 high-quality bacterial genomes, recovered by cultivation (n = 131) and gut metagenomics (n = 80) from wild and farmed fish both in freshwater and seawater. Bacterial genomes were taxonomically assigned to 14 different orders, including 35 distinctive genera and 29 previously undescribed species. Using metatranscriptomics, we functionally characterized key bacterial populations, across five phyla, in the salmon gut. This included the ability to degrade diet-derived fibres and release vitamins and other exometabolites with known beneficial effects, which was supported by genome-scale metabolic modelling and in vitro cultivation of selected bacterial species coupled with untargeted metabolomic studies. Together, the Salmon Microbial Genome Atlas provides a genomic and functional resource to enable future studies on salmon nutrition and health.}, }
@article {pmid39400157, year = {2024}, author = {Gan, B and Wang, K and Zhang, B and Jia, C and Lin, X and Zhao, J and Ding, S}, title = {Dynamic microbiome diversity shaping the adaptation of sponge holobionts in coastal waters.}, journal = {Microbiology spectrum}, volume = {12}, number = {11}, pages = {e0144824}, pmid = {39400157}, issn = {2165-0497}, mesh = {*Porifera/microbiology ; *Microbiota/genetics ; Animals ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Seawater/microbiology ; China ; Biodiversity ; Phylogeny ; Adaptation, Physiological ; }, abstract = {UNLABELLED: The microbial communities associated with sponges contribute to the adaptation of hosts to environments, which are essential for the trophic transformation of benthic-marine coupling. However, little is known about the symbiotic microbial community interactions and adaptative strategies of high- and low-microbial abundance (HMA and LMA) sponges, which represent two typical ecological phenotypes. Here, we compared the 1-year dynamic patterns of microbiomes with the HMA sponge Spongia officinalis and two LMA sponge species Tedania sp. and Haliclona simulans widespread on the coast of China. Symbiotic bacterial communities with the characteristic HMA-LMA dichotomy presented higher diversity and stability in S. officinalis than in Tedania sp. and H. simulans, while archaeal communities showed consistent diversity across all sponges throughout the year. Dissolved oxygen, dissolved inorganic phosphorus, dissolved organic phosphorus, and especially temperature were the major factors affecting the seasonal changes in sponge microbial communities. S. officinalis-associated microbiome had higher diversity, stronger stability, and closer interaction, which adopted a relatively isolated strategy to cope with environmental changes, while Tedania sp. and H. simulans were more susceptible and shared more bacterial Amplicon Sequence Variants (ASVs) with surrounding waters, with an open way facing the uncertainty of the environment. Meta-analysis of the microbiome in composition, diversity, and ecological function from 13 marine sponges further supported that bacterial communities associated with HMA and LMA sponges have evolved two distinct environmental adaptation strategies. We propose that the different adaptive ways of sponges responding to the environment may be responsible for their successful evolution and their competence in global ocean change.<br><br>IMPORTANCE: During long-term evolution, sponge holobionts, among the oldest symbiotic relationships between microbes and metazoans, developed two distinct phenotypes with high- and low-microbial abundance (HMA and LMA). Despite sporadic studies indicating that the characteristic microbial assemblages present in HMA and LMA sponges, the adaptation strategies of symbionts responding to environments are still unclear. This deficiency limits our understanding of the selection of symbionts and the ecological functions during the evolutionary history and the adaptative assessment of HMA and LMA sponges in variable environments. Here, we explored symbiotic communities with two distinct phenotypes in a 1-year dynamic environment and combined with the meta-analysis of 13 sponges. The different strategies of symbionts in adapting to the environment were basically drawn: microbes with LMA were more acclimated to environmental changes, forming relatively loose-connected communities, while HMA developed relatively tight-connected and more similar communities beyond the divergence of species and geographical location.}, }
@article {pmid39396843, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, A}, title = {Host genetics-associated mechanisms in colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {83-122}, doi = {10.1016/bs.adgen.2024.08.003}, pmid = {39396843}, issn = {0065-2660}, mesh = {*Colorectal Neoplasms/genetics ; Humans ; DNA Methylation/genetics ; Epigenesis, Genetic ; Microsatellite Instability ; Cell Transformation, Neoplastic/genetics ; CpG Islands/genetics ; Genetic Predisposition to Disease/genetics ; }, abstract = {Colorectal cancer (CRC) represents the second leading cause of cancer incidence and the third leading cause of cancer deaths worldwide. There is currently a lack of understanding of the onset of CRC, hindering the development of effective prevention strategies, early detection methods and the selection of appropriate therapies. This article outlines the key aspects of host genetics currently known about the origin and development of CRC. The organisation of the colonic crypts is described. It discusses how the transformation of a normal cell to a cancer cell occurs and how that malignant cell can populate an entire colonic crypt, promoting colorectal carcinogenesis. Current knowledge about the cell of origin of CRC is discussed, and the two morphological pathways that can give rise to CRC, the classical and alternative pathways, are presented. Due to the molecular heterogeneity of CRC, each of these pathways has been associated with different molecular mechanisms, including chromosomal and microsatellite genetic instability, as well as the CpG island methylator phenotype. Finally, different CRC classification systems are described based on genetic, epigenetic and transcriptomic alterations, allowing diagnosis and treatment personalisation.}, }
@article {pmid39396842, year = {2024}, author = {González, A and Badiola, I and Fullaondo, A and Rodríguez, J and Odriozola, A}, title = {Personalised medicine based on host genetics and microbiota applied to colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {411-485}, doi = {10.1016/bs.adgen.2024.08.004}, pmid = {39396842}, issn = {0065-2660}, mesh = {Humans ; *Colorectal Neoplasms/genetics/microbiology ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Biomarkers, Tumor/genetics ; Prognosis ; }, abstract = {Colorectal cancer (CRC) ranks second in incidence and third in cancer mortality worldwide. This situation, together with the understanding of the heterogeneity of the disease, has highlighted the need to develop a more individualised approach to its prevention, diagnosis and treatment through personalised medicine. This approach aims to stratify patients according to risk, predict disease progression and determine the most appropriate treatment. It is essential to identify patients who may respond adequately to treatment and those who may be resistant to treatment to avoid unnecessary therapies and minimise adverse side effects. Current research is focused on identifying biomarkers such as specific mutated genes, the type of mutations and molecular profiles critical for the individualisation of CRC diagnosis, prognosis and treatment guidance. In addition, the study of the intestinal microbiota as biomarkers is being incorporated due to the growing scientific evidence supporting its influence on this disease. This article comprehensively addresses the use of current and emerging diagnostic, prognostic and predictive biomarkers in precision medicine against CRC. The effects of host genetics and gut microbiota composition on new approaches to treating this disease are discussed. How the gut microbiota could mitigate the side effects of treatment is reviewed. In addition, strategies to modulate the gut microbiota, such as dietary interventions, antibiotics, and transplantation of faecal microbiota and phages, are discussed to improve CRC prevention and treatment. These findings provide a solid foundation for future research and improving the care of CRC patients.}, }
@article {pmid39396841, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, I and Odriozola, A}, title = {Microbiota and beneficial metabolites in colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {367-409}, doi = {10.1016/bs.adgen.2024.08.002}, pmid = {39396841}, issn = {0065-2660}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Polyphenols/metabolism ; Animals ; }, abstract = {Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related death worldwide. In recent years, the impact of the gut microbiota on the development of CRC has become clear. The gut microbiota is the community of microorganisms living in the gut symbiotic relationship with the host. These microorganisms contribute to the development of CRC through various mechanisms that are not yet fully understood. Increasing scientific evidence suggests that metabolites produced by the gut microbiota may influence CRC development by exerting protective and deleterious effects. This article reviews the metabolites produced by the gut microbiota, which are derived from the intake of complex carbohydrates, proteins, dairy products, and phytochemicals from plant foods and are associated with a reduced risk of CRC. These metabolites include short-chain fatty acids (SCFAs), indole and its derivatives, conjugated linoleic acid (CLA) and polyphenols. Each metabolite, its association with CRC risk, the possible mechanisms by which they exert anti-tumour functions and their relationship with the gut microbiota are described. In addition, other gut microbiota-derived metabolites that are gaining importance for their role as CRC suppressors are included.}, }
@article {pmid39396840, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, A}, title = {Host genetics and microbiota data analysis in colorectal cancer research.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {31-81}, doi = {10.1016/bs.adgen.2024.08.007}, pmid = {39396840}, issn = {0065-2660}, mesh = {*Colorectal Neoplasms/genetics/microbiology ; Humans ; *Computational Biology/methods ; Precision Medicine ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Data Analysis ; }, abstract = {Colorectal cancer (CRC) is a heterogeneous disease with a complex aetiology influenced by a myriad of genetic and environmental factors. Despite advances in CRC research, it is a major burden of disease, with the second highest incidence and third leading cause of cancer deaths worldwide. To individualise diagnosis, prognosis, and treatment of CRC, developing new strategies combining precision medicine and bioinformatic procedures is promising. Precision medicine is based on omics technologies and aims to individualise the management of CRC based on patient host genetic characteristics and microbiota. Bioinformatics is central to the application of personalised medicine because it enables the analysis of large datasets generated by these technologies. At the level of host genetics, bioinformatics allows the identification of mutations, genes, molecular pathways, biomarkers and drugs relevant to colorectal carcinogenesis. At the microbiota level, bioinformatics is fundamental to analysing microbial communities' composition and functionality and developing biomarkers and personalised microbiota-based therapies. This paper explores the host and microbiota genetic data analysis in CRC research.}, }
@article {pmid39396839, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, I and Odriozola, A}, title = {Microbiota and other detrimental metabolites in colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {309-365}, doi = {10.1016/bs.adgen.2024.08.006}, pmid = {39396839}, issn = {0065-2660}, mesh = {*Colorectal Neoplasms/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Diet ; Bile Acids and Salts/metabolism ; Polycyclic Aromatic Hydrocarbons/metabolism ; Animals ; }, abstract = {Increasing scientific evidence demonstrates that gut microbiota plays an essential role in the onset and development of Colorectal cancer (CRC). However, the mechanisms by which these microorganisms contribute to cancer development are complex and far from completely clarified. Specifically, the impact of gut microbiota-derived metabolites on CRC is undeniable, exerting both protective and detrimental effects. This paper examines the effects and mechanisms by which important bacterial metabolites exert detrimental effects associated with increased risk of CRC. Metabolites considered include heterocyclic amines and polycyclic aromatic hydrocarbons, heme iron, secondary bile acids, ethanol, and aromatic amines. It is necessary to delve deeper into the mechanisms of action of these metabolites in CRC and identify the microbiota members involved in their production. Furthermore, since diet is the main factor capable of modifying the intestinal microbiota, conducting studies that include detailed descriptions of dietary interventions is crucial. All this knowledge is essential for developing precision nutrition strategies to optimise a protective intestinal microbiota against CRC.}, }
@article {pmid39396838, year = {2024}, author = {González, A and Odriozola, I and Fullaondo, A and Odriozola, A}, title = {Microbiota and detrimental protein derived metabolites in colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {255-308}, doi = {10.1016/bs.adgen.2024.06.001}, pmid = {39396838}, issn = {0065-2660}, mesh = {*Colorectal Neoplasms/microbiology/metabolism/etiology ; Humans ; *Gastrointestinal Microbiome ; Fermentation ; Risk Factors ; Diet ; Animals ; }, abstract = {Colorectal cancer (CRC) is the third leading cancer in incidence and the second leading cancer in mortality worldwide. There is growing scientific evidence to support the crucial role of the gut microbiota in the development of CRC. The gut microbiota is the complex community of microorganisms that inhabit the host gut in a symbiotic relationship. Diet plays a crucial role in modulating the risk of CRC, with a high intake of red and processed meat being a risk factor for the development of CRC. The production of metabolites derived from protein fermentation by the gut microbiota is considered a crucial element in the interaction between red and processed meat consumption and the development of CRC. This paper examines several metabolites derived from the bacterial fermentation of proteins associated with an increased risk of CRC. These metabolites include ammonia, polyamines, trimethylamine N-oxide (TMAO), N-nitroso compounds (NOC), hydrogen sulphide (H2S), phenolic compounds (p-cresol) and indole compounds (indolimines). These compounds are depicted and reviewed for their association with CRC risk, possible mechanisms promoting carcinogenesis and their relationship with the gut microbiota. Additionally, this paper analyses the evidence related to the role of red and processed meat intake and CRC risk and the factors and pathways involved in bacterial proteolytic fermentation in the large intestine.}, }
@article {pmid39396837, year = {2024}, author = {Orozco-Castaño, C and Mejia-Garcia, A and Zambrano, Y and Combita, AL and Parra-Medina, R and Bonilla, DA and González, A and Odriozola, A}, title = {Construction of an immune gene expression meta signature to assess the prognostic risk of colorectal cancer patients.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {207-254}, doi = {10.1016/bs.adgen.2024.08.005}, pmid = {39396837}, issn = {0065-2660}, mesh = {Humans ; *Colorectal Neoplasms/genetics/immunology ; Prognosis ; *Biomarkers, Tumor/genetics ; *Gene Expression Regulation, Neoplastic ; *Transcriptome ; Gene Expression Profiling ; Proportional Hazards Models ; Male ; Female ; }, abstract = {Despite recent advancements in colorectal cancer (CRC) treatment, particularly with the introduction of immunotherapy and checkpoint inhibitors, the efficacy of these therapies remains limited to a subset of patients. To address this challenge, our study aimed to develop a prognostic biomarker based on immune-related genes to predict better outcomes in CRC patients and aid in treatment decision-making. We comprehensively analysed immune gene expression signatures associated with CRC prognosis to construct an immune meta-signature with prognostic potential. Utilising data from The Cancer Genome Atlas (TCGA), we employed Cox regression to identify immune-related genes with prognostic significance from multiple studies. Subsequently, we compared the expression levels of immune genes, levels of immune cell infiltration, and various immune-related molecules between high-risk and low-risk patient groups. Functional analysis using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses provided insights into the biological pathways associated with the identified prognostic genes. Finally, we validated our findings using a separate CRC cohort from the Gene Expression Omnibus (GEO). Integration of the prognostic genes revealed significant disparities in survival outcomes. Differential expression analysis identified a set of immune-associated genes, which were further refined using LASSO penalisation and Cox regression. Univariate Cox regression analyses confirmed the autonomy of the gene signature as a prognostic indicator for CRC patient survival. Our risk prediction model effectively stratified CRC patients based on their prognosis, with the high-risk group showing enrichment in pro-oncogenic terms and pathways. Immune infiltration analysis revealed an augmented presence of certain immunosuppressive subsets in the high-risk group. Finally, we validated the performance of our prognostic model by applying the risk score equation to a different CRC patient dataset, confirming its prognostic potential in this new cohort. Overall, our study presents a novel immune-related gene signature with promising implications for predicting cancer progression and prognosis, thereby enabling more personalised management strategies for CRC patients.}, }
@article {pmid39396836, year = {2024}, author = {González, A and Fullaondo, A and Odriozola, A}, title = {Microbiota-associated mechanisms in colorectal cancer.}, journal = {Advances in genetics}, volume = {112}, number = {}, pages = {123-205}, doi = {10.1016/bs.adgen.2024.05.002}, pmid = {39396836}, issn = {0065-2660}, mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Bacteria/classification ; }, abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide, ranking third in terms of incidence and second as a cause of cancer-related death. There is growing scientific evidence that the gut microbiota plays a key role in the initiation and development of CRC. Specific bacterial species and complex microbial communities contribute directly to CRC pathogenesis by promoting the neoplastic transformation of intestinal epithelial cells or indirectly through their interaction with the host immune system. As a result, a protumoural and immunosuppressive environment is created conducive to CRC development. On the other hand, certain bacteria in the gut microbiota contribute to protection against CRC. In this chapter, we analysed the relationship of the gut microbiota to CRC and the associations identified with specific bacteria. Microbiota plays a key role in CRC through various mechanisms, such as increased intestinal permeability, inflammation and immune system dysregulation, biofilm formation, genotoxin production, virulence factors and oxidative stress. Exploring the interaction between gut microbiota and tumourigenesis is essential for developing innovative therapeutic approaches in the fight against CRC.}, }
@article {pmid39388223, year = {2024}, author = {Alcaraz, CM and Séneca, J and Kunert, M and Pree, C and Sudo, M and Petersen, JM}, title = {Sulfur-oxidizing symbionts colonize the digestive tract of their lucinid hosts.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39388223}, issn = {1751-7370}, support = {DOC 69/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; *Symbiosis ; *Bivalvia/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; *Gills/microbiology ; *Sulfur/metabolism ; *In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Like many marine invertebrates, marine lucinid clams have an intimate relationship with beneficial sulfur-oxidizing bacteria located within specialized gill cells known as bacteriocytes. Most previous research has focused on the symbionts in the gills of these (and other) symbiotic bivalves, often assuming that the symbionts only persistently colonize the gills, at least in the adult stage. We used 16S rRNA gene sequencing and digital polymerase chain reaction with symbiont-specific primers targeting the soxB gene on the foot, mantle, visceral mass, and gills of the lucinid clam Loripes orbiculatus. We also used fluorescence in situ hybridization with symbiont-specific probes to examine symbiont distribution at the level of the whole holobiont. Despite 40 years of research on these symbioses, we detected previously unknown populations of symbiont cells in several organs, including the digestive tract. As in the well-studied gills, symbionts in the digestive tract may be housed within host cells. A 14-month starvation experiment without hydrogen sulfide to power symbiont metabolism caused a larger reduction in symbiont numbers in the gills compared to the visceral mass, raising the possibility that symbionts in the digestive tract are persistent and may have a distinct physiology and role in the symbiosis compared with the gill symbionts. Our results highlight the unexpectedly complex relationships between marine lucinid clams and their symbionts and challenge the view that chemosynthetic symbionts are restricted to the gills of these hosts.}, }
@article {pmid39392666, year = {2024}, author = {Zhang, N and Qian, Z and He, J and Shen, X and Lei, X and Sun, C and Fan, J and Felton, GW and Shao, Y}, title = {Gut bacteria of lepidopteran herbivores facilitate digestion of plant toxins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {42}, pages = {e2412165121}, pmid = {39392666}, issn = {1091-6490}, support = {32022081//MOST | National Natural Science Foundation of China (NSFC)/ ; CARS-18-ZJ0302//MOA | Earmarked Fund for China Agriculture Research System/ ; LZ22C170001//MOST | NSFC | NSFC-Zhejiang Joint Fund | | Natural Science Foundation of Zhejiang Province (ZJNSF)/ ; }, mesh = {Animals ; *Herbivory ; *Gastrointestinal Microbiome/physiology ; Bombyx/metabolism/microbiology ; Morus ; Symbiosis ; Lepidoptera/microbiology ; Spodoptera/microbiology ; Bacteria/metabolism/genetics/classification ; Digestion ; }, abstract = {Lepidopterans commonly feed on plant material, being the most significant insect herbivores in nature. Despite plant resistance to herbivory, such as producing toxic secondary metabolites, herbivores have developed mechanisms encoded in their genomes to tolerate or detoxify plant defensive compounds. Recent studies also highlight the role of gut microbiota in mediating detoxification in herbivores; however, convincing evidence supporting the significant contribution of gut symbionts is rare in Lepidoptera. Here, we show that the growth of various lepidopteran species was inhibited by a mulberry-derived secondary metabolite, 1-deoxynojirimycin (DNJ); as expected, the specialist silkworm Bombyx mori grew well, but interestingly, gut microbiota of early-instar silkworms was affected by the DNJ level, and several bacterial species responded positively to enriched DNJ. Among these, a bacterial strain isolated from the silkworm gut (Pseudomonas fulva ZJU1) can degrade and utilize DNJ as the sole energy source, and after inoculation into nonspecialists (e.g., beet armyworm Spodoptera exigua), P. fulva ZJU1 increased host resistance to DNJ and significantly promoted growth. We used genomic and transcriptomic analyses to identify genes potentially involved in DNJ degradation, and CRISPR-Cas9-mediated mutagenesis verified the function of ilvB, a key binding protein, in metabolizing DNJ. Furthermore, the ilvB deletion mutant, exhibiting normal bacterial growth, could no longer enhance nonspecialist performance, supporting a role in DNJ degradation in vivo. Therefore, our study demonstrated causality between the gut microbiome and detoxification of plant chemical defense in Lepidoptera, facilitating a mechanistic understanding of host-microbe relationships across this complex, abundant insect group.}, }
@article {pmid39391863, year = {2024}, author = {Martin Bideguren, G and Razgour, O and Alberdi, A}, title = {Quantitative Synthesis of Microbe-Driven Acclimation and Adaptation in Wild Vertebrates.}, journal = {Evolutionary applications}, volume = {17}, number = {10}, pages = {e70025}, pmid = {39391863}, issn = {1752-4571}, abstract = {Microorganisms associated with animals harbour a unique set of functional traits pivotal for the normal functioning of their hosts. This realisation has led researchers to hypothesise that animal-associated microbial communities may boost the capacity of their hosts to acclimatise and adapt to environmental changes, two eco-evolutionary processes with significant applied relevance. Aiming to assess the importance of microorganisms for wild vertebrate conservation, we conducted a quantitative systematic review to evaluate the scientific evidence for the contribution of gut microorganisms to the acclimation and adaptation capacity of wild vertebrate hosts. After screening 1974 publications, we scrutinised the 109 studies that met the inclusion criteria based on 10 metrics encompassing study design, methodology and reproducibility. We found that the studies published so far were not able to resolve the contribution of gut microorganisms due to insufficient study design and research methods for addressing the hypothesis. Our findings underscore the limited application to date of microbiome knowledge in vertebrate conservation and management, highlighting the need for a paradigm shift in research approaches. Considering these results, we advocate for a shift from observational studies to experimental manipulations, where fitness or related indicators are measured, coupled with an update in molecular techniques used to analyse microbial functions. In addition, closer collaboration with conservation managers and practitioners from the inception of the project is needed to encourage meaningful application of microbiome knowledge in adaptive wildlife conservation management.}, }
@article {pmid39382467, year = {2024}, author = {Desikan, P and Rangnekar, A}, title = {Human holobionts: Metaorganisms hidden in plain sight?.}, journal = {The Indian journal of medical research}, volume = {159}, number = {6}, pages = {702-704}, pmid = {39382467}, issn = {0971-5916}, mesh = {Humans ; *Symbiosis ; Microbiota ; Biological Evolution ; }, }
@article {pmid39380028, year = {2024}, author = {Bollati, E and Hughes, DJ and Suggett, DJ and Raina, JB and Kühl, M}, title = {Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {55}, pmid = {39380028}, issn = {2524-4671}, abstract = {Animal guts contain numerous microbes, which are critical for nutrient assimilation and pathogen defence. While corals and other Cnidaria lack a true differentiated gut, they possess semi-enclosed gastrovascular cavities (GVCs), where vital processes such as digestion, reproduction and symbiotic exchanges take place. The microbiome harboured in GVCs is therefore likely key to holobiont fitness, but remains severely understudied due to challenges of working in these small compartments. Here, we developed minimally invasive methodologies to sample the GVC of coral polyps and characterise the microbial communities harboured within. We used glass capillaries, low dead volume microneedles, or nylon microswabs to sample the gastrovascular microbiome of individual polyps from six species of corals, then applied low-input DNA extraction to characterise the microbial communities from these microliter volume samples. Microsensor measurements of GVCs revealed anoxic or hypoxic micro-niches, which persist even under prolonged illumination with saturating irradiance. These niches harboured microbial communities enriched in putatively microaerophilic or facultatively anaerobic taxa, such as Epsilonproteobacteria. Some core taxa found in the GVC of Lobophyllia hemprichii from the Great Barrier Reef were also detected in conspecific colonies held in aquaria, indicating that these associations are unlikely to be transient. Our findings suggest that the coral GVC is chemically and microbiologically similar to the gut of higher Metazoa. Given the importance of gut microbiomes in mediating animal health, harnessing the coral "gut microbiome" may foster novel active interventions aimed at increasing the resilience of coral reefs to the climate crisis.}, }
@article {pmid39379612, year = {2024}, author = {Hermosilla-Albala, N and Silva, FE and Cuadros-Espinoza, S and Fontsere, C and Valenzuela-Seba, A and Pawar, H and Gut, M and Kelley, JL and Ruibal-Puertas, S and Alentorn-Moron, P and Faella, A and Lizano, E and Farias, I and Hrbek, T and Valsecchi, J and Gut, IG and Rogers, J and Farh, KK and Kuderna, LFK and Marques-Bonet, T and Boubli, JP}, title = {Whole genomes of Amazonian uakari monkeys reveal complex connectivity and fast differentiation driven by high environmental dynamism.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1283}, pmid = {39379612}, issn = {2399-3642}, mesh = {Animals ; *Genome ; Genetic Variation ; Rainforest ; Phylogeny ; Ecosystem ; Brazil ; Gene Flow ; Platyrrhini/genetics ; }, abstract = {Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. Nowadays, these two groups present distinct genetic diversity and group-specific variation linked to pathogens. We propose differing hydrology patterns and effectiveness of geographic barriers have modulated the intra-group connectivity and structure of bald and black uakari populations. With this work we have explored the effects of the Amazon rainforest's dynamism on wild primates' genetics and increased the representation of platyrrhine genomes, thus opening the door to future research on the complexity and diversity of primate genomics.}, }
@article {pmid39375799, year = {2024}, author = {Köster, PC and Figueiredo, AM and Maloney, JG and Dashti, A and Bailo, B and Torres, RT and Fonseca, C and Mysterud, A and Habela, M&#xc1; and Rivero-Juarez, A and Vicente, J and Serrano, E and Arnal, MC and de Luco, DF and Armenteros, JA and Balseiro, A and Cardona, GA and Carvalho, J and Hipólito, D and Fernandes, J and Palmeira, JD and Calero-Bernal, R and González-Barrio, D and Santin, M and Carmena, D}, title = {Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula.}, journal = {Veterinary research}, volume = {55}, number = {1}, pages = {133}, pmid = {39375799}, issn = {1297-9716}, support = {PI19CIII/00029//PI19CIII/00029/ ; }, mesh = {Animals ; *Sus scrofa ; Portugal/epidemiology ; Spain/epidemiology ; *Swine Diseases/parasitology/epidemiology ; *Blastocystis/genetics/classification/isolation &amp; purification ; Swine ; *Blastocystis Infections/veterinary/epidemiology/parasitology ; Prevalence ; Feces/parasitology ; Genetic Variation ; }, abstract = {The ongoing increase in wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in the epidemiology of Blastocystis is insufficiently understood. Thus, we investigated the occurrence and subtype diversity of Blastocystis in free-ranging wild boars from the Iberian Peninsula using conventional PCR and next-generation amplicon sequencing of a fragment of the ssu RNA gene. A total of 459 wild boar faecal samples were collected across Spain (n = 360) and Portugal (n = 99) between 2014 and 2021. Blastocystis was present in 15.3% (70/459; 95% CI 12.1-18.9) of the wild boars analysed, and its occurrence was significantly higher in Portugal (34.3%, 34/99; 95% CI 25.1-44.6) than in Spain (10.0%, 36/360; 95% CI 7.1-13.6). Seven Blastocystis subtypes (ST5, ST10b, ST13-ST15, ST24b, and ST43) were detected among the surveyed wild boar populations, with greater variability detected in Portuguese samples. ST5 was identified in all the Blastocystis-positive animals, whereas 14.3% of them harboured ST mixed colonisations. Our results demonstrate that Blastocystis ST5 is particularly adapted to infect wild boars. The additional identification of zoonotic STs reinforces the role of wild boars as spreaders of zoonotic infections with public health significance.}, }
@article {pmid39375020, year = {2024}, author = {Garritano, AN and Zhang, Z and Jia, Y and Allen, MA and Hill, LJ and Kuzhiumparambil, U and Hinkley, C and Raina, JB and Peixoto, RS and Thomas, T}, title = {Simple Porifera holobiont reveals complex interactions between the host, an archaeon, a bacterium, and a phage.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39375020}, issn = {1751-7370}, support = {BAS/1/1095-01-01//ANP R&amp;D levy as "Compromisso de Investimentos com Pesquisa e Desenvolvimento"/ ; }, mesh = {*Symbiosis ; *Archaea/metabolism/genetics ; Animals ; *Bacteriophages/physiology/genetics ; *Porifera/microbiology ; *Bacteria/metabolism/genetics/classification ; Ammonia/metabolism ; Microbiota ; Phylogeny ; Vitamin B 12/metabolism ; }, abstract = {The basal metazoan phylum Porifera (sponges) is increasingly used as a model to investigate ecological and evolutionary features of microbe-animal symbioses. However, sponges often host complex microbiomes, which has hampered our understanding of their interactions with their microbial symbionts. Here, we describe the discovery and characterization of the simplest sponge holobiont reported to date, consisting of the deep-sea glass sponge Aphrocallistes beatrix and two newly-described microbial symbionts: an autotrophic ammonia-oxidizing archaeon and a bacterial heterotroph. Omics analyses and metabolic modeling revealed the dependency of the ammonia-oxidizing archaea on sponge-derived ammonia to drive primary production, which in turn supports the bacterium's growth by providing the dicarboxylate fumarate. Furthermore, virus-mediated archaeal lysis appears crucial to overcome the bacterium's vitamin B12 auxotrophy. These findings reveal that the exchanges of vitamin B12 and dicarboxylate may be evolutionarily conserved features of symbiosis as they can also be found in interactions between free-living marine bacteria, and between microbes and plants or diatoms.}, }
@article {pmid39358872, year = {2024}, author = {Hacquard, S and Martin, FM}, title = {The chemical language of plant-microbe-microbe associations: an introduction to a Virtual Issue.}, journal = {The New phytologist}, volume = {244}, number = {3}, pages = {739-742}, doi = {10.1111/nph.20124}, pmid = {39358872}, issn = {1469-8137}, support = {ANR-11-LABX-0002-01//Laboratory of Excellence ARBRE/ ; //Northwest Institute of Eco-Environment and Resources, Lanzhou, China/ ; //ERC Consolidator Grant MICROBIOSIS/ ; }, mesh = {*Plants/microbiology ; }, }
@article {pmid39358646, year = {2024}, author = {Jiménez-Velásquez, S and Pacheco-Montealegre, ME and Torres-Higuera, L and Uribe-Gutiérrez, L and Burbano-David, D and Dávila-Mora, LL and Renjifo-Ibáñez, C and Caro-Quintero, A}, title = {Genus-targeted markers for the taxonomic identification and monitoring of coagulase-positive and coagulase-negative Staphylococcus species.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {11}, pages = {333}, pmid = {39358646}, issn = {1573-0972}, mesh = {*Staphylococcus/genetics/classification/isolation &amp; purification/enzymology ; *Coagulase/metabolism/genetics ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; DNA Primers/genetics ; Phylogeny ; Staphylococcal Infections/microbiology ; Animals ; Genes, Bacterial/genetics ; Bacterial Proteins/genetics ; Sequence Analysis, DNA ; Multilocus Sequence Typing ; Bacterial Typing Techniques/methods ; Genetic Markers ; High-Throughput Nucleotide Sequencing ; }, abstract = {The Staphylococcus genus comprises multiple pathogenic and opportunistic species that represent a risk to public health. Epidemiological studies require accurate taxonomic classification of isolates with enough resolution to distinguish clonal complexes. Unfortunately, 16 S rRNA molecular analysis and phenotypic characterization cannot distinguish all species and do not offer enough resolution to assess intraspecific diversity. Other approaches, such as Multilocus Sequence Tagging, provide higher resolution; however, they have been developed for Staphylococcus aureus and a few other species. Here, we developed a set of genus-targeted primers using five orthologous genes (pta, tuf, tpi, groEs, and sarA) to identify all Staphylococcus species within the genus. The primers were initially evaluated using 20 strains from the Collection of Microorganisms of Interest in Animal Health from AGROSAVIA (CMISA), and their amplified sequences were compared to a set of 33 Staphylococcus species. This allowed the taxonomic identification of the strains even on close species and the establishment of intraspecies diversity. To enhance the scope and cost-effectiveness of the proposed strategy, we customized the primer sets for an Illumina paired-end amplicon protocol, enabling gene multiplexing. We assessed five genes across 177 strains, generating 880 paired-end libraries from the CMISA. This approach significantly reduced sequencing costs, as all libraries can be efficiently sequenced in a single MiSeq run at a fraction (one-fourth or less) of the cost associated with Sanger sequencing. In summary, this method can be used for precise identification and diversity analysis of Staphylococcus species, offering an advancement over traditional techniques in both resolution and cost-effectiveness.}, }
@article {pmid39346007, year = {2024}, author = {Eisenhofer, R and Alberdi, A and Woodcroft, BJ}, title = {Quantifying microbial DNA in metagenomes improves microbial trait estimation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae111}, pmid = {39346007}, issn = {2730-6151}, abstract = {Shotgun metagenomics is a powerful tool for studying the genomic traits of microbial community members, such as genome size, gene content, etc. While such traits can be used to better understand the ecology and evolution of microbial communities, the accuracy of their estimations can be critically influenced by both known and unknown factors. One factor that can bias trait estimations is the proportion of eukaryotic and viral DNA in a metagenome, as some bioinformatic tools assume that all DNA reads in a metagenome are bacterial or archaeal. Here, we add to a recent debate about the influence of eukaryotic DNA in the estimation of average genome size from a global soil sample dataset using a new bioinformatic tool. Contrary to what was assumed, our reanalysis of this dataset revealed that soil samples can contain a substantial proportion of non-microbial DNA, which severely inflated the original estimates of average genome size. Correcting for this bias significantly improves the statistical support for the negative relationship between average bacterial genome size and soil pH. These results highlight that metagenomes can contain large quantities of non-microbial DNA and that new methods that correct for this can improve microbial trait estimation.}, }
@article {pmid39329334, year = {2024}, author = {Navarro, B and Turina, M}, title = {Viroid and viroid-like elements in plants and plant-associated microbiota: a new layer of biodiversity for plant holobionts.}, journal = {The New phytologist}, volume = {244}, number = {4}, pages = {1216-1222}, doi = {10.1111/nph.20156}, pmid = {39329334}, issn = {1469-8137}, support = {P2022XX55J//European Union-NextGeneration EU, Missione 4, Componente 1, MUR Piano Nazionale di Ripresa e Resilienza (PNRR)/ ; }, mesh = {*Viroids/physiology/genetics ; *Plants/virology/microbiology ; *Biodiversity ; Microbiota ; Symbiosis ; Plant Viruses/physiology ; }, abstract = {The functional relevance of plant-associated microorganisms is theoretically framed within the holobiont concept. The role of viruses in plant holobionts is being recognized both for their direct effects when hosted in plants (cryptic plant viruses) and for their indirect effects when infecting microorganisms associated with plants in tripartite interactions (e.g. mycoviruses and bacteriophages). We argue that viroids, the smallest infectious agents typically infecting only plant hosts, must also be included in plant holobiont studies. The same applies to the recently discovered large number of viroid-like elements infecting hosts of other life kingdoms that are closely associated with plants. Here we also describe in depth the diversity of such viroid-like elements and their initial functional characterization in plant-associated fungi.}, }
@article {pmid39328926, year = {2024}, author = {Duque-Granda, D and Vivero-Gómez, RJ and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX}, title = {Interaction and effects of temperature preference under a controlled environment on the diversity and abundance of the microbiome in Lutzomyia longipalpis (Diptera: Psychodidae).}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {44}, number = {}, pages = {e00857}, pmid = {39328926}, issn = {2215-017X}, abstract = {Characterization of the temperature effects on the abundance and richness of the microbiota of Lutzomyia longipalpis, insect vector of Leishmania infantum in America, is an aspect of pivotal importance to understand the interactions between temperature, bacteria, and Leishmania infection. We developed and used a customized device with a temperature gradient (21-34 °C) to assess the temperature preferences of wild females of Lu. longipalpis collected in a rural area (Ricaurte, Cundinamarca, Colombia). Each replicate consisted of 50 females exposed to the gradient for an hour. At the end of the exposure time, insects were collected and separated by the temperature ranges selected varying from 21 °C to 34 °C. They were organized in 17 pools from which total DNA extracts were obtained, and samples were subjected to 16S rRNA amplicon sequencing analyzes. The most abundant phyla across the different temperature ranges were Proteobacteria (17.22-90.73 %), Firmicutes (5.99-77.21 %) and Actinobacteria (1.56-59.85 %). Results also showed an abundance (30 % to 57.36 %) of Pseudomonas (mainly at temperatures of 21-29 °C and 34 °C) that decreased to 6.55 %-13.20 % at temperatures of 31-33 °C, while Bacillus increase its abundance to 67.24 % at 29-33 °C. Serratia also had a greater representation (49.79 %), specifically in sand flies recovered at 25-27 °C. No significant differences were found at α-diversity level when comparing richness using the Shannon-Wiener, Simpson, and Chao1 indices, while β-diversity differences were found using the Bray-Curtis index (F-value of 3.5073, p-value < 0.013, R-squared of 0,4889), especially in the groups of Lu. longipalpis associated at higher temperatures (29-33 °C). It was also possible to detect the presence of endosymbionts such as Spiroplasma and Arsenophonus in the range of 29-33 °C. Rickettsia was only detected in Lu. longipalpis sand flies recovered between 25-27 °C. It was possible to characterize Lu. longipalpis microbiota in response to intraspecific temperature preferences and observe changes in bacterial communities and endosymbionts at different ranges of said environmental variable, which may be important in its vector competence and environmental plasticity to adapt to new climate change scenarios.}, }
@article {pmid39322283, year = {2024}, author = {Narechania, A and Bobo, D and Deitz, K and DeSalle, R and Planet, PJ and Mathema, B}, title = {Rapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.}, journal = {Genome research}, volume = {34}, number = {10}, pages = {1651-1660}, pmid = {39322283}, issn = {1549-5469}, support = {R01 AI151173/AI/NIAID NIH HHS/United States ; }, mesh = {*SARS-CoV-2/genetics/isolation &amp; purification ; *COVID-19/epidemiology/virology ; Humans ; *Wastewater/virology ; *Genome, Viral ; *Phylogeny ; South Africa/epidemiology ; Pandemics ; }, abstract = {The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic.}, }
@article {pmid39316562, year = {2025}, author = {Kliver, S and Kovacic, I and Mak, S and Sinding, MS and Stagegaard, J and Petersen, B and Nesme, J and Gilbert, MTP}, title = {A chromosome phased diploid genome assembly of African hunting dog (Lycaon pictus).}, journal = {The Journal of heredity}, volume = {116}, number = {1}, pages = {78-87}, doi = {10.1093/jhered/esae052}, pmid = {39316562}, issn = {1465-7333}, support = {CF22-0680//Carlsbergfondet Research Infrastructure/ ; //Danish National Research Foundation/ ; //NovoNordisk Foundation/ ; CF20-0355//Carlsberg Foundation Reintegration Fellowship/ ; }, mesh = {Animals ; *Genome ; *Canidae/genetics ; *Diploidy ; Genomics/methods ; Haplotypes ; }, abstract = {The African hunting dog (Lycaon pictus, 2n = 78) once ranged over most sub-Saharan ecosystems except its deserts and rainforests. However, as a result of (still ongoing) population declines, today they remain only as small fragmented populations. Furthermore, the future of the species remains unclear, due to both anthropogenic pressure and interactions with domestic dogs, thus their preservation is a conservation priority. On the tree of life, the hunting dog is basal to Canis and Cuon and forms a crown group with them, making it a useful species for comparative genomic studies. Here, we present a diploid chromosome-level assembly of an African hunting dog. Assembled according to Vertebrate Genomes Project guidelines from a combination of PacBio HiFi reads and HiC data, it is phased at the level of individual chromosomes. The maternal (pseudo)haplotype (mat) of our assembly has a length of 2.38 Gbp, and 99.36% of the sequence is encompassed by 39 chromosomal scaffolds. The rest is included in only 36 unplaced short scaffolds. At the contig level, the mat consists of only 166 contigs with an N50 of 39 Mbp. BUSCO (Benchmarking Universal Single-Copy Orthologue) analysis showed 95.4% completeness based on Carnivora conservative genes (carnivora_odb10). When compared with other available genomes from subtribe Canina, the quality of the assembly is excellent, typically between the first and third depending on the parameter used, and a significant improvement on previously published genomes for the species. We hope this assembly will play an important role in future conservation efforts and comparative studies of canid genomes.}, }
@article {pmid39314892, year = {2024}, author = {Katirtzoglou, A and Rasmussen, JA and Schindler, DE and Limborg, MT}, title = {Intestinal microbial profiles of wild Alaskan rainbow trout (Oncorhynchus mykiss) characterized by 16S rRNA amplicon data.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {110902}, pmid = {39314892}, issn = {2352-3409}, abstract = {Rainbow trout (Oncorhynchus mykiss) is a dominant aquaculture species of the Salmonidae family, native only to the North Pacific. Recently, the gut microbiome has been shown to reflect the health status and responses to environmental changes in farmed fish. In this analysis we investigated the microbiome composition of the intestinal tract in 20 wild-caught rainbow trout specimens sampled in Alaska, USA. The targeted 16S rRNA gene (V3-V4 region) was sequenced on the Illumina NovaSeq 6000 platform. After quality control, demultiplexing and adapter trimming reads were analyzed using the DADA2 pipeline to obtain Amplicon Sequencing Variants (ASVs) which were subsequently taxonomically assigned. We found two phyla dominating the gut ecosystem present in every sample, Firmicutes and Fusobacteria, followed by lower abundances of Cyanobacteria, Proteobacteria and Bacteroidetes. At the genus level, we found high relative abundances of Cetobacterium and Clostridium sensu stricto 1. Interestingly, we did not identify often dominant genera Mycoplasma, Pseudomonas or Weisella which were prevalent in numerous studies previously, in cultured rainbow trout. Wild fish are exposed to a plethora of unpredictable environmental challenges, ranging from fluctuating water temperatures to variable food availability, as opposed to controlled conditions in production facilities. Examining and comparing the gut ecosystem of wild and reared individuals holds great potential in optimizing management practices for commercially important species. Microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention and increase sustainability in aquaculture production.}, }
@article {pmid39313563, year = {2024}, author = {Arnholdt-Schmitt, B and Noceda, C and Germano, TA and Aziz, S and Thiers, KLL and Oliveira, M and Bharadwaj, R and Mohanapriya, G and Sircar, D and Costa, JH}, title = {Validating alternative oxidase (AOX) gene family as efficient marker consortium for multiple-resilience in Xylella fastidiosa-infected Vitis holobionts.}, journal = {Plant cell reports}, volume = {43}, number = {10}, pages = {236}, pmid = {39313563}, issn = {1432-203X}, mesh = {*Xylella/genetics/physiology ; *Vitis/microbiology/genetics ; *Oxidoreductases/genetics/metabolism ; *Mitochondrial Proteins/genetics/metabolism ; *Plant Proteins/genetics/metabolism ; *Plant Diseases/microbiology/genetics ; Gene Expression Regulation, Plant ; Multigene Family ; Xylem/microbiology/genetics ; }, abstract = {AOX gene family in motion marks in-born efficiency of respiration adjustment; can serve for primer screening, genotype ranking, in vitro-plant discrimination and a SMART perspective for multiple-resilient plant holobiont selection. The bacteria Xylella fastidiosa (Xf) is a climate-dependent, global threat to many crops of high socio-economic value, including grapevine. Currently designed breeding strategies for Xf-tolerant or -resistant genotypes insufficiently address the danger of biodiversity loss by focusing on selected threats, neglecting future environmental conditions. Thus, breeding strategies should be validated across diverse populations and acknowledge temperature changes and drought by minimizing the metabolic-physiologic effects of multiple stress-induced oxygen shortages. This research hypothesizes that multiple-resilient plant holobionts achieve lifelong adaptive robustness through early molecular and metabolic responses in primary stress target cells, which facilitate efficient respiration adjustment and cell cycle down-regulation. To validate this concept open-access transcriptome data were analyzed of xylem tissues of Xf-tolerant and -resistant Vitis holobionts from diverse trials and genetic origins from early hours to longer periods after Xf-inoculation. The results indicated repetitive involvement of alternative oxidase (AOX) transcription in episodes of down-regulated transcripts of cytochrome c oxidase (COX) at various critical time points before disease symptoms emerged. The relation between transcript levels of COX and AOX ('relCOX/AOX') was found promising for plant discrimination and primer screening. Furthermore, transcript levels of xylem-harbored bacterial consortia indicated common regulation with Xf and revealed stress-induced early down-regulation and later enhancement. LPS priming promoted the earlier increase in bacterial transcripts after Xf-inoculation. This proof-of-principle study highlights a SMART perspective for AOX-assisted plant selection towards multiple-resilience that includes Xf-tolerance. It aims to support timely future plant diagnostics and in-field substitution, sustainable agro-management, which protects population diversity and strengthens both conventional breeding and high-tech, molecular breeding research. Furthermore, the results suggested early up-regulation of bacterial microbiota consortia in vascular-enriched tissues as a novel additional trait for future studies on Xf-tolerance.}, }
@article {pmid39311881, year = {2024}, author = {Isaac, P and Mutusamy, P and Yin, LS and Jing Wei, Y and Mohd Salleh, F and Bin Abu Bakar, MAL and Parimannan, S and Rajandas, H}, title = {Complete genome sequence of Serratia marcescens D1_6, isolated from peat soil.}, journal = {Microbiology resource announcements}, volume = {13}, number = {11}, pages = {e0029924}, pmid = {39311881}, issn = {2576-098X}, abstract = {We present a complete genome of Serratia marcescens D1_6 isolated from peat swamp forest. The complete genome for the isolate D1_6 was constructed using data from Oxford Nanopore Technologies and Illumina. The genome of D1_6 has a total length of 4,996,151 bp, comprising a chromosome and a plasmid.}, }
@article {pmid39304531, year = {2024}, author = {Umar, M and Merlin, TS and Puthiyedathu Sajeevan, T}, title = {Genomic insights into symbiosis and host adaptation of sponge-associated novel bacterium, Rossellomorea orangium sp. nov.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnae074}, pmid = {39304531}, issn = {1574-6968}, support = {BT/PR41474/NDB/39/760/2020//Higher Education Department, Government of Kerala/ ; 1422/2021/HEDN//Performance Linked Encouragement for Academic Studies and Endeavour (PLEASE)/ ; CUSAT/PL(UGC).A1/2314/2023//Rashtriya Uchchatar Shiksha Abhiyan/ ; //Kerala State Council for Science, Technology and Environment/ ; //University Grants Commission India/ ; }, mesh = {*Symbiosis ; *Porifera/microbiology ; Animals ; *Genome, Bacterial ; *Phylogeny ; Genomics ; Multigene Family ; Adaptation, Physiological ; Flavobacteriaceae/genetics/classification ; Secondary Metabolism ; Gene Transfer, Horizontal ; }, abstract = {Sponge-associated microorganisms play vital roles in marine sponge ecology. This study presents a genomic investigation of Rossellomorea sp. MCCB 382, isolated from Stelletta sp., reveals insights into its adaptations and symbiotic roles. Phylogenomic study and Overall Genomic Relatedness Index (OGRI) classify MCCB 382 as a novel species, Rossellomorea orangium sp. nov. The genome encodes numerous carbohydrate metabolism enzymes (CAZymes), likely aiding nutrient cycling in the sponge host. Unique eukaryotic-like protein domains hint at potential mechanisms of symbiosis. Defence mechanisms include CRISPR, restriction-modification systems, DNA phosphorothioation, toxin-antitoxin systems, and heavy metal and multidrug resistance genes, indicating adaptation to challenging marine environments. Unlike obligate mutualists, MCCB 382 shows no genome reduction. Furthermore, the presence of mobile genetic elements, horizontal gene transfer, and prophages suggest genetic versatility, implying flexible metabolic potential and capacity for rapid adaptation and symbiosis shifts. MCCB 382 possesses six biosynthetic gene clusters for secondary metabolites, including both type II and III polyketide synthases (PKS), terpenes, (NRPS), NRPS-independent-siderophore, and lassopeptide. Further genome mining using BiGScape revealed four distinct gene cluster families, T2PKS, NRPS-independent-siderophore, lasso peptide, and terpene, presenting opportunities for novel compound elucidation. Our study reveals a symbiotic lifestyle of MCCB 382 with the host sponge, highlighting symbiont factors that aid in establishing and sustaining this relationship. This is the pioneering genomic characterization of a novel Rossellomorea sp. within the sponge Stelletta sp. holobiont.}, }
@article {pmid39301440, year = {2024}, author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and ,  and ,  and ,  and , }, title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton &amp; E. Newton, 1876).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {378}, pmid = {39301440}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.}, }
@article {pmid39299961, year = {2024}, author = {Soltani, J and Sheikh-Ahmadi, A}, title = {Genomic and Chemical Evidence on Biosynthesis of Taxane Diterpenoids in Alternaria Isolates from Cupressaceae.}, journal = {Current microbiology}, volume = {81}, number = {11}, pages = {367}, pmid = {39299961}, issn = {1432-0991}, mesh = {*Alternaria/genetics/metabolism ; *Taxoids/metabolism ; *Biosynthetic Pathways/genetics ; Endophytes/metabolism/genetics/isolation &amp; purification/classification ; Bridged-Ring Compounds/metabolism ; Diterpenes/metabolism ; Paclitaxel/biosynthesis ; Fungal Proteins/genetics/metabolism ; Genomics ; Phylogeny ; }, abstract = {Alternaria species (Deuteromycetes, Ascomycota) as ubiquitous fungi and prolific producers of a variety of toxic compounds are a part of microbiomes of plants, humans, and animals, mainly causing disease, allergic reactions, and toxicosis. However, some species have also been reported as endophytic microorganisms with highly bioactive metabolites. Our previous results indicate that potentially endophytic Alternaria species from Cupressaceae produce bioactive metabolites that possibly contribute to plant holobiont's health. Here, a possible mechanism behind this bioactivity is elucidated. As some endophytic fungi are reported to produce cytotoxic taxane diterpenoids, eight potentially endophytic Alternaria isolates from our collection were analyzed for the presence of the key genes of the paclitaxel (Taxol) biosynthetic pathway, i.e., taxadin synthase (ts), 10-deacetylbaccatin III-10-O-acetyltransferase (dbat), and C-13-phenylpropanoid side-chain CoA acyltransferase (bapt). The presence of all genes, i.e., ts, dbat, and bapt, was detected by PCR in six isolates and dbat and bapt in two isolates. Chemical analyses of the fermentation broths by TLC and HPLC chromatography and IR spectroscopy indicated the synthesis of the final product, i.e., paclitaxel. So, we introduce the synthesis of taxane diterpenoids as a possible mechanism by which Alternaria occupies the plant niches and protects the plant holobiont in the presence of competing microorganisms.}, }
@article {pmid39294150, year = {2024}, author = {Wang, W and Song, W and Majzoub, ME and Feng, X and Xu, B and Tao, J and Zhu, Y and Li, Z and Qian, PY and Webster, NS and Thomas, T and Fan, L}, title = {Decoupling of strain- and intrastrain-level interactions of microbiomes in a sponge holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {8205}, pmid = {39294150}, issn = {2041-1723}, support = {42376113//National Natural Science Foundation of China (National Science Foundation of China)/ ; 91951120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42406103//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41776138//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31861143020//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Microbiota/genetics ; *Porifera/microbiology/virology ; *Symbiosis ; Genetic Variation ; Viruses/genetics/classification ; Phylogeny ; }, abstract = {Holobionts are highly organized assemblages of eukaryotic hosts, cellular microbial symbionts, and viruses, whose interactions and evolution involve complex biological processes. It is largely unknown which specific determinants drive similarity or individuality in genetic diversity between holobionts. Here, we combine short- and long-read sequencing and DNA-proximity-linkage technologies to investigate intraspecific diversity of the microbiomes, including host-resolved viruses, in individuals of a model marine sponge. We find strong impacts of the sponge host and the cellular hosts of viruses on strain-level organization of the holobiont, whereas substantial overlap in nucleotide diversity between holobionts suggests frequent exchanges of microbial cells and viruses at intrastrain level in the local sponge population. Immune-evasive arms races likely restricted virus-host co-evolution at the intrastrain level, generated holobiont-specific genome variations, and linked virus-host genetics through recombination. Our work shows that a decoupling of strain- and intrastrain-level interactions is a key factor in the genetic diversification of holobionts.}, }
@article {pmid39290662, year = {2024}, author = {Thormar, EA and Hansen, SB and Jørgensen, LVG and Limborg, MT}, title = {Sampling fish gut microbiota - A genome-resolved metagenomic approach.}, journal = {Ecology and evolution}, volume = {14}, number = {9}, pages = {e70302}, pmid = {39290662}, issn = {2045-7758}, abstract = {Despite a surge in microbiota-focused studies in teleosts, few have reported functional data on whole metagenomes as it has proven difficult to extract high biomass microbial DNA from fish intestinal samples. The zebrafish is a promising model organism in functional microbiota research, yet studies on the functional landscape of the zebrafish gut microbiota through shotgun based metagenomics remain scarce. Thus, a consensus on an appropriate sampling method accurately representing the zebrafish gut microbiota, or any fish species is lacking. Addressing this, we systematically tested four methods of sampling the zebrafish gut microbiota: collection of faeces from the tank, the whole gut, intestinal content, and the application of ventral pressure to facilitate extrusion of gut material. Additionally, we included water samples as an environmental control to address the potential influence of the environmental microbiota on each sample type. To compare these sampling methods, we employed a combination of genome-resolved metagenomics and 16S metabarcoding techniques. We observed differences among sample types on all levels including sampling, bioinformatic processing, metagenome co-assemblies, generation of metagenome-assembled genomes (MAGs), functional potential, MAG coverage, and population level microdiversity. Comparison to the environmental control highlighted the potential impact of the environmental contamination on data interpretation. While all sample types tested are informative about the zebrafish gut microbiota, the results show that optimal sample type for studying fish microbiomes depends on the specific objectives of the study, and here we provide a guide on what factors to consider for designing functional metagenome-based studies on teleost microbiomes.}, }
@article {pmid39262445, year = {2023}, author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA}, title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {926}, pmid = {39262445}, issn = {2046-1402}, support = {T32 GM139782/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; }, abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.}, }
@article {pmid39256870, year = {2024}, author = {Kløve, S and Stinson, SE and Romme, FO and Butt, J and Graversen, KB and Lund, MAV and Fonvig, CE and Waterboer, T and Perez-Perez, GI and Hansen, T and Holm, JC and Andersen, SB}, title = {Helicobacter pylori seropositivity associates with hyperglycemia, but not obesity, in Danish children and adolescents.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {379}, pmid = {39256870}, issn = {1741-7015}, mesh = {Humans ; Adolescent ; Child ; Denmark/epidemiology ; *Helicobacter pylori ; *Helicobacter Infections/epidemiology/blood ; Male ; Female ; *Hyperglycemia/epidemiology/blood ; Seroepidemiologic Studies ; Young Adult ; Pediatric Obesity/epidemiology/blood/microbiology ; Cohort Studies ; Body Mass Index ; Prevalence ; Blood Glucose/analysis ; }, abstract = {BACKGROUND: Helicobacter pylori colonizes the human stomach and may affect the inflammatory response, hormone production related to energy regulation, and gastrointestinal microbiota composition. Previous studies have explored a potential association between H. pylori infection and pediatric obesity with varying results. Considering the immunomodulatory effects of early-life infection with H. pylori that can confer beneficial effects, we hypothesized that we would find an inverse relationship between H. pylori seropositivity and obesity among Danish children and adolescents.<br><br>METHODS: We assessed H. pylori seroprevalence in 713 subjects from an obesity clinic cohort and 990 subjects from a population-based cohort, aged 6 to 19 years, and examined its association with obesity and other cardiometabolic risk factors.<br><br>RESULTS: No association was found between H. pylori and body mass index standard deviation score (BMI SDS). H. pylori seropositivity was, however, significantly associated with higher fasting plasma glucose levels and the prevalence of hyperglycemia.<br><br>CONCLUSION: While we did not find an association between H. pylori seropositivity and BMI SDS, we observed a significant association with higher fasting plasma&#xa0;glucose levels and increased prevalence of hyperglycemia, suggesting that H. pylori infection may contribute to impaired glucose regulation in Danish children and adolescents.}, }
@article {pmid39256139, year = {2024}, author = {Pepke, ML and Hansen, SB and Limborg, MT}, title = {Telomere dynamics as mediators of gut microbiota-host interactions.}, journal = {Trends in cell biology}, volume = {34}, number = {10}, pages = {805-808}, doi = {10.1016/j.tcb.2024.08.003}, pmid = {39256139}, issn = {1879-3088}, mesh = {Animals ; Humans ; Aging/metabolism ; *Gastrointestinal Microbiome ; *Telomere/metabolism ; }, abstract = {The highly proliferative gut tissue exhibits rapid telomere shortening with systemic effects on the host organism. Recent studies have demonstrated a bidirectionality in interactions between intestinal telomere length dynamics and the composition and activity of the gut microbiome thus linking processes of inflammation, dysbiosis and aging across different vertebrate species.}, }
@article {pmid39253787, year = {2024}, author = {Cheng, S and Gong, X and Xue, W and Kardol, P and Delgado-Baquerizo, M and Ling, N and Chen, X and Liu, M}, title = {Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.}, journal = {The New phytologist}, volume = {244}, number = {4}, pages = {1570-1584}, doi = {10.1111/nph.20118}, pmid = {39253787}, issn = {1469-8137}, support = {42077047//National Foundation of Sciences in China/ ; lzujbky-2022-ct04//Fundamental Research Funds for the Central University of China/ ; 2021YFD1700202//National Key R&amp;D program/ ; }, mesh = {*Nitrogen/metabolism ; *Rhizosphere ; *Microbiota ; *Phylogeny ; Biological Evolution ; Plants/microbiology/metabolism ; Soil Microbiology ; Species Specificity ; Quantitative Trait, Heritable ; }, abstract = {Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.}, }
@article {pmid39245169, year = {2024}, author = {Brulin, L and Ducrocq, S and Estellé, J and Even, G and Martel, S and Merlin, S and Audebert, C and Croiseau, P and Sanchez, MP}, title = {The fecal microbiota of Holstein cows is heritable and genetically correlated to dairy performances.}, journal = {Journal of dairy science}, volume = {107}, number = {12}, pages = {11254-11268}, doi = {10.3168/jds.2024-25003}, pmid = {39245169}, issn = {1525-3198}, mesh = {Animals ; Cattle ; *Feces/microbiology ; Female ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Phenotype ; }, abstract = {The fecal microbiota of ruminants constitutes a diversified community that has been phenotypically associated with a variety of host phenotypes, such as production and health. To gain a better understanding of the complex and interconnected factors that drive the fecal bacterial community, we have aimed to estimate the genetic parameters of the diversity and composition of the fecal microbiota, including heritabilities, genetic correlations among taxa, and genetic correlations between fecal microbiota features and host phenotypes. To achieve this, we analyzed a large population of 1,875 Holstein cows originating from 144 French commercial herds and routinely recorded for production, SCS, and fertility traits. Fecal samples were collected from the animals and subjected to 16S rRNA gene sequencing, with reads classified into amplicon sequence variants (ASV). The estimated α- and β-diversity indices (i.e., Observed Richness, Shannon index, Bray-Curtis and Jaccard dissimilarity matrices) and the abundances of ASV, genera, families, and phyla, normalized by centered-log ratio, were considered as phenotypes. Genetic parameters were calculated using either univariate or bivariate animal models. Heritabilities estimates, ranging from 0.08 to 0.31 for taxa abundances and β-diversity indices, highlight the influence of the host genetics on the composition of the fecal microbiota. Furthermore, genetic correlations estimated within the microbial community and between microbiota features and host traits reveal the complex networks linking all components of the fecal microbiota together and to their host, thus strengthening the holobiont concept. By estimating the heritabilities of microbiota-associated phenotypes, our study quantifies the impact of the host genetics on the fecal microbiota composition. In addition, genetic correlations between taxonomic groups and between taxa abundances and host performance suggest potential applications for selective breeding to improve host traits or promote a healthier microbiota.}, }
@article {pmid39242500, year = {2024}, author = {Zhang, Y and Zhang, Y and Tang, X and Guo, X and Yang, Q and Sun, H and Wang, H and Ling, J and Dong, J}, title = {A transcriptome-wide analysis provides novel insights into how Metabacillus indicus promotes coral larvae metamorphosis and settlement.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {840}, pmid = {39242500}, issn = {1471-2164}, support = {2022YFC3103602//National Key Research and Development Program of China/ ; 2022YFC3102003//National Key Research and Development Program of China/ ; 2022YFC3102004//National Key Research and Development Program of China/ ; 41976147//National Natural Science Foundation of China/ ; U2106208//National Natural Science Foundation of China-Shandong Joint Fund/ ; 2020B1212060058//Science and Technology Planning Project of Guangdong Province, China/ ; }, mesh = {Animals ; *Anthozoa/genetics/growth &amp; development/microbiology ; *Metamorphosis, Biological/genetics ; *Larva/growth &amp; development ; *Gene Expression Profiling ; Transcriptome ; Bacillaceae/genetics/growth &amp; development ; Coral Reefs ; }, abstract = {BACKGROUND: Coral reefs experience frequent and severe disturbances that can overwhelm their natural resilience. In such cases, ecological restoration is essential for coral reef recovery. Sexual reproduction has been reported to present the simplest and most cost-effective means for coral reef restoration. However, larval settlement and post-settlement survival represent bottlenecks for coral recruitment in sexual reproduction. While bacteria play a significant role in triggering coral metamorphosis and settlement in many coral species, the underlying molecular mechanisms remain largely unknown. In this study, we employed a transcriptome-level analysis to elucidate the intricate interactions between bacteria and coral larvae that are crucial for the settlement process.<br><br>RESULTS: High Metabacillus indicus strain cB07 inoculation densities resulted in the successful induction of metamorphosis and settlement of coral Pocillopora damicoris larvae. Compared with controls, inoculated coral larvae exhibited a pronounced increase in the abundance of strain cB07 during metamorphosis and settlement, followed by a significant decrease in total lipid contents during the settled stage. The differentially expressed genes (DEGs) during metamorphosis were significantly enriched in amino acid, protein, fatty acid, and glucose related metabolic pathways. In settled coral larvae induced by strain cB07, there was a significant enrichment of DEGs with essential roles in the establishment of a symbiotic relationship between coral larvae and their symbiotic partners. The photosynthetic efficiency of strain cB07 induced primary polyp holobionts was improved compared to those of the negative controls. In addition, coral primary polyps induced by strain cB07 showed significant improvements in energy storage and survival.<br><br>CONCLUSIONS: Our findings revealed that strain cB07 can promote coral larval settlement and enhance post-settlement survival and fitness. Manipulating coral sexual reproduction with strain cB07 can overcome the current recruitment bottleneck. This innovative approach holds promise for future coral reef restoration efforts.}, }
@article {pmid39228372, year = {2025}, author = {Alexandre, PA and Rodríguez-Ramilo, ST and Mach, N and Reverter, A}, title = {Combining genomics and semen microbiome increases the accuracy of predicting bull prolificacy.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {142}, number = {2}, pages = {237-250}, pmid = {39228372}, issn = {1439-0388}, support = {//CSIRO-INRAE linkage Travel Grant/ ; }, mesh = {Animals ; Male ; Cattle/genetics/microbiology/physiology ; *Genomics/methods ; *Semen/microbiology ; *Microbiota/genetics ; *Fertility/genetics ; Breeding ; Genotype ; Phenotype ; Pedigree ; }, abstract = {Commercial livestock producers need to prioritize genetic progress for health and efficiency traits to address productivity, welfare, and environmental concerns but face challenges due to limited pedigree information in extensive multi-sire breeding scenarios. Utilizing pooled DNA for genotyping and integrating seminal microbiome information into genomic models could enhance predictions of male fertility traits, thus addressing complexities in reproductive performance and inbreeding effects. Using the Angus Australia database comprising genotypes and pedigree data for 78,555 animals, we simulated percentage of normal sperm (PNS) and prolificacy of sires, resulting in 713 sires and 27,557 progeny in the final dataset. Publicly available microbiome data from 45 bulls was used to simulate data for the 713 sires. By incorporating both genomic and microbiome information our models were able to explain a larger proportion of phenotypic variation in both PNS (0.94) and prolificacy (0.56) compared to models using a single data source (e.g., 0.36 and 0.41, respectively, using only genomic information). Additionally, models containing both genomic and microbiome data revealed larger phenotypic differences between animals in the top and bottom quartile of predictions, indicating potential for improved productivity and sustainability in livestock farming systems. Inbreeding depression was observed to affect fertility traits, which makes the incorporation of microbiome information on the prediction of fertility traits even more actionable. Crucially, our inferences demonstrate the potential of the semen microbiome to contribute to the improvement of fertility traits in cattle and pave the way for the development of targeted microbiome interventions to improve reproductive performance in livestock.}, }
@article {pmid39228291, year = {2024}, author = {Martin, EJ and Speak, SA and Urban, L and Morales, HE and van Oosterhout, C}, title = {Sonification of Genomic Data to Represent Genetic Load in Zoo Populations.}, journal = {Zoo biology}, volume = {43}, number = {6}, pages = {513-519}, pmid = {39228291}, issn = {1098-2361}, support = {//E.J.M. was funded by East of Scotland Bioscience Doctoral Training Partnership (EASTBIO) funded by UKRI Biotechnology and Biological Sciences Research Council (BBSRC) Grant Number BB/M010996/1. C.v.O. was funded by the Royal Society International Collaboration Awards (ICA\R1\201194) and the Earth and Life Systems Alliance (ELSA), S.A.S. was funded by a NERC ARIES PhD studentship (T209447) at the UEA and a Research Training Support Grant (RTSG; 100162318RA1). H.M. was funded by an EMBO fellowship (grant 1111-2018) and the European Union's Horizon 2020 research and innovation program under Marie Sk&#x142;odowska-Curie (grant 840519)./ ; }, mesh = {Animals ; *Animals, Zoo/genetics ; Genetic Load ; Columbidae/genetics/physiology ; Genomics ; Endangered Species ; Humans ; Breeding ; }, abstract = {Maintaining a diverse gene pool is important in the captive management of zoo populations, especially in endangered species such as the pink pigeon (Nesoenas mayeri). However, due to the limited number of breeding individuals and relaxed natural selection, the loss of variation and accumulation of harmful variants is inevitable. Inbreeding results in a loss of fitness (i.e., inbreeding depression), principally because related parents are more likely to transmit a copy of the same recessive deleterious genetic variant to their offspring. Genomics-informed captive breeding can manage harmful variants by artificial selection, reducing the genetic load by avoiding the inheritance of two copies of the same harmful variant. To explain this concept in an interactive way to zoo visitors, we developed a sonification game to represent the fitness impacts of harmful variants by detuning notes in a familiar musical melody (i.e., Beethoven's Für Elise). Conceptually, zoo visitors play a game aiming to create the most optimal pink pigeon offspring in terms of inbreeding depression. They select virtual crosses between pink pigeon individuals and listen for the detuning of the melody, which represents the realised load of the resultant offspring. Here we present the sonification algorithm and the results of an online survey to see whether participants could identify the most and least optimal offspring from three potential pink pigeon offspring. Of our 98 respondents, 85 (86.7%) correctly identified the least optimal offspring, 73 (74.5%) correctly identified the most optimal, and 62 (63.3%) identified both the most and least optimal offspring using only the sonification.}, }
@article {pmid39221442, year = {2024}, author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and ,  and ,  and ,  and , }, title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).}, journal = {Wellcome open research}, volume = {9}, number = {}, pages = {312}, pmid = {39221442}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.}, }
@article {pmid39217744, year = {2025}, author = {Pylak, M and Oszust, K and Panek, J and Siegieda, D and Cybulska, J and Zdunek, A and Orzeł, A and Frąc, M}, title = {Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation.}, journal = {Food chemistry}, volume = {462}, number = {}, pages = {140943}, doi = {10.1016/j.foodchem.2024.140943}, pmid = {39217744}, issn = {1873-7072}, mesh = {*Soil Microbiology ; *Fruit/chemistry/microbiology/metabolism ; *Rubus/chemistry/microbiology/metabolism/growth &amp; development ; *Soil/chemistry ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification/growth &amp; development ; *Fungi/metabolism/growth &amp; development ; Agriculture ; Microbiota ; }, abstract = {Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.}, }
@article {pmid39216737, year = {2024}, author = {Chen, J and Yu, X and Yu, K and Chen, B and Qin, Z and Liao, Z and Ma, Y and Xu, L and Wang, Y}, title = {Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China.}, journal = {Environmental research}, volume = {262}, number = {Pt 1}, pages = {119848}, doi = {10.1016/j.envres.2024.119848}, pmid = {39216737}, issn = {1096-0953}, mesh = {*Anthozoa/microbiology/physiology ; Animals ; China ; Salinity ; Stress, Physiological ; Symbiosis ; Rain ; Floods ; Adaptation, Physiological ; Coral Reefs ; Microbiota ; }, abstract = {Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.}, }
@article {pmid39216249, year = {2024}, author = {Guo, D and Li, Z and Zhang, Y and Zhang, W and Wang, C and Zhang, DX and Liu, F and Gao, Z and Xu, B and Wang, N}, title = {The effect of lambda-cyhalothrin nanocapsules on the gut microbial communities and immune response of the bee elucidates the potential environmental impact of emerging nanopesticides.}, journal = {Journal of hazardous materials}, volume = {479}, number = {}, pages = {135650}, doi = {10.1016/j.jhazmat.2024.135650}, pmid = {39216249}, issn = {1873-3336}, mesh = {Animals ; Bees/drug effects/microbiology/immunology ; *Pyrethrins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Nitriles/toxicity ; *Insecticides/toxicity ; *Nanocapsules/toxicity ; Superoxide Dismutase/metabolism ; Catalase/metabolism ; }, abstract = {Emerging nanopesticides are gradually gaining widespread application in agriculture due to their excellent properties, but their potential risks to pollinating insects are not fully understood. In this study, lambda-cyhalothrin nanocapsules (LC-NCs) were constructed by electrostatic self-assembly method with iron mineralization optimization, and their effects on bee gut microbial communities and host immune-related factors were investigated. Microbiome sequencing revealed that LC-NCs increase the diversity of gut microbial communities and reduce the complexity of network features, disrupting the overall structure of the microbial communities. In addition, LC-NCs also had systemic effects on the immune response of bees, including increased activity of SOD and CAT enzymes and expression of their genes, as well as downregulation of Defensin1. Furthermore, we noticed that the immune system of the host was activated simultaneously with a rise in the abundance of beneficial bacteria in the gut. Our research emphasizes the importance of both the host and gut microbiota of holobiont in revealing the potential risks of LC-NCs to environmental indicators of honey bees, and provides references for exploring the interactions between host-microbiota systems under exogenous stress. At the same time, we hope that more research can focus on the potential impacts of nanopesticides on the ecological environment.}, }
@article {pmid39210412, year = {2024}, author = {Barnes, CJ and Bünner, MS and Ramírez-Flores, MR and Nielsen, IB and Ramos-Madrigal, J and Zharikova, D and McLaughlin, CM and Gilbert, MT and Sawers, RJH}, title = {The ancestral environment of teosinte populations shapes their root microbiome.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {64}, pmid = {39210412}, issn = {2524-6372}, abstract = {BACKGROUND: The composition of the root microbiome affects the host's growth, with variation in the host genome associated with microbiome variation. However, it is not known whether this intra-specific variation of root microbiomes is a consequence of plants performing targeted manipulations of them to adapt to their local environment or varying passively with other traits. To explore the relationship between the genome, environment and microbiome, we sampled seeds from teosinte populations across its native range in Mexico. We then grew teosinte accessions alongside two modern maize lines in a common garden experiment. Metabarcoding was performed using universal bacterial and fungal primers to profile their root microbiomes.<br><br>RESULTS: The root microbiome varied between the two modern maize lines and the teosinte accessions. We further found that variation of the teosinte genome, the ancestral environment (temperature/elevation) and root microbiome were all correlated. Multiple microbial groups significantly varied in relative abundance with temperature/elevation, with an increased abundance of bacteria associated with cold tolerance found in teosinte accessions taken from high elevations.<br><br>CONCLUSIONS: Our results suggest that variation in the root microbiome is pre-conditioned by the genome for the local environment (i.e. non-random). Ultimately, these claims would be strengthened by confirming that these differences in the root microbiome impact host phenotype, for example, by confirming that the root microbiomes of high-elevation teosinte populations enhance cold tolerance.}, }
@article {pmid39209587, year = {2024}, author = {Limborg, MT and Winther-Have, CS and Morueta-Holme, N and Gilbert, MTP and Rasmussen, JA}, title = {The overlooked biodiversity loss.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {10}, pages = {889-891}, doi = {10.1016/j.tree.2024.08.001}, pmid = {39209587}, issn = {1872-8383}, mesh = {Animals ; *Biodiversity ; Biological Coevolution ; Conservation of Natural Resources ; Ecosystem ; *Extinction, Biological ; Host Microbial Interactions ; Microbiota ; }, abstract = {As most life-forms exist as holobionts, reduction of host-level biodiversity drives parallel habitat losses to their host-adapted microorganisms. The holobiont concept helps us to understand how species are habitats for - often ignored - coevolved microorganisms also worthy of conservation. Indeed, loss of host-associated microbial biodiversity may accelerate the extinction risks of their host.}, }
@article {pmid39203380, year = {2024}, author = {Bai, C and Wang, Q and Xu, J and Zhang, H and Huang, Y and Cai, L and Zheng, X and Yang, M}, title = {Impact of Nutrient Enrichment on Community Structure and Co-Occurrence Networks of Coral Symbiotic Microbiota in Duncanopsammia peltata: Zooxanthellae, Bacteria, and Archaea.}, journal = {Microorganisms}, volume = {12}, number = {8}, pages = {}, pmid = {39203380}, issn = {2076-2607}, support = {2022YFC3102003//the National Key Research and Development Program of China/ ; 2022ZD01//the Fund of Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, MNR)/ ; 2019017//the Scientific Research Foundation of the Third Institute of Oceanography, Ministry of Natural Resources of China/ ; 41976127//the National Natural Science Foundation of China/ ; 2023J06043//the Fujian Provincial Natural Science Funds for Distinguished Young Scholar/ ; }, abstract = {Symbiotic microorganisms in reef-building corals, including algae, bacteria, archaea, fungi, and viruses, play critical roles in the adaptation of coral hosts to adverse environmental conditions. However, their adaptation and functional relationships in nutrient-rich environments have yet to be fully explored. This study investigated Duncanopsammia peltata and the surrounding seawater and sediments from protected and non-protected areas in the summer and winter in Dongshan Bay. High-throughput sequencing was used to characterize community changes, co-occurrence patterns, and factors influencing symbiotic coral microorganisms (zooxanthellae, bacteria, and archaea) in different environments. The results showed that nutrient enrichment in the protected and non-protected areas was the greatest in December, followed by the non-protected area in August. In contrast, the August protected area had the lowest nutrient enrichment. Significant differences were found in the composition of the bacterial and archaeal communities in seawater and sediments from different regions. Among the coral symbiotic microorganisms, the main dominant species of zooxanthellae is the C1 subspecies (42.22-56.35%). The dominant phyla of bacteria were Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota. Only in the August protected area did a large number (41.98%) of SAR324_cladeMarine_group_B exist. The August protected and non-protected areas and December protected and non-protected areas contained beneficial bacteria as biomarkers. They were Nisaea, Spiroplasma, Endozoicomonas, and Bacillus. No pathogenic bacteria appeared in the protected area in August. The dominant phylum in Archaea was Crenarchaeota. These symbiotic coral microorganisms' relative abundances and compositions vary with environmental changes. The enrichment of dissolved inorganic nitrogen in environmental media is a key factor affecting the composition of coral microbial communities. Co-occurrence analysis showed that nutrient enrichment under anthropogenic disturbances enhanced the interactions between coral symbiotic microorganisms. These findings improve our understanding of the adaptations of coral holobionts to various nutritional environments.}, }
@article {pmid39196422, year = {2024}, author = {Toloza-Moreno, DL and Yockteng, R and Pérez-Zuñiga, JI and Salinas-Castillo, C and Caro-Quintero, A}, title = {Implications of Domestication in Theobroma cacao L. Seed-Borne Microbial Endophytes Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {108}, pmid = {39196422}, issn = {1432-184X}, mesh = {*Cacao/microbiology ; *Endophytes/genetics/classification/isolation &amp; purification/physiology ; *Seeds/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Domestication ; Microbiota ; Fungi/genetics/classification/isolation &amp; purification ; Genotype ; Biodiversity ; }, abstract = {The study of plant-microbe interactions is a rapidly growing research field, with increasing attention to the role of seed-borne microbial endophytes in protecting the plant during its development from abiotic and biotic stresses. Recent evidence suggests that seed microbiota is crucial in establishing the plant microbial community, affecting its composition and structure, and influencing plant physiology and ecology. For Theobroma cacao L., the diversity and composition of vertically transmitted microbes have yet to be addressed in detail. We explored the composition and diversity of seed-borne endophytes in cacao pods of commercial genotypes (ICS95, IMC67), recently liberated genotypes from AGROSAVIA (TCS01, TCS19), and landraces from Tumaco (Colombia) (AC9, ROS1, ROS2), to evaluate microbial vertical transmission and establishment in various tissues during plant development. We observed a higher abundance of Pseudomonas and Pantoea genera in the landraces and AGROSAVIA genotypes, while the commercial genotypes presented a higher number of bacteria species but in low abundance. In addition, all the genotypes and plant tissues showed a high percentage of fungi of the genus Penicillium. These results indicate that domestication in cacao has increased bacterial endophyte diversity but has reduced their abundance. We isolated some of these seed-borne endophytes to evaluate their potential as growth promoters and found that Bacillus, Pantoea, and Pseudomonas strains presented high production of indole acetic acid and ACC deaminase activity. Our results suggest that cacao domestication could lead to the loss of essential bacteria for seedling establishment and development. This study improves our understanding of the relationship and interaction between perennial plants and seed-borne microbiota.}, }
@article {pmid39191812, year = {2024}, author = {Feng, Y and Wei, R and Chen, Q and Shang, T and Zhou, N and Wang, Z and Chen, Y and Chen, G and Zhang, G and Dong, K and Zhong, Y and Zhao, H and Hu, F and Zheng, H}, title = {Host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {72}, pmid = {39191812}, issn = {2055-5008}, mesh = {Animals ; *Host Specificity ; *Bacteriophages/genetics/physiology ; *Gastrointestinal Microbiome ; Bees/virology/microbiology ; *Bacteria/virology/genetics/classification ; *Phylogeny ; Metagenomics/methods ; Metagenome ; }, abstract = {Cophylogeny has been identified between gut bacteria and their animal host and is highly relevant to host health, but little research has extended to gut bacteriophages. Here we use bee model to investigate host specificity and cophylogeny in the "animal-gut bacteria-phage" tripartite system. Through metagenomic sequencing upon different bee species, the gut phageome revealed a more variable composition than the gut bacteriome. Nevertheless, the bacteriome and the phageome showed a significant association of their dissimilarity matrices, indicating a reciprocal interaction between the two kinds of communities. Most of the gut phages were host generalist at the viral cluster level but host specialist at the viral OTU level. While the dominant gut bacteria Gilliamella and Snodgrassella exhibited matched phylogeny with bee hosts, most of their phages showed a diminished level of cophylogeny. The evolutionary rates of the bee, the gut bacteria and the gut phages showed a remarkably increasing trend, including synonymous and non-synonymous substitution and gene content variation. For all of the three codiversified tripartite members, however, their genes under positive selection and genes involving gain/loss during evolution simultaneously enriched the functions into metabolism of nutrients, therefore highlighting the tripartite coevolution that results in an enhanced ecological fitness for the whole holobiont.}, }
@article {pmid39189963, year = {2025}, author = {Battilani, D and Gargiulo, R and Caniglia, R and Fabbri, E and Madrigal, JR and Fontsere, C and Ciucani, MM and Gopalakrishnan, S and Girardi, M and Fracasso, I and Mastroiaco, M and Ciucci, P and Vernesi, C}, title = {Beyond population size: Whole-genome data reveal bottleneck legacies in the peninsular Italian wolf.}, journal = {The Journal of heredity}, volume = {116}, number = {1}, pages = {10-23}, pmid = {39189963}, issn = {1465-7333}, support = {DOT1326JZS-17; CUP B85F21005360001//University of Rome "La Sapienza"/ ; }, mesh = {*Wolves/genetics ; Animals ; Italy ; *Population Density ; *Genetics, Population ; *Genetic Variation ; Inbreeding ; Genome ; Conservation of Natural Resources ; }, abstract = {Preserving genetic diversity and adaptive potential while avoiding inbreeding depression is crucial for the long-term conservation of natural populations. Despite demographic increases, traces of past bottleneck events at the genomic level should be carefully considered for population management. From this perspective, the peninsular Italian wolf is a paradigmatic case. After being on the brink of extinction in the late 1960s, peninsular Italian wolves rebounded and recolonized most of the peninsula aided by conservation measures, including habitat and legal protection. Notwithstanding their demographic recovery, a comprehensive understanding of the genomic consequences of the historical bottleneck in Italian wolves is still lacking. To fill this gap, we sequenced whole genomes of 13 individuals sampled in the core historical range of the species in Central Italy to conduct population genomic analyses, including a comparison with wolves from two highly-inbred wolf populations (i.e. Scandinavia and Isle Royale). We found that peninsular Italian wolves, despite their recent recovery, still exhibit relatively low genetic diversity, a small effective population size, signatures of inbreeding, and a non-negligible genetic load. Our findings indicate that the peninsular Italian wolf population is still susceptible to bottleneck legacies, which could lead to local inbreeding depression in case of population reduction or fragmentations. This study emphasizes the importance of considering key genetic parameters to design appropriate long-term conservation management plans.}, }
@article {pmid39189551, year = {2024}, author = {Poupin, MJ and González, B}, title = {Embracing complexity in plant-microbiome systems.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e70000}, pmid = {39189551}, issn = {1758-2229}, support = {ACT210052//Agencia Nacional de Investigaci&#xf3;n y Desarrollo PIA/ANILLOS/ ; NCN2021_010//Agencia Nacional de Investigaci&#xf3;n y Desarrollo-Millennium Science Initiative Program/ ; 1230472//Agencia Nacional de Investigaci&#xf3;n y Desarrollo - FONDECYT/ ; FB0002//Agencia NAcional de Investigaci&#xf3;n y Desarrollo - PIA/BASAL/ ; }, mesh = {*Microbiota ; *Plants/microbiology ; *Bacteria/genetics/classification ; Fungi/genetics/classification/physiology ; Archaea/classification/genetics ; Ecosystem ; }, abstract = {Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.}, }
@article {pmid39187231, year = {2024}, author = {Jefferson, T and Henley, EM and Erwin, PM and Lager, C and Perry, R and Chernikhova, D and Powell-Palm, MJ and Ushijima, B and Hagedorn, M}, title = {Evaluating the coral microbiome during cryopreservation.}, journal = {Cryobiology}, volume = {117}, number = {}, pages = {104960}, doi = {10.1016/j.cryobiol.2024.104960}, pmid = {39187231}, issn = {1090-2392}, mesh = {*Anthozoa/microbiology ; Animals ; *Cryopreservation/methods ; *Microbiota ; *Vitrification ; Coral Reefs ; Bacteria/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Coral reefs are threatened by various local and global stressors, including elevated ocean temperatures due to anthropogenic climate change. Coral cryopreservation could help secure the diversity of threatened corals. Recently, isochoric vitrification was used to demonstrate that coral fragments lived to 24 hr post-thaw; however, in this study, they were stressed post-thaw. The microbial portion of the coral holobiont has been shown to affect host fitness and the impact of cryopreservation treatment on coral microbiomes is unknown. Therefore, we examined the coral-associated bacterial communities pre- and post-cryopreservation treatments, with a view towards informing potential future stress reduction strategies. We characterized the microbiome of the Hawaiian finger coral, Porites compressa in the wild and at seven steps during the isochoric vitrification process. We observed significant changes in microbiome composition, including: 1) the natural wild microbiomes of P. compressa were dominated by Endozoicomonadaceae (76.5 % relative abundance) and consistent between samples, independent of collection location across Kāne'ohe Bay; 2) Endozoicomonadaceae were reduced to <6.9 % in captivity, and further reduced to <0.5 % relative abundance after isochoric vitrification; and 3) Vibrionaceae dominated communities post-thaw (58.5-74.7 % abundance). Thus, the capture and cryopreservation processes, are implicated as possible causal agents of dysbiosis characterized by the loss of putatively beneficial symbionts (Endozoicomonadaceae) and overgrowth of potential pathogens (Vibrionaceae). Offsetting these changes with probiotic restoration treatments may alleviate cryopreservation stress and improve post-thaw husbandry.}, }
@article {pmid39184395, year = {2024}, author = {Gastaldi, M and Pankey, MS and Svendsen, G and Medina, A and Firstater, F and Narvarte, M and Lozada, M and Lesser, M}, title = {Holobiont dysbiosis or acclimatation? Shift in the microbial taxonomic diversity and functional composition of a cosmopolitan sponge subjected to chronic pollution in a Patagonian bay.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17707}, pmid = {39184395}, issn = {2167-8359}, mesh = {Animals ; *Porifera/microbiology ; *Microbiota ; Argentina ; *Dysbiosis/microbiology ; Acclimatization ; Bays/microbiology ; Water Pollutants, Chemical/adverse effects/analysis ; }, abstract = {Dysbiosis and acclimatization are two starkly opposing outcomes of altered holobiont associations in response to environmental pollution. This study assesses whether shifts in microbial taxonomic composition and functional profiles of the cosmopolitan sponge Hymeniacidon perlevis indicate dysbiotic or acclimatized responses to water pollution. To do so, sponge and water samples were collected in a semi-enclosed environment (San Antonio Bay, Patagonia, Argentina) from variably polluted sites (i.e., eutrophication, heavy metal contamination). We found significant differences in the microbiome of H. perlevis with respect to the pollution history of the sites. Several indicators suggested that acclimatization, rather than dysbiosis, explained the microbiome response to higher pollution: 1) the distinction of the sponge microbiome from the water microbiome; 2) low similarity between the sponge and water microbiomes at the most polluted site; 3) the change in microbiome composition between sponges from the different sites; 4) a high similarity in the microbiome among sponge individuals within sites; 5) a similar ratio of common sponge microbes to opportunistic microbes between sponges at the most and least polluted sites; and 6) a distinctive functional profile of the sponge microbiome at the most polluted site. This profile indicated a more expansive metabolic repertoire, including the degradation of pollutants and the biosynthesis of secondary metabolites, suggesting a relevant role of these microbial communities in the adaptation of the holobiont to organic pollution. Our results shed light on the rearrangement of the H. perlevis microbiome that could allow it to successfully colonize sites with high anthropogenic impact while resisting dysbiosis.}, }
@article {pmid39165397, year = {2024}, author = {Jacob, M and Thomas, PK and Giebel, HA and Billerbeck, S and Simon, M and Striebel, M and Dlugosch, L}, title = {Cross-domain diversity effects: linking diatom species richness, intraspecific richness, and biomass production to host-associated bacterial diversity.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae046}, pmid = {39165397}, issn = {2730-6151}, abstract = {Interactions between bacteria and microalgae are important for the functioning of aquatic ecosystems, yet interactions based on the biodiversity of these two taxonomic domains have been scarcely studied. Specifically, it is unclear whether a positive biodiversity-productivity relationship in phytoplankton is largely facilitated by niche partitioning among the phytoplankton organisms themselves or whether associated bacterial communities play an additional role in modifying these diversity effects. Moreover, the effects of intraspecific diversity in phytoplankton communities on bacterial community diversity have not been tested. To address these points, we factorially manipulated both species and intraspecific richness of three diatoms to test the effects of diatom species/strain diversity on biomass production and bacterial diversity in algae-bacteria communities. The results show that diatom intraspecific diversity has significant positive effects on culture biomass and the diversity of the associated free-living bacterial community (0.2-3 μm size fraction), which are comparable in magnitude to species diversity effects. However, there were little to no effects of diatom diversity on host-associated bacterial diversity (>3 μm size fraction), or of bacterial diversity on biomass production. These results suggest a decoupling of bacterial diversity from the diatom diversity-productivity relationship and provide early insights regarding the relations between diversity across domains in aquatic ecosystems.}, }
@article {pmid39164135, year = {2025}, author = {Cook, LSJ and Briscoe, AG and Fonseca, VG and Boenigk, J and Woodward, G and Bass, D}, title = {Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment.}, journal = {Trends in microbiology}, volume = {33}, number = {1}, pages = {48-65}, doi = {10.1016/j.tim.2024.07.003}, pmid = {39164135}, issn = {1878-4380}, mesh = {Animals ; Bacteria/genetics/classification/metabolism ; *Biodiversity ; *DNA, Environmental ; *Ecosystem ; Environmental Monitoring ; Microbiota/genetics ; }, abstract = {Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.}, }
@article {pmid39163656, year = {2024}, author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q}, title = {Significant response of coral-associated bacteria and their carbohydrate-active enzymes diversity to coral bleaching.}, journal = {Marine environmental research}, volume = {201}, number = {}, pages = {106694}, doi = {10.1016/j.marenvres.2024.106694}, pmid = {39163656}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/enzymology ; Symbiosis ; Microbiota ; }, abstract = {Analysis of bacterial carbohydrate-active enzymes (CAZymes) contributes significantly to comprehending the response exhibited by coral symbionts to the external environment. This study explored the impact of bleaching on the bacteria and their CAZymes in coral Favites sp. through metagenomic sequencing. Notably, principal coordinates analysis (PCoA) unveiles substantial difference in bacterial communities between bleached and unbleached corals. Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidota, and Chloroflexi, exhibit noteworthy alterations during coral bleaching. CAZymes profiles in bleached coral disclosed a significant increase in Glycosyltransferases (GTs) abundance, suggesting an intensified biosynthesis of polysaccharides. Conversely, there is a marked reduction in other CAZymes abundance in bleached coral. Proteobacteria, Bacteroidota, Chlorobi, and Planctomycetota exhibit greater contributions to CAZymes in bleached corals, with Rhodobacterales, Cytophagales, Burkholderiales, Caulobacterales, and Hyphomicrobiales being the main contributors. While Acidobacteria, Actinobacteria, and Chloroflexi demonstrate higher contributions to CAZymes in unbleached corals. The changes in bacteria and their CAZymes reflect the ecological adaptability of coral holobionts when facing environmental stress. The alterations in CAZymes composition caused by bleaching events may have profound impacts on coral nutrient absorption and ecosystem stability. Therefore, understanding the dynamic changes in CAZymes is crucial for assessing the health and recovery potential of coral ecosystems.}, }
@article {pmid39151124, year = {2024}, author = {Katirtzoglou, A and Hansen, SB and Sveier, H and Martin, MD and Brealey, JC and Limborg, MT}, title = {Genomic context determines the effect of DNA methylation on gene expression in the gut epithelium of Atlantic salmon (Salmo salar).}, journal = {Epigenetics}, volume = {19}, number = {1}, pages = {2392049}, pmid = {39151124}, issn = {1559-2308}, mesh = {Animals ; *DNA Methylation ; *Salmo salar/genetics/metabolism ; *Epigenesis, Genetic ; Intestinal Mucosa/metabolism ; Transcription Initiation Site ; }, abstract = {The canonical view of DNA methylation, a pivotal epigenetic regulation mechanism in eukaryotes, dictates its role as a suppressor of gene activity, particularly within promoter regions. However, this view is being challenged as it is becoming increasingly evident that the connection between DNA methylation and gene expression varies depending on the genomic location and is therefore more complex than initially thought. We examined DNA methylation levels in the gut epithelium of Atlantic salmon (Salmo salar) using whole-genome bisulfite sequencing, which we correlated with gene expression data from RNA sequencing of the same gut tissue sample (RNA-seq). Assuming epigenetic signals might be pronounced between distinctive phenotypes, we compared large and small fish, finding 22 significant associations between 22 differentially methylated regions and 21 genes. We did not detect significant methylation differences between large and small fish. However, we observed a consistent signal of methylation levels around the transcription start sites (TSS), being negatively correlated with the expression levels of those genes. We found both negative and positive associations of methylation levels with gene expression further upstream or downstream of the TSS, revealing a more unpredictable pattern. The 21 genes showing significant methylation-expression correlations were involved in biological processes related to salmon health, such as growth and immune responses. Deciphering how DNA methylation affects the expression of such genes holds great potential for future applications. For instance, our results suggest the importance of genomic context in targeting epigenetic modifications to improve the welfare of aquaculture species like Atlantic salmon.}, }
@article {pmid39148013, year = {2024}, author = {Hoenicka, H and Bein, S and Starczak, M and Graf, W and Hanelt, D and Gackowski, D}, title = {β-Aminobutyric acid promotes stress tolerance, physiological adjustments, as well as broad epigenetic changes at DNA and RNA nucleobases in field elms (Ulmus minor).}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {779}, pmid = {39148013}, issn = {1471-2229}, mesh = {*Epigenesis, Genetic ; *RNA, Plant/genetics ; Stress, Physiological/genetics ; Aminobutyrates/pharmacology ; DNA, Plant/genetics ; }, abstract = {BACKGROUND: β-Aminobutyric acid (BABA) has been successfully used to prime stress resistance in numerous plant species; however, its effectiveness in forest trees has been poorly explored thus far. This study aimed to investigate the influence of BABA on morphological, physiological, and epigenetic parameters in field elms under various growth conditions. Epigenetic changes were assessed in both DNA and RNA through the use of reversed-phase ultra-performance liquid chromatography (UPLC) coupled with sensitive mass spectrometry.<br><br>RESULTS: The presented results confirm the influence of BABA on the development, physiology, and stress tolerance in field elms. However, the most important findings are related to the broad epigenetic changes promoted by this amino acid, which involve both DNA and RNA. Our findings confirm, for the first time, that BABA influences not only well-known epigenetic markers in plants, such as 5-methylcytosine, but also several other non-canonical nucleobases, such as 5-hydroxymethyluracil, 5-formylcytosine, 5-hydroxymethylcytosine, N6-methyladenine, uracil (in DNA) and thymine (in RNA). The significant effect on the levels of N6-methyladenine, the main bacterial epigenetic marker, is particularly noteworthy. In this case, the question arises as to whether this effect is due to epigenetic changes in the microbiome, the plant genome, or both.<br><br>CONCLUSIONS: The plant phenotype is the result of complex interactions between the plant's DNA, the microbiome, and the environment. We propose that different types of epigenetic changes in the plant and microbiome may play important roles in the largely unknown memory process that enables plants to adapt faster to changing environmental conditions.}, }
@article {pmid39137959, year = {2024}, author = {Saha, M and Dittami, SM and Chan, CX and Raina, JB and Stock, W and Ghaderiardakani, F and Valathuparambil Baby John, AM and Corr, S and Schleyer, G and Todd, J and Cardini, U and Bengtsson, MM and Prado, S and Skillings, D and Sonnenschein, EC and Engelen, AH and Wang, G and Wichard, T and Brodie, J and Leblanc, C and Egan, S}, title = {Progress and future directions for seaweed holobiont research.}, journal = {The New phytologist}, volume = {244}, number = {2}, pages = {364-376}, doi = {10.1111/nph.20018}, pmid = {39137959}, issn = {1469-8137}, support = {LT0028/2022-L//Human Frontier Science Programme/ ; ALTF 192-2021//European Molecular Biology Organization (EMBO) Postdoctoral Fellowship/ ; }, mesh = {*Seaweed/physiology/microbiology ; Symbiosis ; Research ; Ecosystem ; Microbiota ; }, abstract = {In the marine environment, seaweeds (i.e. marine macroalgae) provide a wide range of ecological services and economic benefits. Like land plants, seaweeds do not provide these services in isolation, rather they rely on their associated microbial communities, which together with the host form the seaweed holobiont. However, there is a poor understanding of the mechanisms shaping these complex seaweed-microbe interactions, and of the evolutionary processes underlying these interactions. Here, we identify the current research challenges and opportunities in the field of seaweed holobiont biology. We argue that identifying the key microbial partners, knowing how they are recruited, and understanding their specific function and their relevance across all seaweed life history stages are among the knowledge gaps that are particularly important to address, especially in the context of the environmental challenges threatening seaweeds. We further discuss future approaches to study seaweed holobionts, and how we can apply the holobiont concept to natural or engineered seaweed ecosystems.}, }
@article {pmid39128929, year = {2024}, author = {Nahor, O and Israel, &#xc1; and Barger, N and Rubin-Blum, M and Luzzatto-Knaan, T}, title = {Epiphytic microbiome associated with intertidal seaweeds in the Mediterranean Sea: comparative analysis of bacterial communities across seaweed phyla.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {18631}, pmid = {39128929}, issn = {2045-2322}, mesh = {Mediterranean Sea ; *Seaweed/microbiology/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Phylogeny ; Ecosystem ; }, abstract = {The complex interactions between epiphytic bacteria and marine macroalgae are still poorly understood, with limited knowledge about their community structure, interactions, and functions. This study focuses on comparing epiphytic prokaryotes community structure between three seaweed phyla; Chlorophyta, Rhodophyta, and Heterokontophyta in an easternmost rocky intertidal site of the Mediterranean Sea. By taking a snapshot approach and simultaneously collecting seaweed samples from the same habitat, we minimize environmental variations that could affect epiphytic bacterial assembly, thereby emphasizing host specificity. Through 16S rRNA gene amplicon sequencing, we identified that the microbial community composition was more similar within the same seaweed phylum host compared to seaweed host from other phyla. Furthermore, exclusive Amplicon Sequence Variants (ASVs) were identified for each algal phyla despite sharing higher taxonomic classifications across the other phyla. Analysis of niche breadth indices uncovers distinctive affinities and potential specialization among seaweed host phyla, with 39% of all ASVs identified as phylum specialists and 13% as generalists. Using taxonomy function prediction, we observed that the taxonomic variability does not significantly impact functional redundancy, suggesting resilience to disturbance. The study concludes that epiphytic bacteria composition is connected to host taxonomy, possibly influenced by shared morphological and chemical traits among genetically related hosts, implying a potential coevolutionary relationship between specific bacteria and their host seaweeds.}, }
@article {pmid39120056, year = {2024}, author = {Di Gesù, CM and Buffington, SA}, title = {The early life exposome and autism risk: a role for the maternal microbiome?.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2385117}, pmid = {39120056}, issn = {1949-0984}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; R01 HD109095/HD/NICHD NIH HHS/United States ; R01 HD109780/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/etiology ; Female ; Pregnancy ; Exposome ; Gastrointestinal Microbiome ; Risk Factors ; Genetic Predisposition to Disease ; Animals ; Autistic Disorder/etiology/microbiology ; }, abstract = {Autism spectrum disorders (ASD) are highly heritable, heterogeneous neurodevelopmental disorders characterized by clinical presentation of atypical social, communicative, and repetitive behaviors. Over the past 25 years, hundreds of ASD risk genes have been identified. Many converge on key molecular pathways, from translational control to those regulating synaptic structure and function. Despite these advances, therapeutic approaches remain elusive. Emerging data unearthing the relationship between genetics, microbes, and immunity in ASD suggest an integrative physiology approach could be paramount to delivering therapeutic breakthroughs. Indeed, the advent of large-scale multi-OMIC data acquisition, analysis, and interpretation is yielding an increasingly mechanistic understanding of ASD and underlying risk factors, revealing how genetic susceptibility interacts with microbial genetics, metabolism, epigenetic (re)programming, and immunity to influence neurodevelopment and behavioral outcomes. It is now possible to foresee exciting advancements in the treatment of some forms of ASD that could markedly improve quality of life and productivity for autistic individuals. Here, we highlight recent work revealing how gene X maternal exposome interactions influence risk for ASD, with emphasis on the intrauterine environment and fetal neurodevelopment, host-microbe interactions, and the evolving therapeutic landscape for ASD.}, }
@article {pmid39119491, year = {2024}, author = {Passera, A and Escudero-Martinez, C}, title = {Editorial: Genome and metagenome interactions in the plant holobiont for plant health and productivity.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1463795}, pmid = {39119491}, issn = {1664-462X}, }
@article {pmid39119209, year = {2024}, author = {Clokie, MRJ and Sicheritz-Pontén, T}, title = {Editorial June 2024.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {5}, number = {2}, pages = {43}, doi = {10.1089/phage.2024.0020}, pmid = {39119209}, issn = {2641-6549}, }
@article {pmid39116436, year = {2025}, author = {Voolstra, CR and Alderdice, R and Colin, L and Staab, S and Apprill, A and Raina, JB}, title = {Standardized Methods to Assess the Impacts of Thermal Stress on Coral Reef Marine Life.}, journal = {Annual review of marine science}, volume = {17}, number = {1}, pages = {193-226}, doi = {10.1146/annurev-marine-032223-024511}, pmid = {39116436}, issn = {1941-0611}, mesh = {Animals ; *Anthozoa/physiology ; Climate Change ; *Coral Reefs ; Global Warming ; *Heat-Shock Response/physiology ; Oceans and Seas ; Seawater/chemistry ; Stress, Physiological ; Temperature ; Environmental Monitoring/methods ; }, abstract = {The Earth's oceans have absorbed more than 90% of the excess, climate change-induced atmospheric heat. The resulting rise in oceanic temperatures affects all species and can lead to the collapse of marine ecosystems, including coral reefs. Here, we review the range of methods used to measure thermal stress impacts on reef-building corals, highlighting current standardization practices and necessary refinements to fast-track discoveries and improve interstudy comparisons. We also present technological developments that will undoubtedly enhance our ability to record and analyze standardized data. Although we use corals as an example, the methods described are widely employed in marine sciences, and our recommendations therefore apply to all species and ecosystems. Enhancing collaborative data collection efforts, implementing field-wide standardized protocols, and ensuring data availability through dedicated, openly accessible databases will enable large-scale analysis and monitoring of ecosystem changes, improving our predictive capacities and informing active intervention to mitigate climate change effects on marine life.}, }
@article {pmid39110680, year = {2024}, author = {Krishnakant Kushwaha, S and Wu, Y and Leonardo Avila, H and Anand, A and Sicheritz-Pontén, T and Millard, A and Amol Marathe, S and Nobrega, FL}, title = {Comprehensive blueprint of Salmonella genomic plasticity identifies hotspots for pathogenicity genes.}, journal = {PLoS biology}, volume = {22}, number = {8}, pages = {e3002746}, pmid = {39110680}, issn = {1545-7885}, mesh = {*Salmonella/genetics/pathogenicity ; *Genome, Bacterial/genetics ; Virulence/genetics ; Humans ; Genomics/methods ; Multigene Family ; Phylogeny ; Plasmids/genetics ; Salmonella Infections/microbiology ; Prophages/genetics ; Evolution, Molecular ; }, abstract = {Understanding the dynamic evolution of Salmonella is vital for effective bacterial infection management. This study explores the role of the flexible genome, organised in regions of genomic plasticity (RGP), in shaping the pathogenicity of Salmonella lineages. Through comprehensive genomic analysis of 12,244 Salmonella spp. genomes covering 2 species, 6 subspecies, and 46 serovars, we uncover distinct integration patterns of pathogenicity-related gene clusters into RGP, challenging traditional views of gene distribution. These RGP exhibit distinct preferences for specific genomic spots, and the presence or absence of such spots across Salmonella lineages profoundly shapes strain pathogenicity. RGP preferences are guided by conserved flanking genes surrounding integration spots, implicating their involvement in regulatory networks and functional synergies with integrated gene clusters. Additionally, we emphasise the multifaceted contributions of plasmids and prophages to the pathogenicity of diverse Salmonella lineages. Overall, this study provides a comprehensive blueprint of the pathogenicity potential of Salmonella. This unique insight identifies genomic spots in nonpathogenic lineages that hold the potential for harbouring pathogenicity genes, providing a foundation for predicting future adaptations and developing targeted strategies against emerging human pathogenic strains.}, }
@article {pmid39107841, year = {2024}, author = {Murphy, RM and Sinotte, VM and Cuesta-Maté, A and Renelies-Hamilton, J and Lenz-Strube, M and Poulsen, M}, title = {Shaping the tripartite symbiosis: are termite microbiome functions directed by the environmentally acquired fungal cultivar?.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {44}, pmid = {39107841}, issn = {2524-4671}, abstract = {Microbiome assembly critically impacts the ability of hosts to access beneficial symbiont functions. Fungus-farming termites have co-evolved with a fungal cultivar as a primary food source and complex gut microbiomes, which collectively perform complementary degradation of plant biomass. A large subset of the bacterial community residing within termite guts are inherited (vertically transmitted) from parental colonies, while the fungal symbiont is, in most termite species, acquired from the environment (horizontally transmitted). It has remained unknown how the gut microbiota sustains incipient colonies prior to the acquisition of the fungal cultivar, and how, if at all, bacterial contributions are modulated by fungus garden establishment. Here, we test the latter by determining the composition and predicted functions of the gut microbiome using metabarcoding and shotgun metagenomics, respectively. We focus our functional predictions on bacterial carbohydrate-active enzyme and nitrogen cycling genes and verify compositional patterns of the former through enzyme activity assays. Our findings reveal that the vast majority of microbial functions are encoded in the inherited microbiome, and that the establishment of fungal gardens incurs only minor modulations of predicted bacterial capacities for carbohydrate and nitrogen metabolism. While we cannot rule out that other symbiont functions are gained post-fungus garden establishment, our findings suggest that fungus-farming termite hosts are equipped with a near-complete set of gut microbiome functions at the earliest stages of colony life. This inherited, incipient bacterial microbiome likely contributes to the high extent of functional specificity and coevolution observed between termite hosts, gut microbiomes, and the fungal cultivar.}, }
@article {pmid39095694, year = {2024}, author = {He, X and Zou, J and Chen, Q and Qin, X and Liu, Y and Zeng, L and Su, H}, title = {Microbial and transcriptional response of Acropora valida and Turbinaria peltata to Vibrio coralliilyticus challenge: insights into corals disease resistance.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {288}, pmid = {39095694}, issn = {1471-2180}, mesh = {*Anthozoa/microbiology/genetics/immunology ; Animals ; *Vibrio/genetics ; *Disease Resistance/genetics ; Symbiosis/genetics ; Microbiota/genetics ; Coral Reefs ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Coral diseases are significant drivers of global coral reef degradation, with pathogens dominated by Vibrio coralliilyticus playing a prominent role in the development of coral diseases. Coral phenotype, symbiotic microbial communities, and host transcriptional regulation have been well-established as factors involved in determining coral disease resistance, but the underlying mechanisms remain incompletely understood.<br><br>METHODS: This study employs high-throughput sequencing to analyse the symbiotic microbial and transcriptional response of the hosts in order to evaluate the disease resistance of Acropora valida and Turbinaria peltata exposed to Vibrio coralliilyticus.<br><br>RESULTS: A. valida exhibited pronounced bleaching and tissue loss within 7&#xa0;h of pathogen infection, whereas T. peltata showed no signs of disease throughout the experiment. Microbial diversity analyses revealed that T. peltata had a more flexible microbial community and a higher relative abundance of potential beneficial bacteria compared to A. valida. Although Vibrio inoculation resulted in a more significant decrease in the Symbiodiniaceae density of A. valida compared to that of T. peltata, it did not lead to recombination of the coral host and Symbiodiniaceae in either coral species. RNA-seq analysis revealed that the interspecific differences in the transcriptional regulation of hosts after Vibrio inoculation. Differentially expressed genes in A. valida were mainly enriched in the pathways associated with energy supply and immune response, such as G protein-coupled receptor signaling, toll-like receptor signaling, regulation of TOR signaling, while these genes in T. peltata were mainly involved in the pathway related to immune homeostasis and ion transport, such as JAK-STAT signaling pathway and regulation of ion transport.<br><br>CONCLUSIONS: Pathogenic challenges elicit different microbial and transcriptional shifts across coral species. This study offers novel insights into molecular mechanisms of coral resistance to disease.}, }
@article {pmid39090391, year = {2024}, author = {Sun, PF and Lu, MR and Liu, YC and Shaw, BJP and Lin, CP and Chen, HW and Lin, YF and Hoh, DZ and Ke, HM and Wang, IF and Lu, MJ and Young, EB and Millett, J and Kirschner, R and Lin, YJ and Chen, YL and Tsai, IJ}, title = {An acidophilic fungus promotes prey digestion in a carnivorous plant.}, journal = {Nature microbiology}, volume = {9}, number = {10}, pages = {2522-2537}, pmid = {39090391}, issn = {2058-5276}, mesh = {*Drosera/metabolism ; Animals ; *Symbiosis ; *Plant Leaves/microbiology/metabolism ; Carnivorous Plant/metabolism/genetics ; Oxylipins/metabolism ; Insecta/microbiology ; Cyclopentanes/metabolism ; Transcriptome ; Carnivory ; Fungi/genetics/metabolism/classification ; }, abstract = {Leaves of the carnivorous sundew plants (Drosera spp.) secrete mucilage that hosts microorganisms, but whether this microbiota contributes to prey digestion is unclear. We identified the acidophilic fungus Acrodontium crateriforme as the dominant species in the mucilage microbial communities, thriving in multiple sundew species across the global range. The fungus grows and sporulates on sundew glands as its preferred acidic environment, and its presence in traps increased the prey digestion process. A. crateriforme has a reduced genome similar to other symbiotic fungi. During A. crateriforme-Drosera spatulata coexistence and digestion of prey insects, transcriptomes revealed significant gene co-option in both partners. Holobiont expression patterns during prey digestion further revealed synergistic effects in several gene families including fungal aspartic and sedolisin peptidases, facilitating prey digestion in leaves, as well as nutrient assimilation and jasmonate signalling pathway expression. This study establishes that botanical carnivory is defined by adaptations involving microbial partners and interspecies interactions.}, }
@article {pmid39089083, year = {2024}, author = {Duret, M and Wallner, A and Buée, M and Aziz, A}, title = {Rhizosphere microbiome assembly, drivers and functions in perennial ligneous plant health.}, journal = {Microbiological research}, volume = {287}, number = {}, pages = {127860}, doi = {10.1016/j.micres.2024.127860}, pmid = {39089083}, issn = {1618-0623}, mesh = {*Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Plant Roots/microbiology ; *Plants/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/physiology ; }, abstract = {Plants shape and interact continuously with their rhizospheric microbiota, which play a key role in plant health and resilience. However, plant-associated microbial community can be shaped by several factors including plant phenotype and cropping system. Thus, understanding the interplay between microbiome assembly during the onset of plant-pathogen interactions and long-lasting resistance traits in ligneous plants remains a major challenge. To date, such attempts were mainly investigated in herbaceous plants, due to their phenotypic characteristics and their short life cycle. However, only few studies have focused on the microbial structure, dynamic and their drivers in perennial ligneous plants. Ligneous plants coevolved in interaction with specific fungal and bacterial communities that differ from those of annual plants. The specificities of such ligneous plants in shaping their own functional microbial communities could be dependent on their high heterozygosis, physiological and molecular status associated to seasonality and their aging processes, root system and above-ground architectures, long-lasting climatic variations, and specific cultural practices. This article provides an overview of the specific characteristics of perennial ligneous plants that are likely to modulate symbiotic interactions in the rhizosphere, thus affecting the plant's fitness and systemic immunity. Plant and microbial traits contributing to the establishment of plant-microbiome interactions and the adaptation of this holobiont are also discussed.}, }
@article {pmid39076113, year = {2024}, author = {Ruggeri, M and Million, WC and Hamilton, L and Kenkel, CD}, title = {Microhabitat acclimatization alters sea anemone-algal symbiosis and thermal tolerance across the intertidal zone.}, journal = {Ecology}, volume = {105}, number = {9}, pages = {e4388}, doi = {10.1002/ecy.4388}, pmid = {39076113}, issn = {1939-9170}, support = {//USC Wrigley Institute for Environmental Studies/ ; //Wrigley Bakus Fellowship/ ; //Wrigley Summer Fellowship/ ; //Victoria J. Bertics Fellowship/ ; }, mesh = {*Symbiosis ; Animals ; *Sea Anemones/physiology ; *Ecosystem ; Acclimatization/physiology ; Thermotolerance ; Microalgae/physiology ; }, abstract = {Contemporary symbioses in extreme environments can give an insight into mechanisms that stabilize species interactions during environmental change. The intertidal sea anemone, Anthopleura elegantissima, engages in a nutritional symbiosis with microalgae similar to tropical coral, but withstands more intense environmental fluctuations during tidal inundations. In this study, we compare baseline symbiotic traits and their sensitivity to thermal stress within and among anemone aggregations across the intertidal using a laboratory-based tank experiment to better understand how fixed genotypic and plastic environmental effects contribute to the successful maintenance of this symbiosis in extreme habitats. High intertidal anemones had lower baseline symbiont-to-host cell ratios under control conditions, but their symbionts had higher baseline photosynthetic efficiency compared to low intertidal anemone symbionts. Symbiont communities were identical across all samples, suggesting that shifts in symbiont density and photosynthetic performance could be an acclimatory mechanism to maintain symbiosis in different environments. Despite lower baseline symbiont-to-host cell ratios, high intertidal anemones maintained greater symbiont-to-host cell ratios under heat stress compared with low intertidal anemones, suggesting greater thermal tolerance of high intertidal holobionts. However, the thermal tolerance of clonal anemones acclimatized to different zones was not explained by tidal height alone, indicating additional environmental variables contribute to physiological differences. Host genotype significantly influenced anemone weight, but only explained a minor proportion of variation among symbiotic traits and their response to thermal stress, further implicating environmental history as the primary driver of holobiont tolerance. These results indicate that this symbiosis is highly plastic and may be able to acclimatize to climate change over ecological timescales, defying the convention that symbiotic organisms are more susceptible to environmental stress.}, }
@article {pmid39072987, year = {2024}, author = {Yan, G and Wei, T and Lan, Y and Xu, T and Qian, P}, title = {Different parts of the mussel Gigantidas haimaensis holobiont responded differently to deep-sea sampling stress.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12881}, pmid = {39072987}, issn = {1749-4877}, support = {2019B030302004//Major Project of Basic and Applied Basic Research of Guangdong Province/ ; 2021HJ01//PI project of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 16101822//HKSAR government/ ; C2013-22G//HKSAR government/ ; }, abstract = {Acute environmental changes cause stress during conventional deep-sea biological sampling without in situ fixation and affect gene expressions of samples collected. However, the degree of influence and underlying mechanisms are hardly investigated. Here, we conducted comparative transcriptomic analyses between in situ and onboard fixed gills and between in situ and onboard fixed mantles of deep-sea mussel Gigantidas haimaensis to assess the effects of incidental sampling stress. Results showed that transcription, translation, and energy metabolism were upregulated in onboard fixed gills and mantles, thereby mobilizing rapid gene expression to tackle the stress. Autophagy and phagocytosis that related to symbiotic interactions between the host and endosymbiont were downregulated in the onboard fixed gills. These findings demonstrated that symbiotic gill and nonsymbiotic mantle responded differently to sampling stress, and symbiosis in the gill was perturbed. Further comparative metatranscriptomic analysis between in situ and onboard fixed gills revealed that stress response genes, peptidoglycan biosynthesis, and methane fixation were upregulated in the onboard fixed endosymbiotic Gammaproteobacteria inside the gills, implying that energy metabolism of the endosymbiont was increased to cope with sampling stress. Furthermore, comparative analysis between the mussel G. haimaensis and the limpet Bathyacmaea lactea transcriptomes resultedidentified six transcription factor orthologs upregulated in both onboard fixed mussel mantles and limpets, including sharply increased early growth response protein 1 and Kruppel-like factor 5. They potentially play key roles in initiating the response of sampled deep-sea macrobenthos to sampling stress. Our results clearly show that in situ fixed biological samples are vital for studying deep-sea environmental adaptation.}, }
@article {pmid39071805, year = {2024}, author = {Gilbert, SF}, title = {Inter-kingdom communication and the sympoietic way of life.}, journal = {Frontiers in cell and developmental biology}, volume = {12}, number = {}, pages = {1427798}, pmid = {39071805}, issn = {2296-634X}, abstract = {Organisms are now seen as holobionts, consortia of several species that interact metabolically such that they sustain and scaffold each other's existence and propagation. Sympoiesis, the development of the symbiotic relationships that form holobionts, is critical for our understanding the origins and maintenance of biodiversity. Rather than being the read-out of a single genome, development has been found to be sympoietic, based on multigenomic interactions between zygote-derived cells and symbiotic microbes. These symbiotic and sympoietic interactions are predicated on the ability of cells from different kingdoms of life (e.g., bacteria and animals) to communicate with one another and to have their chemical signals interpreted in a manner that facilitates development. Sympoiesis, the creation of an entity by the interactions of other entities, is commonly seen in embryogenesis (e.g., the creation of lenses and retinas through the interaction of brain and epidermal compartments). In holobiont sympoiesis, interactions between partners of different domains of life interact to form organs and biofilms, wherein each of these domains acts as the environment for the other. If evolution is forged by changes in development, and if symbionts are routinely involved in our development, then changes in sympoiesis can constitute an important factor in evolution.}, }
@article {pmid39066224, year = {2024}, author = {Caetano-Anollés, G}, title = {Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment.}, journal = {Viruses}, volume = {16}, number = {7}, pages = {}, pmid = {39066224}, issn = {1999-4915}, support = {ILLU-802-909 and ILLU-483-625//National Institute of Food and Agriculture/ ; Illinois Campus Cluster Program (ICCP), and Blue Waters supercomputing allocations//National Center for Supercomputing Applications/ ; }, mesh = {*Phylogeny ; *Viruses/genetics/classification ; *Genome, Viral ; *Evolution, Molecular ; *Protein Domains ; Genomics/methods ; }, abstract = {Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.}, }
@article {pmid39047050, year = {2024}, author = {Marzinelli, EM and Thomas, T and Vadillo Gonzalez, S and Egan, S and Steinberg, PD}, title = {Seaweeds as holobionts: Current state, challenges, and potential applications.}, journal = {Journal of phycology}, volume = {60}, number = {4}, pages = {785-796}, doi = {10.1111/jpy.13485}, pmid = {39047050}, issn = {1529-8817}, mesh = {*Seaweed ; *Microbiota ; Symbiosis ; }, abstract = {Seaweeds play a strong ecological and economical role along the world's coastlines, where they support industries (e.g., aquaculture, bioproducts) and essential ecosystem services (e.g., biodiversity, fisheries, carbon capture). Evidence from wild and cultured seaweeds suggests that microorganisms play crucial roles in their health and functioning, prompting the need for considering seaweeds and their microbiome as a coherent entity or "holobiont." Here we show that the number of studies investigating seaweed hosts and their microbiome have increased in the last two decades. This likely reflects the increase in the appreciation of the importance of microbiomes for eukaryotic hosts, improved molecular approaches used to characterize their interactions, and increasing interest in commercial use of seaweeds. However, although increasing, most studies of seaweed holobionts have focused on (i) a few seaweed species of ecological or commercial significance, (ii) interactions involving only bacteria, and (iii) descriptive rather than experimental approaches. The relatively few experimental studies have mostly focused on manipulating abiotic factors to examine responses of seaweeds and their microbiome. Of the few studies that directly manipulated microorganisms to investigate their effects on seaweeds, most were done in laboratory or aquaria. We emphasize the need to move beyond the descriptions of patterns to experimental approaches for understanding causation and mechanisms. We argue that such experimental approaches are necessary for a better understanding of seaweed holobionts, for management actions for wild and cultivated seaweeds, and to better integrate studies of seaweed holobionts with the broader fields of seaweed ecology and biology, which are strongly experimental.}, }
@article {pmid39037435, year = {2024}, author = {Liu, X and Liu, S and Yu, Z and Guo, X and Zhang, R and Sun, H and Zhang, Y}, title = {Cognatishimia coralii sp. nov., a marine bacterium isolated from seawater surrounding corals.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {7}, pages = {}, doi = {10.1099/ijsem.0.006467}, pmid = {39037435}, issn = {1466-5034}, mesh = {*Anthozoa/microbiology ; *Phylogeny ; *Seawater/microbiology ; *Base Composition ; *RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; *Fatty Acids/analysis ; Animals ; China ; *Bacterial Typing Techniques ; *Sequence Analysis, DNA ; *Coral Reefs ; Ubiquinone/analogs &amp; derivatives ; Nucleic Acid Hybridization ; }, abstract = {Coral reefs are declining due to the rising seawater temperature. Bacteria within and surrounding corals play key roles in maintaining the homeostasis of the coral holobiont. Research on coral-related bacteria could provide benefits for coral reef restoration. During the isolation of coral-associated bacteria, a Gram-stain-negative, motile bacterium (D5M38[T]) was isolated from seawater surrounding corals in Daya Bay, Shenzhen, PR China. Phylogenetic analysis revealed that strain D5M38[T] represents a novel species in the genus Cognatishimia. The temperature range for strain D5M38[T] growth was 10-40 °C, and the optimum temperature was 37 °C. The salinity range for the growth of this isolate was from 0 to 4.0 %, with an optimal salinity level of 0.5 %. The pH range necessary for strain D5M38[T] growth was between pH 5.0 and 9.0, with an optimal pH being 7.5. The predominant fatty acid was summed feature 8 (65.0 %). The major respiratory quinone was Q-10. The DNA G+C content was 56.8 %. The genome size was 3.88 Mb. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain D5M38[T] and its two closest neighbours, Cognatishimia activa LMG 29900[T] and Cognatishimia maritima KCTC 23347[T], were 73.2/73.6%, 73.2/73.6% and 19.7/19.5%, respectively. Strain D5M38[T] was clearly distinct from its closest neighbours C. activa LMG 29900[T] and C. maritima KCTC 23347[T], with 16S rRNA gene sequence similarity values of 97.5 and 97.3 %, respectively. The phylogenetic analysis, along with the ANI, AAI, and dDDH values, demonstrated that strain D5M38[T] is a member of the genus Cognatishimia, and is distinct from the other two recognized species within this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain D5M38[T]. Thus, strain D5M38[T] is considered to be classified as representing a novel species in the genus Cognatishimia, for which the name Cognatishimia coralii sp. nov. is proposed. The type strain is D5M38[T] (=MCCC 1K08692[T]=KCTC 8160[T]).}, }
@article {pmid39036359, year = {2024}, author = {Rolli, E and Ghitti, E and Mapelli, F and Borin, S}, title = {Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1429096}, pmid = {39036359}, issn = {1664-462X}, abstract = {INTRODUCTION: The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.<br><br>METHODS: Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.<br><br>RESULTS: Arabidopsis exposure to 70 &#xb5;M PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-&#x3b2;-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.<br><br>DISCUSSION: These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.}, }
@article {pmid39030686, year = {2024}, author = {Wallace, BA and Varona, NS and Hesketh-Best, PJ and Stiffler, AK and Silveira, CB}, title = {Globally distributed bacteriophage genomes reveal mechanisms of tripartite phage-bacteria-coral interactions.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39030686}, issn = {1751-7370}, support = {UM PRA 2022-2547//University of Miami Provost Research Award/ ; 2023353157//National Science Foundation Graduate Research Fellowship Program/ ; //University of Miami Holmes Fellowship/ ; //Kushlan Graduate Research Support Award/ ; 2023349872//NSF Graduate Research Fellowship Program/ ; //University of Miami Dean's Fellowship/ ; PG015171//Maytag Fellowship/ ; 80NSSC23K0676//National Aeronautics and Space Administration Exobiology Program/ ; }, mesh = {*Bacteriophages/genetics/isolation &amp; purification/classification ; *Anthozoa/virology/microbiology ; *Genome, Viral ; Animals ; *Bacteria/virology/genetics/classification ; Metagenome ; Symbiosis ; Coral Reefs ; Virome/genetics ; Prophages/genetics ; }, abstract = {Reef-building corals depend on an intricate community of microorganisms for functioning and resilience. The infection of coral-associated bacteria by bacteriophages can modify bacterial ecological interactions, yet very little is known about phage functions in the holobiont. This gap stems from methodological limitations that have prevented the recovery of high-quality viral genomes and bacterial host assignment from coral samples. Here, we introduce a size fractionation approach that increased bacterial and viral recovery in coral metagenomes by 9-fold and 2-fold, respectively, and enabled the assembly and binning of bacterial and viral genomes at relatively low sequencing coverage. We combined these viral genomes with those derived from 677 publicly available metagenomes, viromes, and bacterial isolates from stony corals to build a global coral virus database of over 20,000 viral genomic sequences spanning four viral realms. The tailed bacteriophage families Kyanoviridae and Autographiviridae were the most abundant, replacing groups formerly referred to as Myoviridae and Podoviridae, respectively. Prophage and CRISPR spacer linkages between these viruses and 626 bacterial metagenome-assembled genomes and bacterial isolates showed that most viruses infected Alphaproteobacteria, the most abundant class, and less abundant taxa like Halanaerobiia and Bacteroidia. A host-phage-gene network identified keystone viruses with the genomic capacity to modulate bacterial metabolic pathways and direct molecular interactions with eukaryotic cells. This study reveals the genomic basis of nested symbioses between bacteriophage, bacteria, and the coral host and its endosymbiotic algae.}, }
@article {pmid39030648, year = {2024}, author = {Moretti, LG and Crusciol, CAC and Leite, MFA and Momesso, L and Bossolani, JW and Costa, OYA and Hungria, M and Kuramae, EE}, title = {Diverse bacterial consortia: key drivers of rhizosoil fertility modulating microbiome functions, plant physiology, nutrition, and soybean grain yield.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {50}, pmid = {39030648}, issn = {2524-6372}, support = {2016/23699-8; 2018/14892-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 151120/2020-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {Soybean cultivation in tropical regions relies on symbioses with nitrogen-fixing Bradyrhizobium and plant growth-promoting bacteria (PGPBs), reducing environmental impacts of N fertilizers and pesticides. We evaluate the effects of soybean inoculation with different bacterial consortia combined with PGPBs or microbial secondary metabolites (MSMs) on rhizosoil chemistry, plant physiology, plant nutrition, grain yield, and rhizosphere microbial functions under field conditions over three growing seasons with four treatments: standard inoculation of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens consortium (SI); SI plus foliar spraying with Bacillus subtilis (SI + Bs); SI plus foliar spraying with Azospirillum brasilense (SI + Az); and SI plus seed application of MSMs enriched in lipo-chitooligosaccharides extracted from B. diazoefficiens and Rhizobium tropici (SI + MSM). Rhizosphere microbial composition, diversity, and function was assessed by metagenomics. The relationships between rhizosoil chemistry, plant nutrition, grain yield, and the abundance of microbial taxa and functions were determined by generalized joint attribute modeling. The bacterial consortia had the most significant impact on rhizosphere soil fertility, which in turn affected the bacterial community, plant physiology, nutrient availability, and production. Cluster analysis identified microbial groups and functions correlated with shifts in rhizosoil chemistry and plant nutrition. Bacterial consortia positively modulated specific genera and functional pathways involved in biosynthesis of plant secondary metabolites, amino acids, lipopolysaccharides, photosynthesis, bacterial secretion systems, and sulfur metabolism. The effects of the bacterial consortia on the soybean holobiont, particularly the rhizomicrobiome and rhizosoil fertility, highlight the importance of selecting appropriate consortia for desired outcomes. These findings have implications for microbial-based agricultural practices that enhance crop productivity, quality, and sustainability.}, }
@article {pmid39030484, year = {2024}, author = {Siegieda, D and Panek, J and Frąc, M}, title = {Ecological processes of bacterial microbiome assembly in healthy and dysbiotic strawberry farms.}, journal = {BMC plant biology}, volume = {24}, number = {1}, pages = {692}, pmid = {39030484}, issn = {1471-2229}, support = {BIOSTRATEG3/344433/16/NCBR/2018//Narodowe Centrum Bada&#x144; i Rozwoju/ ; }, mesh = {*Fragaria/microbiology ; *Microbiota ; *Soil Microbiology ; *Rhizosphere ; *Bacteria/classification/genetics ; Plant Roots/microbiology ; Plant Shoots/microbiology ; Farms ; }, abstract = {The bacterial microbiome plays crucial role in plants' resistance to diseases, nutrient uptake and productivity. We examined the microbiome characteristics of healthy and unhealthy strawberry farms, focusing on soil (bulk soil, rhizosphere soil) and plant (roots and shoots). The relative abundance of most abundant taxa were correlated with the chemical soil properties and shoot niche revealed the least amount of significant correlations between the two. While alpha and beta diversities did not show differences between health groups, we identified a number of core taxa (16-59) and marker bacterial taxa for each healthy (Unclassified Tepidisphaerales, Ohtaekwangia, Hydrocarboniphaga) and dysbiotic (Udaeobacter, Solibacter, Unclassified Chitinophagales, Unclassified Nitrosomonadaceae, Nitrospira, Nocardioides, Tardiphaga, Skermanella, Pseudomonas, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Curtobacterium) niche. We also revealed selective pressure of strawberry rhizosphere soil and roots plants in unhealthy plantations increased stochastic ecological processes of bacterial microbiome assembly in shoots. Our findings contribute to understanding sustainable agriculture and plant-microbiome interactions.}, }
@article {pmid39030351, year = {2024}, author = {Gong, S and Liang, J and Xu, L and Wang, Y and Li, J and Jin, X and Yu, K and Zhang, Y}, title = {Diel transcriptional responses of coral-Symbiodiniaceae holobiont to elevated temperature.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {882}, pmid = {39030351}, issn = {2399-3642}, mesh = {*Anthozoa/genetics/physiology ; Animals ; *Symbiosis ; Circadian Rhythm/genetics ; Transcription, Genetic ; Hot Temperature ; Dinoflagellida/genetics/physiology ; Temperature ; }, abstract = {Coral exhibits diel rhythms in behavior and gene transcription. However, the influence of elevated temperature, a key factor causing coral bleaching, on these rhythms remains poorly understood. To address this, we examined physiological, metabolic, and gene transcription oscillations in the Acropora tenuis-Cladocopium sp. holobiont under constant darkness (DD), light-dark cycle (LD), and LD with elevated temperature (HLD). Under LD, the values of photosystem II efficiency, reactive oxygen species leakage, and lipid peroxidation exhibited significant diel oscillations. These oscillations were further amplified during coral bleaching under HLD. Gene transcription analysis identified 24-hour rhythms for specific genes in both coral and Symbiodiniaceae under LD. Notably, these rhythms were disrupted in coral and shifted in Symbiodiniaceae under HLD. Importantly, we identified over 20 clock or clock-controlled genes in this holobiont. Specifically, we suggested CIPC (CLOCK-interacting pacemaker-like) gene as a core clock gene in coral. We observed that the transcription of two abundant rhythmic genes encoding glycoside hydrolases (CBM21) and heme-binding protein (SOUL) were dysregulated by elevated temperature. These findings indicate that elevated temperatures disrupt diel gene transcription rhythms in the coral-Symbiodiniaceae holobiont, affecting essential symbiosis processes, such as carbohydrate utilization and redox homeostasis. These disruptions may contribute to the thermal bleaching of coral.}, }
@article {pmid39026872, year = {2024}, author = {Ostridge, HJ and Fontsere, C and Lizano, E and Soto, DC and Schmidt, JM and Saxena, V and Alvarez-Estape, M and Barratt, CD and Gratton, P and Bocksberger, G and Lester, JD and Dieguez, P and Agbor, A and Angedakin, S and Assumang, AK and Bailey, E and Barubiyo, D and Bessone, M and Brazzola, G and Chancellor, R and Cohen, H and Coupland, C and Danquah, E and Deschner, T and Dotras, L and Dupain, J and Egbe, VE and Granjon, AC and Head, J and Hedwig, D and Hermans, V and Hernandez-Aguilar, RA and Jeffery, KJ and Jones, S and Junker, J and Kadam, P and Kaiser, M and Kalan, AK and Kambere, M and Kienast, I and Kujirakwinja, D and Langergraber, KE and Lapuente, J and Larson, B and Laudisoit, A and Lee, KC and Llana, M and Maretti, G and Martín, R and Meier, A and Morgan, D and Neil, E and Nicholl, S and Nixon, S and Normand, E and Orbell, C and Ormsby, LJ and Orume, R and Pacheco, L and Preece, J and Regnaut, S and Robbins, MM and Rundus, A and Sanz, C and Sciaky, L and Sommer, V and Stewart, FA and Tagg, N and Tédonzong, LR and van Schijndel, J and Vendras, E and Wessling, EG and Willie, J and Wittig, RM and Yuh, YG and Yurkiw, K and Vigilant, L and Piel, A and Boesch, C and Kühl, HS and Dennis, MY and Marques-Bonet, T and Arandjelovic, M and Andrés, AM}, title = {Local genetic adaptation to habitat in wild chimpanzees.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39026872}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; DP2 MH119424/MH/NIMH NIH HHS/United States ; R01 MH132818/MH/NIMH NIH HHS/United States ; }, abstract = {How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees.}, }
@article {pmid38999024, year = {2024}, author = {Schwarcz, S and Nyerges, P and Bíró, TI and Janka, E and Bai, P and Mikó, E}, title = {Cytostatic Bacterial Metabolites Interfere with 5-Fluorouracil, Doxorubicin and Paclitaxel Efficiency in 4T1 Breast Cancer Cells.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {13}, pages = {}, pmid = {38999024}, issn = {1420-3049}, support = {FK128387, K142141, TKP2021-EGA-19, TKP-EGA-20//NKFIH/ ; POST-COVID2021-33//Grant from the Hungarian Academy of Sciences/ ; &#xda;NKP-23-3-II-DE-151, &#xda;NKP-23-3-I-DE-184, &#xda;NKP-23-4-II-DE-172//&#xda;NKP-23/ ; }, mesh = {*Paclitaxel/pharmacology ; *Fluorouracil/pharmacology ; *Doxorubicin/pharmacology ; *Breast Neoplasms/drug therapy/metabolism/pathology ; Female ; *Cytostatic Agents/pharmacology ; *Cell Proliferation/drug effects ; Cell Line, Tumor ; Humans ; Mice ; Animals ; Bacteria/drug effects/metabolism ; Antineoplastic Agents/pharmacology ; Indoles/pharmacology ; }, abstract = {The microbiome is capable of modulating the bioavailability of chemotherapy drugs, mainly due to metabolizing these agents. Multiple cytostatic bacterial metabolites were recently identified that have cytostatic effects on cancer cells. In this study, we addressed the question of whether a set of cytostatic bacterial metabolites (cadaverine, indolepropionic acid and indoxylsulfate) can interfere with the cytostatic effects of the chemotherapy agents used in the management of breast cancer (doxorubicin, gemcitabine, irinotecan, methotrexate, rucaparib, 5-fluorouracil and paclitaxel). The chemotherapy drugs were applied in a wide concentration range to which a bacterial metabolite was added in a concentration within its serum reference range, and the effects on cell proliferation were assessed. There was no interference between gemcitabine, irinotecan, methotrexate or rucaparib and the bacterial metabolites. Nevertheless, cadaverine and indolepropionic acid modulated the Hill coefficient of the inhibitory curve of doxorubicin and 5-fluorouracil. Changes to the Hill coefficient implicate alterations to the kinetics of the binding of the chemotherapy agents to their targets. These effects have an unpredictable significance from the clinical or pharmacological perspective. Importantly, indolepropionic acid decreased the IC50 value of paclitaxel, which is a potentially advantageous combination.}, }
@article {pmid38996487, year = {2024}, author = {Sandoval-Velasco, M and Dudchenko, O and Rodríguez, JA and Pérez Estrada, C and Dehasque, M and Fontsere, C and Mak, SST and Khan, R and Contessoto, VG and Oliveira Junior, AB and Kalluchi, A and Zubillaga Herrera, BJ and Jeong, J and Roy, RP and Christopher, I and Weisz, D and Omer, AD and Batra, SS and Shamim, MS and Durand, NC and O'Connell, B and Roca, AL and Plikus, MV and Kusliy, MA and Romanenko, SA and Lemskaya, NA and Serdyukova, NA and Modina, SA and Perelman, PL and Kizilova, EA and Baiborodin, SI and Rubtsov, NB and Machol, G and Rath, K and Mahajan, R and Kaur, P and Gnirke, A and Garcia-Treviño, I and Coke, R and Flanagan, JP and Pletch, K and Ruiz-Herrera, A and Plotnikov, V and Pavlov, IS and Pavlova, NI and Protopopov, AV and Di Pierro, M and Graphodatsky, AS and Lander, ES and Rowley, MJ and Wolynes, PG and Onuchic, JN and Dalén, L and Marti-Renom, MA and Gilbert, MTP and Aiden, EL}, title = {Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3541-3562.e51}, doi = {10.1016/j.cell.2024.06.002}, pmid = {38996487}, issn = {1097-4172}, support = {R35 GM146852/GM/NIGMS NIH HHS/United States ; R35 GM147467/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Mammoths/genetics ; *Genome/genetics ; Female ; *Skin ; Elephants/genetics ; Chromatin/genetics ; Fossils ; DNA, Ancient/analysis ; Mice ; Humans ; X Chromosome/genetics ; }, abstract = {Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus primigenius) that died 52,000 years ago retained its ancient genome architecture. We use PaleoHi-C to map chromatin contacts and assemble its genome, yielding 28 chromosome-length scaffolds. Chromosome territories, compartments, loops, Barr bodies, and inactive X chromosome (Xi) superdomains persist. The active and inactive genome compartments in mammoth skin more closely resemble Asian elephant skin than other elephant tissues. Our analyses uncover new biology. Differences in compartmentalization reveal genes whose transcription was potentially altered in mammoths vs. elephants. Mammoth Xi has a tetradic architecture, not bipartite like human and mouse. We hypothesize that, shortly after this mammoth's death, the sample spontaneously freeze-dried in the Siberian cold, leading to a glass transition that preserved subfossils of ancient chromosomes at nanometer scale.}, }
@article {pmid38989465, year = {2024}, author = {Nanetti, E and Scicchitano, D and Palladino, G and Interino, N and Corlatti, L and Pedrotti, L and Zanetti, F and Pagani, E and Esposito, E and Brambilla, A and Grignolio, S and Marotti, I and Turroni, S and Fiori, J and Rampelli, S and Candela, M}, title = {The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.}, journal = {iScience}, volume = {27}, number = {7}, pages = {110194}, pmid = {38989465}, issn = {2589-0042}, abstract = {Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.}, }
@article {pmid38986611, year = {2024}, author = {Odriozola, I and Rasmussen, JA and Gilbert, MTP and Limborg, MT and Alberdi, A}, title = {A practical introduction to holo-omics.}, journal = {Cell reports methods}, volume = {4}, number = {7}, pages = {100820}, pmid = {38986611}, issn = {2667-2375}, mesh = {Humans ; *Microbiota ; Metabolomics ; Genomics ; Proteomics/methods ; Computational Biology/methods ; Animals ; Host Microbial Interactions/genetics ; }, abstract = {Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.}, }
@article {pmid38981551, year = {2024}, author = {Roik, A and Wall, M and Dobelmann, M and Nietzer, S and Brefeld, D and Fiesinger, A and Reverter, M and Schupp, PJ and Jackson, M and Rutsch, M and Strahl, J}, title = {Trade-offs in a reef-building coral after six years of thermal acclimation.}, journal = {The Science of the total environment}, volume = {949}, number = {}, pages = {174589}, doi = {10.1016/j.scitotenv.2024.174589}, pmid = {38981551}, issn = {1879-1026}, mesh = {*Anthozoa/physiology ; Animals ; *Coral Reefs ; *Acclimatization/physiology ; Temperature ; }, abstract = {There is growing evidence that reef-building corals can acclimate to novel and challenging thermal conditions. However, potential trade-offs that accompany acclimation remain largely unexplored. We investigated physiological trade-offs in colonies of a globally abundant coral species (Pocillopora acuta) that were acclimated ex situ to an elevated temperature of 31 °C (i.e., 1 °C above their bleaching threshold) for six years. By comparing them to conspecifics maintained at a cooler temperature, we found that the energy storage of corals was prioritized over skeletal growth at the elevated temperature. This was associated with the formation of higher density skeletons, lower calcification rates and consequently lower skeletal extension rates, which entails ramifications for future reef-building processes, structural complexity and reef community composition. Furthermore, symbionts were physiologically compromised at 31 °C and had overall lower energy reserves, likely due to increased exploitation by their host, resulting in an overall lower stress resilience of the holobiont. Our study shows how biological trade-offs of thermal acclimation unfold, helping to refine our picture of future coral reef trajectories. Importantly, our observations in this six-year study do not align with observations of short-term studies, where elevated temperatures were often associated with the depletion of energy reserves, highlighting the importance of studying acclimation of organisms at relevant biological scales.}, }
@article {pmid38979873, year = {2024}, author = {Chávez-González, JD and Flores-Núñez, VM and Merino-Espinoza, IU and Partida-Martínez, LP}, title = {Desert plants, arbuscular mycorrhizal fungi and associated bacteria: Exploring the diversity and role of symbiosis under drought.}, journal = {Environmental microbiology reports}, volume = {16}, number = {4}, pages = {e13300}, pmid = {38979873}, issn = {1758-2229}, support = {//CONAHCYT (Consejo Nacional de Humanidades Ciencias y Tecnologias)/ ; A1-S-9889//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; IDEAGTO/CONV/014/2022//IDEA GTO/ ; }, mesh = {*Mycorrhizae/physiology/classification/genetics ; *Symbiosis ; *Droughts ; *Desert Climate ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Agave/microbiology ; Biodiversity ; Plant Roots/microbiology ; }, abstract = {Desert plants, such as Agave tequilana, A. salmiana and Myrtillocactus geometrizans, can survive harsh environmental conditions partly due to their symbiotic relationships with microorganisms, including arbuscular mycorrhizal fungi (AMF). Interestingly, some of these fungi also harbour endosymbiotic bacteria. Our research focused on investigating the diversity of these AMFs and their associated bacteria in these plants growing in arid soil. We found that agaves have a threefold higher AMF colonization than M. geometrizans. Metabarcoding techniques revealed that the composition of AMF communities was primarily influenced by the plant host, while the bacterial communities were more affected by the specific plant compartment or niche they inhabited. We identified both known and novel endofungal bacterial taxa, including Burkholderiales, and confirmed their presence within AMF spores using multiphoton microscopy. Our study also explored the effects of drought on the symbiosis between A. tequilana and AMF. We discovered that the severity of drought conditions could modulate the strength of this symbiosis and its outcomes for the plant holobiont. Severe drought conditions prevented the formation of this symbiosis, while moderate drought conditions promoted it, thereby conferring drought tolerance in A. tequilana. This research sheds light on the diversity of AMF and associated bacteria in Crassulacean Acid Metabolism (CAM) plants and underscores the crucial role of drought as a factor modulating the symbiosis between A. tequilana and AMF. Further research is needed to understand the role of endofungal bacteria in this response.}, }
@article {pmid38974189, year = {2024}, author = {Cham, AK and Adams, AK and Wadl, PA and Ojeda-Zacarías, MDC and Rutter, WB and Jackson, DM and Shoemaker, DD and Yencho, GC and Olukolu, BA}, title = {Metagenome-enabled models improve genomic predictive ability and identification of herbivory-limiting genes in sweetpotato.}, journal = {Horticulture research}, volume = {11}, number = {7}, pages = {uhae135}, pmid = {38974189}, issn = {2662-6810}, abstract = {Plant-insect interactions are often influenced by host- or insect-associated metagenomic community members. The relative abundance of insects and the microbes that modulate their interactions were obtained from sweetpotato (Ipomoea batatas) leaf-associated metagenomes using quantitative reduced representation sequencing and strain/species-level profiling with the Qmatey software. Positive correlations were found between whitefly (Bemisia tabaci) and its endosymbionts (Candidatus Hamiltonella defensa, Candidatus Portiera aleyrodidarum, and Rickettsia spp.) and negative correlations with nitrogen-fixing bacteria that implicate nitric oxide in sweetpotato-whitefly interaction. Genome-wide associations using 252 975 dosage-based markers, and metagenomes as a covariate to reduce false positive rates, implicated ethylene and cell wall modification in sweetpotato-whitefly interaction. The predictive abilities (PA) for whitefly and Ocypus olens abundance were high in both populations (68%-69% and 33.3%-35.8%, respectively) and 69.9% for Frankliniella occidentalis. The metagBLUP (gBLUP) prediction model, which fits the background metagenome-based Cao dissimilarity matrix instead of the marker-based relationship matrix (G-matrix), revealed moderate PA (35.3%-49.1%) except for O. olens (3%-10.1%). A significant gain in PA after modeling the metagenome as a covariate (gGBLUP, ≤11%) confirms quantification accuracy and that the metagenome modulates phenotypic expression and might account for the missing heritability problem. Significant gains in PA were also revealed after fitting allele dosage (≤17.4%) and dominance effects (≤4.6%). Pseudo-diploidized genotype data underperformed for dominance models. Including segregation-distorted loci (SDL) increased PA by 6%-17.1%, suggesting that traits associated with fitness cost might benefit from the inclusion of SDL. Our findings confirm the holobiont theory of host-metagenome co-evolution and underscore its potential for breeding within the context of G × G × E interactions.}, }
@article {pmid38972908, year = {2024}, author = {Ma, C and Xu, C and Zhang, T and Mu, Q and Lv, J and Xing, Q and Yang, Z and Xu, Z and Guan, Y and Chen, C and Ni, K and Dai, X and Ding, W and Hu, J and Bao, Z and Wang, S and Liu, P}, title = {Tracking the hologenome dynamics in aquatic invertebrates by the holo-2bRAD approach.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {827}, pmid = {38972908}, issn = {2399-3642}, support = {32130107//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Aquatic Organisms/genetics ; Invertebrates/genetics/physiology ; Microbiota ; Polymorphism, Single Nucleotide ; }, abstract = {The "hologenome" concept is an increasingly popular way of thinking about microbiome-host for marine organisms. However, it is challenging to track hologenome dynamics because of the large amount of material, with tracking itself usually resulting in damage or death of the research object. Here we show the simple and efficient holo-2bRAD approach for the tracking of hologenome dynamics in marine invertebrates (i.e., scallop and shrimp) from one holo-2bRAD library. The stable performance of our approach was shown with high genotyping accuracy of 99.91% and a high correlation of r > 0.99 for the species-level profiling of microorganisms. To explore the host-microbe association underlying mass mortality events of bivalve larvae, core microbial species changed with the stages were found, and two potentially associated host SNPs were identified. Overall, our research provides a powerful tool with various advantages (e.g., cost-effective, simple, and applicable for challenging samples) in genetic, ecological, and evolutionary studies.}, }
@article {pmid38965478, year = {2024}, author = {Yang, J and Woo, JJ and Sesal, C and Gökalsın, B and Eldem, V and Açıkgöz, B and Başaran, TI and Kurtuluş, G and Hur, JS}, title = {Continental scale comparison of mycobiomes in Parmelia and Peltigera lichens from Turkey and South Korea.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {243}, pmid = {38965478}, issn = {1471-2180}, support = {NRF-2021K2A9A1A06086000//National Research Foundation of Korea/ ; 2023R1A6C101B022//Korea Basic Science Institute/ ; 221N004//Turkish Technological Research Council/ ; }, mesh = {*Mycobiome ; Republic of Korea ; Turkey ; *Lichens/microbiology/classification ; *DNA, Fungal/genetics ; Ascomycota/classification/isolation &amp; purification/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Fungi/classification/isolation &amp; purification/genetics ; Parmeliaceae/genetics ; }, abstract = {BACKGROUND: Lichens, traditionally considered as a simple partnership primarily between mycobiont and photobiont, are, in reality, complex holobionts comprised of a multitude of microorganisms. Lichen mycobiome represents fungal community residing within lichen thalli. While it is acknowledged that factors like the host lichen species and environmental conditions influence the structure of the lichen mycobiome, the existing research remains insufficient. To investigate which factor, host genus or location, has a greater impact on the lichen mycobiome, we conducted a comparative analysis of mycobiomes within Parmelia and Peltigera collected from both Turkey and South Korea, using high-throughput sequencing based on internal transcribed spacer region amplification.<br><br>RESULTS: Overall, the lichen mycobiome was dominated by Capnodiales (Dothideomycetes), regardless of host or location. At the order level, the taxonomic composition was not significantly different according to lichen genus host or geographical distance. Hierarchical clustering of the top 100 abundant ASVs did not clearly indicate whether the lichen mycobiome was more influenced by host genus or location. Analyses of community similarity and partitioning variables revealed that the structure of the lichen mycobiome is more significantly influenced by location than by host genus. When analyzing the core mycobiome by host genus, the Peltigera mycobiome contained more ASV members than the Parmelia mycobiome. These two core mycobiomes also share common fungal strains, including basidiomycete yeast. Additionally, we used chi-squared tests to identify host genus-specialists and location-specialists.<br><br>CONCLUSIONS: By comparing lichen mycobiomes of the same genera across different countries, our study advances our comprehension of these microbial communities. Our study elucidates that, although host species play a contributory role, geographic distance exerts a more pronounced impact on the structure of lichen mycobiome. We have made foundational contributions to understanding the lichen mycobiome occupying ecologically crucial niches. We anticipate that broader global-scale investigations into the fungal community structures will provide more detailed insights into fungal residents within lichens.}, }
@article {pmid38964709, year = {2024}, author = {Williams, CE and Fontaine, SS}, title = {Commentary: The microbial dependence continuum: Towards a comparative physiology approach to understand host reliance on microbes.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {296}, number = {}, pages = {111690}, doi = {10.1016/j.cbpa.2024.111690}, pmid = {38964709}, issn = {1531-4332}, mesh = {Animals ; Biological Evolution ; Herbivory ; Host Microbial Interactions/physiology ; *Microbiota/physiology ; Physiology, Comparative ; }, abstract = {Comparative physiologists often compare physiological traits across organisms to understand the selective pressures influencing their evolution in different environments. Traditionally focused on the organisms themselves, comparative physiology has more recently incorporated studies of the microbiome-the communities of microbes living in and on animals that influence host physiology. In this commentary, we describe the utility of applying a comparative framework to study the microbiome, particularly in understanding how hosts vary in their dependence on microbial communities for physiological function, a concept we term the "microbial dependence continuum". This hypothesis suggests that hosts exist on a spectrum ranging from high to low reliance on their microbiota. Certain physiological traits may be highly dependent on microbes for proper function in some species but microbially independent in others. Comparative physiology can elucidate the selective pressures driving species along this continuum. Here, we discuss the microbial dependence continuum in detail and how comparative physiology can be useful to study it. Then, we discuss two example traits, herbivory and flight, where comparative physiology has helped reveal the selective pressures influencing host dependence on microbial communities. Lastly, we discuss useful experimental approaches for studying the microbial dependence continuum in a comparative physiology context.}, }
@article {pmid38963125, year = {2024}, author = {Kobel, CM and Merkesvik, J and Burgos, IMT and Lai, W and Øyås, O and Pope, PB and Hvidsten, TR and Aho, VTE}, title = {Integrating host and microbiome biology using holo-omics.}, journal = {Molecular omics}, volume = {20}, number = {7}, pages = {438-452}, doi = {10.1039/d4mo00017j}, pmid = {38963125}, issn = {2515-4184}, mesh = {*Microbiota ; Humans ; Host Microbial Interactions/genetics ; Animals ; Symbiosis ; Proteomics/methods ; Metabolomics/methods ; Genomics/methods ; }, abstract = {Holo-omics is the use of omics data to study a host and its inherent microbiomes - a biological system known as a "holobiont". A microbiome that exists in such a space often encounters habitat stability and in return provides metabolic capacities that can benefit their host. Here we present an overview of beneficial host-microbiome systems and propose and discuss several methodological frameworks that can be used to investigate the intricacies of the many as yet undefined host-microbiome interactions that influence holobiont homeostasis. While this is an emerging field, we anticipate that ongoing methodological advancements will enhance the biological resolution that is necessary to improve our understanding of host-microbiome interplay to make meaningful interpretations and biotechnological applications.}, }
@article {pmid38960756, year = {2024}, author = {Robinson, JM and Barnes, AD and Fickling, N and Costin, S and Sun, X and Breed, MF}, title = {Food webs in food webs: the micro-macro interplay of multilayered networks.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {10}, pages = {913-922}, doi = {10.1016/j.tree.2024.06.006}, pmid = {38960756}, issn = {1872-8383}, mesh = {*Food Chain ; Animals ; Microbiota ; Models, Biological ; Host Microbial Interactions ; Ecosystem ; }, abstract = {Food webs are typically defined as being macro-organism-based (e.g., plants, mammals, birds) or microbial (e.g., bacteria, fungi, viruses). However, these characterizations have limits. We propose a multilayered food web conceptual model where microbial food webs are nested within food webs composed of macro-organisms. Nesting occurs through host-microbe interactions, which influence the health and behavior of host macro-organisms, such that host microbiomes likely alter population dynamics of interacting macro-organisms and vice versa. Here, we explore the theoretical underpinnings of multilayered food webs and the implications of this new conceptual model on food web ecology. Our framework opens avenues for new empirical investigations into complex ecological networks and provides a new lens through which to view a network's response to ecosystem changes.}, }
@article {pmid38943206, year = {2024}, author = {Larzul, C and Estellé, J and Borey, M and Blanc, F and Lemonnier, G and Billon, Y and Thiam, MG and Quinquis, B and Galleron, N and Jardet, D and Lecardonnel, J and Plaza Oñate, F and Rogel-Gaillard, C}, title = {Driving gut microbiota enterotypes through host genetics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {116}, pmid = {38943206}, issn = {2049-2618}, support = {Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; Enterotypig//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Feces/microbiology ; Bacteria/classification/genetics ; Metagenomics/methods ; Prevotella/genetics/classification ; Ruminococcus/genetics ; Treponema/genetics ; }, abstract = {BACKGROUND: Population stratification based on interindividual variability in gut microbiota composition has revealed the existence of several ecotypes named enterotypes in humans and various animal species. Enterotypes are often associated with environmental factors including diet, but knowledge of the role of host genetics remains scarce. Moreover, enterotypes harbor functionalities likely associated with varying abilities and susceptibilities of their host. Previously, we showed that under controlled conditions, 60-day-old pig populations consistently split into two enterotypes with either Prevotella and Mitsuokella (PM enterotype) or Ruminococcus and Treponema (RT enterotype) as keystone taxa. Here, our aim was to rely on pig as a model to study the influence of host genetics to assemble enterotypes, and to provide clues on enterotype functional differences and their links with growth traits.<br><br>RESULTS: We established two pig lines contrasted for abundances of the genera pairs specifying each enterotype at 60&#xa0;days of age and assessed them for fecal microbiota composition and growth throughout three consecutive generations. Response to selection across three generations revealed, per line, an increase in the prevalence of the selected enterotype and in the average relative abundances of directly and indirectly selected bacterial genera. The PM enterotype was found less diverse than the RT enterotype but more efficient for piglet growth during the post-weaning period. Shotgun metagenomics revealed differentially abundant bacterial species between the two enterotypes. By using the KEGG Orthology database, we show that functions related to starch degradation and polysaccharide metabolism are enriched in the PM enterotype, whereas functions related to general nucleoside transport and peptide/nickel transport are enriched in the RT enterotype. Our results also suggest that the PM and RT enterotypes might differ in the metabolism of valine, leucin, and isoleucine, favoring their biosynthesis and degradation, respectively.<br><br>CONCLUSION: We experimentally demonstrated that enterotypes are functional ecosystems that can be selected as a whole by exerting pressure on the host genetics. We also highlight that holobionts should be considered as units of selection in breeding programs. These results pave the way for a holistic use of host genetics, microbiota diversity, and enterotype functionalities to understand holobiont shaping and adaptation. Video Abstract.}, }
@article {pmid38942016, year = {2024}, author = {Dehasque, M and Morales, HE and Díez-Del-Molino, D and Pečnerová, P and Chacón-Duque, JC and Kanellidou, F and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Nikolskiy, P and Danilov, GK and Giannì, M and van der Sluis, L and Higham, T and Heintzman, PD and Oskolkov, N and Gilbert, MTP and Götherström, A and van der Valk, T and Vartanyan, S and Dalén, L}, title = {Temporal dynamics of woolly mammoth genome erosion prior to extinction.}, journal = {Cell}, volume = {187}, number = {14}, pages = {3531-3540.e13}, doi = {10.1016/j.cell.2024.05.033}, pmid = {38942016}, issn = {1097-4172}, mesh = {Animals ; *Mammoths/genetics ; *Extinction, Biological ; *Genome/genetics ; *Mutation ; Siberia ; Phylogeny ; Evolution, Molecular ; Time Factors ; }, abstract = {A number of species have recently recovered from near-extinction. Although these species have avoided the immediate extinction threat, their long-term viability remains precarious due to the potential genetic consequences of population declines, which are poorly understood on a timescale beyond a few generations. Woolly mammoths (Mammuthus primigenius) became isolated on Wrangel Island around 10,000 years ago and persisted for over 200 generations before becoming extinct around 4,000 years ago. To study the evolutionary processes leading up to the mammoths' extinction, we analyzed 21 Siberian woolly mammoth genomes. Our results show that the population recovered quickly from a severe bottleneck and remained demographically stable during the ensuing six millennia. We find that mildly deleterious mutations gradually accumulated, whereas highly deleterious mutations were purged, suggesting ongoing inbreeding depression that lasted for hundreds of generations. The time-lag between demographic and genetic recovery has wide-ranging implications for conservation management of recently bottlenecked populations.}, }
@article {pmid38930599, year = {2024}, author = {Liu, Y and Wu, H and Shu, Y and Hua, Y and Fu, P}, title = {Symbiodiniaceae and Ruegeria sp. Co-Cultivation to Enhance Nutrient Exchanges in Coral Holobiont.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, pmid = {38930599}, issn = {2076-2607}, abstract = {The symbiotic relationship between corals and their associated microorganisms is crucial for the health of coral reef eco-environmental systems. Recently, there has been a growing interest in unraveling how the manipulation of symbiont nutrient cycling affects the stress tolerance in the holobiont of coral reefs. However, most studies have primarily focused on coral-Symbiodiniaceae-bacterial interactions as a whole, neglecting the interactions between Symbiodiniaceae and bacteria, which remain largely unexplored. In this study, we proposed a hypothesis that there exists an inner symbiotic loop of Symbiodiniaceae and bacteria within the coral symbiotic loop. We conducted experiments to demonstrate how metabolic exchanges between Symbiodiniaceae and bacteria facilitate the nutritional supply necessary for cellular growth. It was seen that the beneficial bacterium, Ruegeria sp., supplied a nitrogen source to the Symbiodiniaceae strain Durusdinium sp., allowing this dinoflagellate to thrive in a nitrogen-free medium. The Ruegeria sp.-Durusdinium sp. interaction was confirmed through [15]N-stable isotope probing-single cell Raman spectroscopy, in which [15]N infiltrated into the bacterial cells for intracellular metabolism, and eventually the labeled nitrogen source was traced within the macromolecules of Symbiodiniaceae cells. The investigation into Symbiodiniaceae loop interactions validates our hypothesis and contributes to a comprehensive understanding of the intricate coral holobiont. These findings have the potential to enhance the health of coral reefs in the face of global climate change.}, }
@article {pmid38930577, year = {2024}, author = {Hernández-Zulueta, J and Rubio-Bueno, S and Zamora-Tavares, MDP and Vargas-Ponce, O and Rodríguez-Troncoso, AP and Rodríguez-Zaragoza, FA}, title = {Metabarcoding the Bacterial Assemblages Associated with Toxopneustes roseus in the Mexican Central Pacific.}, journal = {Microorganisms}, volume = {12}, number = {6}, pages = {}, pmid = {38930577}, issn = {2076-2607}, abstract = {The Mexican Central Pacific (MCP) region has discontinuous coral ecosystems with different protection and anthropogenic disturbance. Characterizing the bacterial assemblage associated with the sea urchin Toxopneustes roseus and its relationship with environmental variables will contribute to understanding the species' physiology and ecology. We collected sea urchins from coral ecosystems at six sites in the MCP during the summer and winter for two consecutive years. The spatial scale represented the most important variation in the T. roseus bacteriome, particularly because of Isla Isabel National Park (PNII). Likewise, spatial differences correlated with habitat structure variables, mainly the sponge and live coral cover. The PNII exhibited highly diverse bacterial assemblages compared to other sites, characterized by families associated with diseases and environmental stress (Saprospiraceae, Flammeovirgaceae, and Xanthobacteraceae). The remaining five sites presented a constant spatiotemporal pattern, where the predominance of the Campylobacteraceae and Helicobacteraceae families was key to T. roseus' holobiont. However, the dominance of certain bacterial families, such as Enterobacteriaceae, in the second analyzed year suggests that Punto B and Islas e islotes de Bahía Chamela Sanctuary were exposed to sewage contamination. Overall, our results improve the understanding of host-associated bacterial assemblages in specific time and space and their relationship with the environmental condition.}, }
@article {pmid38923181, year = {2024}, author = {Bogale, AT and Braun, M and Bernhardt, J and Zühlke, D and Schiefelbein, U and Bog, M and Scheidegger, C and Zengerer, V and Becher, D and Grube, M and Riedel, K and Bengtsson, MM}, title = {The microbiome of the lichen Lobaria pulmonaria varies according to climate on a subcontinental scale.}, journal = {Environmental microbiology reports}, volume = {16}, number = {3}, pages = {e13289}, pmid = {38923181}, issn = {1758-2229}, support = {//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Lichens/microbiology/physiology ; *Microbiota ; *Climate ; Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Seasons ; Genotype ; }, abstract = {The Lobaria pulmonaria holobiont comprises algal, fungal, cyanobacterial and bacterial components. We investigated L. pulmonaria's bacterial microbiome in the adaptation of this ecologically sensitive lichen species to diverse climatic conditions. Our central hypothesis posited that microbiome composition and functionality aligns with subcontinental-scale (a stretch of ~1100 km) climatic parameters related to temperature and precipitation. We also tested the impact of short-term weather dynamics, sampling season and algal/fungal genotypes on microbiome variation. Metaproteomics provided insights into compositional and functional changes within the microbiome. Climatic variables explained 41.64% of microbiome variation, surpassing the combined influence of local weather and sampling season at 31.63%. Notably, annual mean temperature and temperature seasonality emerged as significant climatic drivers. Microbiome composition correlated with algal, not fungal genotype, suggesting similar environmental recruitment for the algal partner and microbiome. Differential abundance analyses revealed distinct protein compositions in Sub-Atlantic Lowland and Alpine regions, indicating differential microbiome responses to contrasting environmental/climatic conditions. Proteins involved in oxidative and cellular stress were notably different. Our findings highlight microbiome plasticity in adapting to stable climates, with limited responsiveness to short-term fluctuations, offering new insights into climate adaptation in lichen symbiosis.}, }
@article {pmid38922379, year = {2024}, author = {Mikó, E and Sipos, A and Tóth, E and Lehoczki, A and Fekete, M and Sebő, &#xc9; and Kardos, G and Bai, P}, title = {Guideline for designing microbiome studies in neoplastic diseases.}, journal = {GeroScience}, volume = {46}, number = {5}, pages = {4037-4057}, pmid = {38922379}, issn = {2509-2723}, support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; FK146852//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; TKP2021-EGA-19//NFKIH/ ; POST-COVID2021-33//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; NKM2022-30//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; }, mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Research Design ; }, abstract = {Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.}, }
@article {pmid38918405, year = {2024}, author = {Paës, C and Beaumont, M and Gidenne, T and Bébin, K and Duperray, J and Gohier, C and Guené-Grand, E and Rebours, G and Castinel, A and Barilly, C and Gabinaud, B and Bannelier, C and Gress, L and Laperruque, F and Aymard, P and Debrusse, AM and Cauquil, L and Pascal, G and Combes, S}, title = {A multi-omics dataset of the response to early plant polysaccharide ingestion in rabbits.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {684}, pmid = {38918405}, issn = {2052-4463}, mesh = {Animals ; Rabbits ; *Polysaccharides ; *Gastrointestinal Microbiome ; Transcriptome ; Cecum ; Weaning ; Metabolome ; Multiomics ; }, abstract = {The transition from a milk-based diet to exclusive solid feeding deeply modifies microbiota-host crosstalk. Specifically, early ingestion of plant polysaccharides would be one of the main nutritional components to drive host-microbiota-interaction. To capture the effects of polysaccharides early-life nutrition (starch vs rapidly fermentable fiber) on the holobiont development, we investigated on the one hand the gut bacteriome and metabolome and on the other hand the transcriptome of two host gut tissues. Rabbit model was used to study post-natal co-development of the gut microbiota and its host around weaning transition. The assessment of the microbial composition of the gut appendix together with the caecum was provided for the first time. Gene expression signatures were analyzed along the gut (ileum and caecum) through high-throughput qPCR. The data collected were completed by the analysis of animal growth changes and time-series assessment of blood biomarkers. Those accessible and reusable data could help highlight the gut development dynamics as well as biological adaptation processes at the onset of solid feeding.}, }
@article {pmid38905343, year = {2024}, author = {Buschi, E and Dell'Anno, A and Tangherlini, M and Candela, M and Rampelli, S and Turroni, S and Palladino, G and Esposito, E and Martire, ML and Musco, L and Stefanni, S and Munari, C and Fiori, J and Danovaro, R and Corinaldesi, C}, title = {Resistance to freezing conditions of endemic Antarctic polychaetes is enhanced by cryoprotective proteins produced by their microbiome.}, journal = {Science advances}, volume = {10}, number = {25}, pages = {eadk9117}, pmid = {38905343}, issn = {2375-2548}, mesh = {*Polychaeta/microbiology ; Animals ; Antarctic Regions ; *Microbiota ; *Freezing ; Phylogeny ; Bacterial Proteins/metabolism/genetics ; }, abstract = {The microbiome plays a key role in the health of all metazoans. Whether and how the microbiome favors the adaptation processes of organisms to extreme conditions, such as those of Antarctica, which are incompatible with most metazoans, is still unknown. We investigated the microbiome of three endemic and widespread species of Antarctic polychaetes: Leitoscoloplos geminus, Aphelochaeta palmeri, and Aglaophamus trissophyllus. We report here that these invertebrates contain a stable bacterial core dominated by Meiothermus and Anoxybacillus, equipped with a versatile genetic makeup and a unique portfolio of proteins useful for coping with extremely cold conditions as revealed by pangenomic and metaproteomic analyses. The close phylosymbiosis between Meiothermus and Anoxybacillus and these Antarctic polychaetes indicates a connection with their hosts that started in the past to support holobiont adaptation to the Antarctic Ocean. The wide suite of bacterial cryoprotective proteins found in Antarctic polychaetes may be useful for the development of nature-based biotechnological applications.}, }
@article {pmid38903121, year = {2024}, author = {Bougiouri, K and Aninta, SG and Charlton, S and Harris, A and Carmagnini, A and Piličiauskienė, G and Feuerborn, TR and Scarsbrook, L and Tabadda, K and Blaževičius, P and Parker, HG and Gopalakrishnan, S and Larson, G and Ostrander, EA and Irving-Pease, EK and Frantz, LAF and Racimo, F}, title = {Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38903121}, issn = {2692-8205}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R[2]>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.}, }
@article {pmid38892721, year = {2024}, author = {Mafra, D and Borges, NA and Baptista, BG and Martins, LF and Borland, G and Shiels, PG and Stenvinkel, P}, title = {What Can the Gut Microbiota of Animals Teach Us about the Relationship between Nutrition and Burden of Lifestyle Diseases?.}, journal = {Nutrients}, volume = {16}, number = {11}, pages = {}, pmid = {38892721}, issn = {2072-6643}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Humans ; Life Style ; Nutritional Status ; Chronic Disease ; }, abstract = {The gut microbiota performs several crucial roles in a holobiont with its host, including immune regulation, nutrient absorption, synthesis, and defense against external pathogens, significantly influencing host physiology. Disruption of the gut microbiota has been linked to various chronic conditions, including cardiovascular, kidney, liver, respiratory, and intestinal diseases. Studying how animals adapt their gut microbiota across their life course at different life stages and under the dynamics of extreme environmental conditions can provide valuable insights from the natural world into how the microbiota modulates host biology, with a view to translating these into treatments or preventative measures for human diseases. By modulating the gut microbiota, opportunities to address many complications associated with chronic diseases appear. Such a biomimetic approach holds promise for exploring new strategies in healthcare and disease management.}, }
@article {pmid38892420, year = {2024}, author = {Qadri, QR and Lai, X and Zhao, W and Zhang, Z and Zhao, Q and Ma, P and Pan, Y and Wang, Q}, title = {Exploring the Interplay between the Hologenome and Complex Traits in Bovine and Porcine Animals Using Genome-Wide Association Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {11}, pages = {}, pmid = {38892420}, issn = {1422-0067}, support = {2023YFD1300404//National Key Research and Development Program of China/ ; 2022KJCX49//Sanya Science and Technology Innovation Project/ ; ZDYF2024XDNY186//Hainan Province Science and Technology Special Fund/ ; 22ZR1431500//Natural Science Foundation of Shanghai/ ; 2021C02068&#x2013;1//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; }, mesh = {Animals ; *Genome-Wide Association Study ; *Polymorphism, Single Nucleotide ; Cattle/genetics ; Swine/genetics ; *Quantitative Trait Loci ; Gastrointestinal Microbiome/genetics ; Rumen/microbiology/metabolism ; Phenotype ; Methane/metabolism ; Milk/metabolism ; Genome ; }, abstract = {Genome-wide association studies (GWAS) significantly enhance our ability to identify trait-associated genomic variants by considering the host genome. Moreover, the hologenome refers to the host organism's collective genetic material and its associated microbiome. In this study, we utilized the hologenome framework, called Hologenome-wide association studies (HWAS), to dissect the architecture of complex traits, including milk yield, methane emissions, rumen physiology in cattle, and gut microbial composition in pigs. We employed four statistical models: (1) GWAS, (2) Microbial GWAS (M-GWAS), (3) HWAS-CG (hologenome interaction estimated using COvariance between Random Effects Genome-based restricted maximum likelihood (CORE-GREML)), and (4) HWAS-H (hologenome interaction estimated using the Hadamard product method). We applied Bonferroni correction to interpret the significant associations in the complex traits. The GWAS and M-GWAS detected one and sixteen significant SNPs for milk yield traits, respectively, whereas the HWAS-CG and HWAS-H each identified eight SNPs. Moreover, HWAS-CG revealed four, and the remaining models identified three SNPs each for methane emissions traits. The GWAS and HWAS-CG detected one and three SNPs for rumen physiology traits, respectively. For the pigs' gut microbial composition traits, the GWAS, M-GWAS, HWAS-CG, and HWAS-H identified 14, 16, 13, and 12 SNPs, respectively. We further explored these associations through SNP annotation and by analyzing biological processes and functional pathways. Additionally, we integrated our GWA results with expression quantitative trait locus (eQTL) data using transcriptome-wide association studies (TWAS) and summary-based Mendelian randomization (SMR) methods for a more comprehensive understanding of SNP-trait associations. Our study revealed hologenomic variability in agriculturally important traits, enhancing our understanding of host-microbiome interactions.}, }
@article {pmid38891668, year = {2024}, author = {Recchia, M and Ghidini, S and Romeo, C and Scali, F and Maisano, AM and Guadagno, F and De Luca, S and Ianieri, A and Alborali, GL}, title = {An Integrated Analysis of Abattoir Lung Lesion Scores and Antimicrobial Use in Italian Heavy Pig Finishing Farms.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {11}, pages = {}, pmid = {38891668}, issn = {2076-2615}, support = {CLASSYFARM project (CUP: E55F21002890001)//Italian Ministry of Health/ ; }, abstract = {Respiratory diseases significantly affect intensive pig finishing farms, causing production losses and increased antimicrobial use (AMU). Lesion scoring at slaughter has been recognized as a beneficial practice to evaluate herd management. The integrated analysis of abattoir lesion scores and AMU data could improve decision-making by providing feedback to veterinarians and farmers on the effectiveness of antimicrobial treatments, thus rationalizing their use. This study compared lung and pleural lesion scores collected at Italian pig slaughterhouses with on-farm AMU, estimated through a treatment index per 100 days (TI100). Overall, 24,752 pig carcasses, belonging to 236 batches from 113 finishing farms, were inspected. Bronchopneumonia and chronic pleuritis were detected in 55% and 48% of the examined pigs, respectively. Antimicrobials were administered in 97% of the farms during the six months prior to slaughter (median TI100 = 5.2), notwithstanding compliance with the mandatory withdrawal period. EMA category B (critical) antimicrobials were administered in 15.2% of cases (median TI100 = 0.06). The lung score was not associated with the total AMU, but significant, positive associations were found with the past use of critical antimicrobials (p = 0.041) and macrolides (p = 0.044). This result highlights the potential of abattoir lung lesion monitoring to rationalize antimicrobial stewardship efforts, contributing to AMU reduction.}, }
@article {pmid38886248, year = {2024}, author = {Bartels, N and Matthews, JL and Lawson, CA and Possell, M and Hughes, DJ and Raina, JB and Suggett, DJ}, title = {Paired metabolomics and volatilomics provides insight into transient high light stress response mechanisms of the coral Montipora mollis.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {20}, number = {4}, pages = {66}, pmid = {38886248}, issn = {1573-3890}, mesh = {Animals ; *Anthozoa/metabolism ; *Metabolomics/methods ; *Light ; *Stress, Physiological ; Volatile Organic Compounds/metabolism/analysis ; Photosystem II Protein Complex/metabolism ; }, abstract = {The coral holobiont is underpinned by complex metabolic exchanges between different symbiotic partners, which are impacted by environmental stressors. The chemical diversity of the compounds produced by the holobiont is high and includes primary and secondary metabolites, as well as volatiles. However, metabolites and volatiles have only been characterised in isolation so far. Here, we applied a paired metabolomic-volatilomic approach to characterise holistically the chemical response of the holobiont under stress. Montipora mollis fragments were subjected to high-light stress (8-fold higher than the controls) for 30 min. Photosystem II (PSII) photochemical efficiency values were 7-fold higher in control versus treatment corals immediately following high-light exposure, but returned to pre-stress levels after 30 min of recovery. Under high-light stress, we identified an increase in carbohydrates (> 5-fold increase in arabinose and fructose) and saturated fatty acids (7-fold increase in myristic and oleic acid), together with a decrease in fatty acid derivatives in both metabolites and volatiles (e.g., 80% decrease in oleamide and nonanal), and other antioxidants (~ 85% decrease in sorbitol and galactitol). These changes suggest short-term light stress induces oxidative stress. Correlation analysis between volatiles and metabolites identified positive links between sorbitol, galactitol, six other metabolites and 11 volatiles, with four of these compounds previously identified as antioxidants. This suggests that these 19 compounds may be related and share similar functions. Taken together, our findings demonstrate how paired metabolomics-volatilomics may illuminate broader metabolic shifts occurring under stress and identify linkages between uncharacterised compounds to putatively determine their functions.}, }
@article {pmid38884497, year = {2024}, author = {Han, S and Akhtar, MR and Xia, X}, title = {Functions and regulations of insect gut bacteria.}, journal = {Pest management science}, volume = {80}, number = {10}, pages = {4828-4840}, doi = {10.1002/ps.8261}, pmid = {38884497}, issn = {1526-4998}, support = {31871968//National Natural Science Foundation of China/ ; MIMCP-202302//Open Project of Fujian Key Laboratory of Crop Pest Monitoring and Control/ ; KFB23024A//Science and Technology Innovation Fund of Fujian Agriculture and Forestry University/ ; }, mesh = {Animals ; *Insecta/microbiology/physiology ; *Gastrointestinal Microbiome ; *Symbiosis ; Bacteria/metabolism/genetics ; }, abstract = {The insect gut is a complicated ecosystem that inhabits a large number of symbiotic bacteria. As an important organ of the host insect, the symbiotic bacteria of the insect gut play very important roles in regulating physiological and metabolic processes. Recently, much progress has been made in the study of symbiotic bacteria in insect guts with the development of high-throughput sequencing technology and molecular biology. This review summarizes the primary functions of symbiotic bacteria in insect guts, such as enhancing insecticide resistance, facilitating food digestion, promoting detoxification, and regulating mating behavior and egg hatching. It also addresses some possible pathways of gut bacteria symbiont regulation governed by external habitats, physiological conditions and immunity of the host insect. This review provides solid foundations for further studies on novel theories, new technologies and practical applications of symbiotic bacteria in insect guts. © 2024 Society of Chemical Industry.}, }
@article {pmid38879040, year = {2024}, author = {Zhang, L and Vaccari, F and Bandini, F and Puglisi, E and Trevisan, M and Lucini, L}, title = {The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome.}, journal = {The Science of the total environment}, volume = {945}, number = {}, pages = {174001}, doi = {10.1016/j.scitotenv.2024.174001}, pmid = {38879040}, issn = {1879-1026}, mesh = {*Lactuca/microbiology ; *Rhizosphere ; *Plant Roots/microbiology ; *Soil Pollutants/metabolism ; *Microplastics/toxicity ; *Metabolome ; Soil Microbiology ; Microbiota/drug effects ; Particle Size ; }, abstract = {Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation. Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.}, }
@article {pmid38864655, year = {2024}, author = {McCaw, BA and Leonard, AM and Stevenson, TJ and Lancaster, LT}, title = {A role of epigenetic mechanisms in regulating female reproductive responses to temperature in a pest beetle.}, journal = {Insect molecular biology}, volume = {33}, number = {5}, pages = {516-533}, doi = {10.1111/imb.12933}, pmid = {38864655}, issn = {1365-2583}, support = {BB/M010996/1//UKRI Biotechnology and Biological Sciences Research Council (BBSRC)/ ; //University of Aberdeen/ ; }, mesh = {Animals ; *Coleoptera/genetics/physiology ; *Epigenesis, Genetic ; Female ; *DNA Methylation ; *Reproduction/genetics ; Temperature ; Male ; Cytidine/analogs &amp; derivatives/pharmacology ; Climate Change ; }, abstract = {Many species are threatened by climate change and must rapidly respond to survive in changing environments. Epigenetic modifications, such as DNA methylation, can facilitate plastic responses by regulating gene expression in response to environmental cues. Understanding epigenetic responses is therefore essential for predicting species' ability to rapidly adapt in the context of global environmental change. Here, we investigated the functional significance of different methylation-associated cellular processes on temperature-dependent life history in seed beetles, Callosobruchus maculatus Fabricius 1775 (Coleoptera: Bruchidae). We assessed changes under thermal stress in (1) DNA methyltransferase (Dnmt1 and Dnmt2) expression levels, (2) genome-wide methylation and (3) reproductive performance, with (2) and (3) following treatment with 3-aminobenzamide (3AB) and zebularine (Zeb) over two generations. These drugs are well-documented to alter DNA methylation across the tree of life. We found that Dnmt1 and Dnmt2 were expressed throughout the body in males and females, but were highly expressed in females compared with males and exhibited temperature dependence. However, whole-genome methylation did not significantly vary with temperature, and only marginally or inconclusively with drug treatment. Both 3AB and Zeb led to profound temperature-dependent shifts in female reproductive life history trade-off allocation, often increasing fitness compared with control beetles. Mismatch between magnitude of treatment effects on DNA methylation versus life history effects suggest potential of 3AB and Zeb to alter reproductive trade-offs via changes in DNA repair and recycling processes, rather than or in addition to (subtle) changes in DNA methylation. Together, our results suggest that epigenetic mechanisms relating to Dnmt expression, DNA repair and recycling pathways, and possibly DNA methylation, are strongly implicated in modulating insect life history trade-offs in response to temperature change.}, }
@article {pmid38858806, year = {2024}, author = {Brüssow, F and Bruessow, F and Brüssow, H}, title = {The role of the plant microbiome for forestry, agriculture and urban greenspace in times of environmental change.}, journal = {Microbial biotechnology}, volume = {17}, number = {6}, pages = {e14482}, pmid = {38858806}, issn = {1751-7915}, mesh = {*Microbiota ; *Agriculture/methods ; *Climate Change ; Forestry ; Plants/microbiology ; Fungi/classification/genetics/isolation &amp; purification/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {This Lilliput article provides a literature overview on ecological effects of the plant microbiome with a focus on practical application in forestry, agriculture and urban greenspace under the spectre of climate change. After an overview of the mostly bacterial microbiome of the model plant Arabidopsis thaliana, worldwide data from forests reveal ecological differentiation with respect to major guilds of predominantly fungal plant root symbionts. The plant-microbiome association forms a new holobiont, an integrated unit for ecological adaptation and evolutionary selection. Researchers explored the impact of the microbiome on the capacity of plants to adapt to changing climate conditions. They investigated the impact of the microbiome in reforestation programs, after wildfire, drought, salination and pollution events in forestry, grasslands and agriculture. With increasing temperatures plant populations migrate to higher latitudes and higher altitudes. Ecological studies compared the dispersal capacity of plant seeds with that of soil microbes and the response of soil and root microbes to experimental heating of soils. These studies described a succession of microbiome associations and the kinetics of a release of stored soil carbon into the atmosphere enhancing global warming. Scientists explored the impact of synthetic microbial communities (SynComs) on rice productivity or tea quality; of whole soil addition in grassland restoration; or single fungal inoculation in maize fields. Meta-analyses of fungal inoculation showed overall a positive effect, but also a wide variation in effect sizes. Climate change will be particularly prominent in urban areas ("urban heat islands") where more than half of the world population is living. Urban landscape architecture will thus have an important impact on human health and studies started to explore the contribution of the microbiome from urban greenspace to ecosystem services.}, }
@article {pmid38857541, year = {2024}, author = {Spooren, J and van Bentum, S and Thomashow, LS and Pieterse, CMJ and Weller, DM and Berendsen, RL}, title = {Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes.}, journal = {Annual review of phytopathology}, volume = {62}, number = {1}, pages = {1-30}, doi = {10.1146/annurev-phyto-021622-100127}, pmid = {38857541}, issn = {1545-2107}, mesh = {*Soil Microbiology ; *Microbiota ; *Plant Diseases/microbiology ; *Plants/microbiology ; Plant Immunity ; Soil/chemistry ; }, abstract = {Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.}, }
@article {pmid38851755, year = {2024}, author = {Paix, B and van der Valk, E and de Voogd, NJ}, title = {Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {37}, pmid = {38851755}, issn = {2524-6372}, support = {16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules.<br><br>RESULTS: An overall change of bacterial &#x3b2;-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome.<br><br>CONCLUSIONS: This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.}, }
@article {pmid38846022, year = {2024}, author = {Yakovleva, E and Danilova, I and Maximova, I and Shabaev, A and Dmitrieva, A and Belov, A and Klyukina, A and Perfilieva, K and Bonch-Osmolovskaya, E and Markov, A}, title = {Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster.}, journal = {Microbiome research reports}, volume = {3}, number = {2}, pages = {19}, pmid = {38846022}, issn = {2771-5965}, abstract = {Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter, potentially beneficial to D. melanogaster, decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.}, }
@article {pmid38839511, year = {2024}, author = {Pepke, ML and Hansen, SB and Limborg, MT}, title = {Unraveling host regulation of gut microbiota through the epigenome-microbiome axis.}, journal = {Trends in microbiology}, volume = {32}, number = {12}, pages = {1229-1240}, doi = {10.1016/j.tim.2024.05.006}, pmid = {38839511}, issn = {1878-4380}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Epigenesis, Genetic ; *Epigenome ; Animals ; *Host Microbial Interactions/genetics ; }, abstract = {Recent studies of dynamic interactions between epigenetic modifications of a host organism and the composition or activity of its associated gut microbiota suggest an opportunity for the host to shape its microbiome through epigenetic alterations that lead to changes in gene expression and noncoding RNA activity. We use insights from microbiota-induced epigenetic changes to review the potential of the host to epigenetically regulate its gut microbiome, from which a bidirectional 'epigenome-microbiome axis' emerges. This axis embeds environmentally induced variation, which may influence the adaptive evolution of host-microbe interactions. We furthermore present our perspective on how the epigenome-microbiome axis can be understood and investigated within a holo-omic framework with potential applications in the applied health and food sciences.}, }
@article {pmid38830414, year = {2024}, author = {Koll, R and Theilen, J and Hauten, E and Woodhouse, JN and Thiel, R and Möllmann, C and Fabrizius, A}, title = {Network-based integration of omics, physiological and environmental data in real-world Elbe estuarine Zander.}, journal = {The Science of the total environment}, volume = {942}, number = {}, pages = {173656}, doi = {10.1016/j.scitotenv.2024.173656}, pmid = {38830414}, issn = {1879-1026}, mesh = {Animals ; *Estuaries ; Environmental Monitoring ; Gills/microbiology ; Microbiota ; Transcriptome ; RNA, Ribosomal, 16S ; Climate Change ; Perches/physiology/microbiology ; }, abstract = {Coastal and estuarine environments are under endogenic and exogenic pressures jeopardizing survival and diversity of inhabiting biota. Information of possible synergistic effects of multiple (a)biotic stressors and holobiont interaction are largely missing in estuaries like the Elbe but are of importance to estimate unforeseen effects on animals' physiology. Here, we seek to leverage host-transcriptional RNA-seq and gill mucus microbial 16S rRNA metabarcoding data coupled with physiological and abiotic measurements in a network analysis approach to decipher the impact of multiple stressors on the health of juvenile Sander lucioperca along one of the largest European estuaries. We find mesohaline areas characterized by gill tissue specific transcriptional responses matching osmosensing and tissue remodeling. Liver transcriptomes instead emphasized that zander from highly turbid areas were undergoing starvation which was supported by compromised body condition. Potential pathogenic bacteria, including Shewanella, Acinetobacter, Aeromonas and Chryseobacterium, dominated the gill microbiome along the freshwater transition and oxygen minimum zone. Their occurrence coincided with a strong adaptive and innate transcriptional immune response in host gill and enhanced energy demand in liver tissue supporting their potential pathogenicity. Taken together, we show physiological responses of a fish species and its microbiome to abiotic factors whose impact is expected to increase with consequences of climate change. We further present a method for the close-meshed detection of the main stressors and bacterial species with disease potential in a highly productive ecosystem.}, }
@article {pmid38825980, year = {2024}, author = {Hernández, M and Ancona, S and Hereira-Pacheco, S and Díaz de la Vega-Pérez, AH and Alberdi, A and Navarro-Noya, YE}, title = {Seasonal dietary changes relate to gut microbiota composition depending on the host species but do not correlate with gut microbiota diversity in arthropod-eating lizards.}, journal = {Molecular ecology}, volume = {33}, number = {14}, pages = {e17426}, doi = {10.1111/mec.17426}, pmid = {38825980}, issn = {1365-294X}, support = {205945//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT)/ ; 883//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT)/ ; 967648//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT)/ ; CF-2019-137748//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as (CONAHCYT)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Lizards/microbiology ; *Seasons ; *Diet ; Mexico ; *Bacteria/classification/genetics ; Arthropods/microbiology ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {The animal gut microbiota is strongly influenced by environmental factors that shape their temporal dynamics. Although diet is recognized as a major driver of gut microbiota variation, dietary patterns have seldom been linked to gut microbiota dynamics in wild animals. Here, we analysed the gut microbiota variation between dry and rainy seasons across four Sceloporus species (S. aeneus, S. bicanthalis, S. grammicus and S. spinosus) from central Mexico in light of temporal changes in diet composition. The lizard microbiota was dominated by Firmicutes (now Bacillota) and Bacteroidota, and the closely related species S. aeneus and S. bicanthalis shared a great number of core bacterial taxa. We report species-specific seasonal changes in gut microbiota diversity and composition: greater alpha diversity during the dry compared to the rainy season in S. bicanthalis, the opposite pattern in S. aeneus, and no seasonal differences in S. grammicus and S. spinosus. Our findings indicated a positive association between gut bacterial composition and dietary composition for S. bicanthalis and S. grammicus, but bacterial diversity did not increase linearly with dietary richness in any lizard species. In addition, seasonality affected bacterial composition, and microbial community similarity increased between S. aeneus and S. bicanthalis, as well as between S. grammicus and S. spinosus. Together, our results illustrate that seasonal variation and dietary composition play a role in shaping gut microbiota in lizard populations, but this is not a rule and other ecological factors influence microbiota variation.}, }
@article {pmid38825966, year = {2024}, author = {Herlemann, DPR and Tammert, H and Kivistik, C and Käiro, K and Kisand, V}, title = {Distinct biogeographical patterns in snail gastrointestinal tract bacterial communities compared with sediment and water.}, journal = {MicrobiologyOpen}, volume = {13}, number = {3}, pages = {e13}, pmid = {38825966}, issn = {2045-8827}, support = {MOBTT24//Eesti Teadusagentuur/ ; PUT1389//Eesti Teadusagentuur/ ; Leibniz Institute for Baltic Sea Research Warnem&#xfc;//Leibniz-Institut f&#xfc;r Ostseeforschung Warnem&#xfc;nde/ ; Shallow Water Processes and Transitions//Leibniz-Institut f&#xfc;r Ostseeforschung Warnem&#xfc;nde/ ; MOBTT24//European Regional Development Fund/ ; P190250PKKH//Eesti Maa&#xfc;likool/ ; P200028PKKH//Eesti Maa&#xfc;likool/ ; }, mesh = {*Geologic Sediments/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Tract/microbiology ; Animals ; *Snails/microbiology ; Germany ; Denmark ; Gastrointestinal Microbiome/genetics ; Water Microbiology ; Biodiversity ; Estonia ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; }, abstract = {The factors that influence the distribution of bacterial community composition are not well understood. The role of geographical patterns, which suggest limited dispersal, is still a topic of debate. Bacteria associated with hosts face unique dispersal challenges as they often rely on their hosts, which provide specific environments for their symbionts. In this study, we examined the effect of biogeographic distances on the bacterial diversity and composition of bacterial communities in the gastrointestinal tract of Ampullaceana balthica. We compared the effects on the host-associated bacterial community to those on bacterial communities in water and sediment. This comparison was made using 16S ribosomal RNA gene sequencing. We found that the bacterial communities we sampled in Estonia, Denmark, and Northern Germany varied between water, sediment, and the gastrointestinal tract. They also varied between countries within each substrate. This indicates that the type of substrate is a dominant factor in determining bacterial community composition. We separately analyzed the turnover rates of water, sediment, and gastrointestinal bacterial communities over increasing geographic distances. We observed that the turnover rate was lower for gastrointestinal bacterial communities compared to water bacterial communities. This implies that the composition of gastrointestinal bacteria remains relatively stable over distances, while water bacterial communities exhibit greater variability. However, the gastrointestinal tract had the lowest percentage of country-specific amplicon sequence variants, suggesting bacterial colonization from local bacterial communities. Since the overlap between the water and gastrointestinal tract was highest, it appears that the gastrointestinal bacterial community is colonized by the water bacterial community. Our study confirmed that biogeographical patterns in host-associated communities differ from those in water and sediment bacterial communities. These host-associated communities consist of numerous facultative symbionts derived from the water bacterial community.}, }
@article {pmid38821056, year = {2024}, author = {Swisa, A and Kieckhaefer, J and Daniel, SG and El-Mekkoussi, H and Kolev, HM and Tigue, M and Jin, C and Assenmacher, CA and Dohnalová, L and Thaiss, CA and Karlsson, NG and Bittinger, K and Kaestner, KH}, title = {The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation.}, journal = {Developmental cell}, volume = {59}, number = {16}, pages = {2069-2084.e8}, pmid = {38821056}, issn = {1878-1551}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; R01 DK139049/DK/NIDDK NIH HHS/United States ; R01 DK053839/DK/NIDDK NIH HHS/United States ; P30 DK019525/DK/NIDDK NIH HHS/United States ; R37 DK053839/DK/NIDDK NIH HHS/United States ; R01 139049/NH/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Glycosylation ; *Hepatocyte Nuclear Factor 3-alpha/metabolism/genetics ; *Hepatocyte Nuclear Factor 3-beta/metabolism/genetics ; *Intestinal Mucosa/metabolism/microbiology ; Mice, Inbred C57BL ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics/pathology ; Dysbiosis/microbiology/metabolism/genetics ; Symbiosis ; }, abstract = {Evolutionary adaptation of multicellular organisms to a closed gut created an internal microbiome differing from that of the environment. Although the composition of the gut microbiome is impacted by diet and disease state, we hypothesized that vertebrates promote colonization by commensal bacteria through shaping of the apical surface of the intestinal epithelium. Here, we determine that the evolutionarily ancient FOXA transcription factors control the composition of the gut microbiome by establishing favorable glycosylation on the colonic epithelial surface. FOXA proteins bind to regulatory elements of a network of glycosylation enzymes, which become deregulated when Foxa1 and Foxa2 are deleted from the intestinal epithelium. As a direct consequence, microbial composition shifts dramatically, and spontaneous inflammatory bowel disease ensues. Microbiome dysbiosis was quickly reversed upon fecal transplant into wild-type mice, establishing a dominant role for the host epithelium, in part mediated by FOXA factors, in controlling symbiosis in the vertebrate holobiont.}, }
@article {pmid38814337, year = {2024}, author = {Filek, K and Vuković, BB and Žižek, M and Kanjer, L and Trotta, A and Di Bello, A and Corrente, M and Bosak, S}, title = {Loggerhead Sea Turtles as Hosts of Diverse Bacterial and Fungal Communities.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {79}, pmid = {38814337}, issn = {1432-184X}, support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; }, mesh = {Animals ; *Turtles/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; Microbiota ; Cloaca/microbiology ; Mycobiome ; Biodiversity ; Gastrointestinal Microbiome ; Biofilms ; }, abstract = {Research on microbial communities associated with wild animals provides a valuable reservoir of knowledge that could be used for enhancing their rehabilitation and conservation. The loggerhead sea turtle (Caretta caretta) is a globally distributed species with its Mediterranean population categorized as least concern according to the IUCN Red List of Threatened Species as a result of robust conservation efforts. In our study, we aimed to further understand their biology in relation to their associated microorganisms. We investigated epi- and endozoic bacterial and endozoic fungal communities of cloaca, oral mucosa, carapace biofilm. Samples obtained from 18 juvenile, subadult, and adult turtles as well as 8 respective enclosures, over a 3-year period, were analysed by amplicon sequencing of 16S rRNA gene and ITS2 region of nuclear ribosomal gene. Our results reveal a trend of decreasing diversity of distal gut bacterial communities with the age of turtles. Notably, Tenacibaculum species show higher relative abundance in juveniles than in adults. Differential abundances of taxa identified as Tenacibaculum, Moraxellaceae, Cardiobacteriaceae, and Campylobacter were observed in both cloacal and oral samples in addition to having distinct microbial compositions with Halioglobus taxa present only in oral samples. Fungal communities in loggerheads' cloaca were diverse and varied significantly among individuals, differing from those of tank water. Our findings expand the known microbial diversity repertoire of loggerhead turtles, highlighting interesting taxa specific to individual body sites. This study provides a comprehensive view of the loggerhead sea turtle bacterial microbiota and marks the first report of distal gut fungal communities that contributes to establishing a baseline understanding of loggerhead sea turtle holobiont.}, }
@article {pmid38808038, year = {2024}, author = {Stephens, D and Faghihi, Z and Moniruzzaman, M}, title = {Widespread occurrence and diverse origins of polintoviruses influence lineage-specific genome dynamics in stony corals.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae039}, pmid = {38808038}, issn = {2057-1577}, abstract = {Stony corals (Order: Scleractinia) are central to vital marine habitats known as coral reefs. Numerous stressors in the Anthropocene are contributing to the ongoing decline in coral reef health and coverage. While viruses are established modulators of marine microbial dynamics, their interactions within the coral holobiont and impact on coral health and physiology remain unclear. To address this key knowledge gap, we investigated diverse stony coral genomes for 'endogenous' viruses. Our study uncovered a remarkable number of integrated viral elements recognized as 'Polintoviruses' (Class Polintoviricetes) in thirty Scleractinia genomes; with several species harboring hundreds to thousands of polintoviruses. We reveal massive paralogous expansion of polintoviruses in stony coral genomes, alongside the presence of integrated elements closely related to Polinton-like viruses (PLVs), a group of viruses that exist as free virions. These results suggest multiple integrations of polintoviruses and PLV-relatives, along with paralogous expansions, shaped stony coral genomes. Re-analysis of existing gene expression data reveals all polintovirus structural and non-structural hallmark genes are expressed, providing support for free virion production from polintoviruses. Our results, revealing a significant diversity of polintovirus across the Scleractinia order, open a new research avenue into polintovirus and their possible roles in disease, genomic plasticity, and environmental adaptation in this key group of organisms.}, }
@article {pmid38792833, year = {2024}, author = {Lima, LFO and Alker, AT and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Pre-Bleaching Coral Microbiome Is Enriched in Beneficial Taxa and Functions.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792833}, issn = {2076-2607}, abstract = {Coral reef health is tightly connected to the coral holobiont, which is the association between the coral animal and a diverse microbiome functioning as a unit. The coral holobiont depends on key services such as nitrogen and sulfur cycling mediated by the associated bacteria. However, these microbial services may be impaired in response to environmental changes, such as thermal stress. A perturbed microbiome may lead to coral bleaching and disease outbreaks, which have caused an unprecedented loss in coral cover worldwide, particularly correlated to a warming ocean. The response mechanisms of the coral holobiont under high temperatures are not completely understood, but the associated microbial community is a potential source of acquired heat-tolerance. Here we investigate the effects of increased temperature on the taxonomic and functional profiles of coral surface mucous layer (SML) microbiomes in relationship to coral-algal physiology. We used shotgun metagenomics in an experimental setting to understand the dynamics of microbial taxa and genes in the SML microbiome of the coral Pseudodiploria strigosa under heat treatment. The metagenomes of corals exposed to heat showed high similarity at the level of bacterial genera and functional genes related to nitrogen and sulfur metabolism and stress response. The coral SML microbiome responded to heat with an increase in the relative abundance of taxa with probiotic potential, and functional genes for nitrogen and sulfur acquisition. Coral-algal physiology significantly explained the variation in the microbiome at taxonomic and functional levels. These consistent and specific microbial taxa and gene functions that significantly increased in proportional abundance in corals exposed to heat are potentially beneficial to coral health and thermal resistance.}, }
@article {pmid38792817, year = {2024}, author = {Marcos, AT and Rus, MJ and Areal-Quecuty, V and Simon-Soro, A and Navarro-Pando, JM}, title = {Distinct Gastrointestinal and Reproductive Microbial Patterns in Female Holobiont of Infertility.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792817}, issn = {2076-2607}, support = {JMNP//INEBIR/ ; 2022/00000333//Program for Emerging Research by Universidad de Sevilla/ ; }, abstract = {The microbiota is in symbiosis with the human body as a holobiont. Infertility conditions affect the female reproductive tract (FRT) and its resident microbiota. However, a disturbance in homeostasis could influence the FRT and other distal body sites, such as the gastrointestinal tract (GIT). We included 21 patients with endometriosis and other infertility-associated diseases with clinical profiles and biological samples from the FRT (endometrium, endometrial fluid, and vagina), and GIT samples (oral and feces). We performed a 16S rRNA analysis of site-specific microbial communities and estimated diversity metrics. The study found body site-specific microbial patterns in the FRT-GIT. In both study groups, Lactobacillus was the most shared Amplicon Sequence Variant (ASV), a precise identifier of microbial sequences, between endometrial and vagina samples. However, shared Gardnerella and Enterobacteriaceae ASVs were linked to other conditions but not endometriosis. Remarkably, Haemophilus was a specific GIT-shared taxon in endometriosis cases. In conclusion, infertility influences distinctly the FRT and GIT microbiomes, with endometriosis showing unique microbial characteristics. We proposed the concept of 'female holobiont' as a community that comprises the host and microbes that must maintain overall homeostasis across all body sites to ensure a woman's health. Insights into these microbial patterns not only advance our understanding of the pathophysiology of infertility but also open new avenues for developing microbe-based therapeutic interventions aimed at restoring microbial balance, thereby enhancing fertility prospects.}, }
@article {pmid38792734, year = {2024}, author = {Dietert, RR and Dietert, JM}, title = {Examining Sound, Light, and Vibrations as Tools to Manage Microbes and Support Holobionts, Ecosystems, and Technologies.}, journal = {Microorganisms}, volume = {12}, number = {5}, pages = {}, pmid = {38792734}, issn = {2076-2607}, abstract = {The vast array of interconnected microorganisms across Earth's ecosystems and within holobionts has been called the "Internet of Microbes." Bacteria and archaea are masters of energy and information collection, storage, transformation, and dissemination using both "wired" and wireless (at a distance) functions. Specific tools affecting microbial energy and information functions offer effective strategies for managing microbial populations within, between, and beyond holobionts. This narrative review focuses on microbial management using a subset of physical modifiers of microbes: sound and light (as well as related vibrations). These are examined as follows: (1) as tools for managing microbial populations, (2) as tools to support new technologies, (3) as tools for healing humans and other holobionts, and (4) as potential safety dangers for microbial populations and their holobionts. Given microbial sensitivity to sound, light, and vibrations, it is critical that we assign a higher priority to the effects of these physical factors on microbial populations and microbe-laden holobionts. We conclude that specific sound, light, and/or vibrational conditions are significant therapeutic tools that can help support useful microbial populations and help to address the ongoing challenges of holobiont disease. We also caution that inappropriate sound, light, and/or vibration exposure can represent significant hazards that require greater recognition.}, }
@article {pmid38782905, year = {2024}, author = {Yee, SW and Ferrández-Peral, L and Alentorn-Moron, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Wolfreys, FD and Yang, J and Gestwicki, JE and Capra, JA and Artursson, P and Newman, JW and Marquès-Bonet, T and Giacomini, KM}, title = {Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4380}, pmid = {38782905}, issn = {2041-1723}, support = {GM117163//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 EY032161/EY/NEI NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; GM139875//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM117163/GM/NIGMS NIH HHS/United States ; EY032161//U.S. Department of Health &amp; Human Services | NIH | National Eye Institute (NEI)/ ; }, mesh = {Animals ; Humans ; Amino Acid Sequence ; Estradiol/metabolism ; HEK293 Cells ; Hominidae/genetics/metabolism ; Mutation, Missense ; Organic Cation Transport Proteins/metabolism/genetics ; *Primates/genetics ; Pseudogenes ; Substrate Specificity ; }, abstract = {SLC22A10 is an orphan transporter with unknown substrates and function. The goal of this study is to elucidate its substrate specificity and functional characteristics. In contrast to orthologs from great apes, human SLC22A10, tagged with green fluorescent protein, is not expressed on the plasma membrane. Cells expressing great ape SLC22A10 orthologs exhibit significant accumulation of estradiol-17β-glucuronide, unlike those expressing human SLC22A10. Sequence alignments reveal a proline at position 220 in humans, which is a leucine in great apes. Replacing proline with leucine in SLC22A10-P220L restores plasma membrane localization and uptake function. Neanderthal and Denisovan genomes show proline at position 220, akin to modern humans, indicating functional loss during hominin evolution. Human SLC22A10 is a unitary pseudogene due to a fixed missense mutation, P220, while in great apes, its orthologs transport sex steroid conjugates. Characterizing SLC22A10 across species sheds light on its biological role, influencing organism development and steroid homeostasis.}, }
@article {pmid38782891, year = {2024}, author = {Schwarcz, S and Kovács, P and Nyerges, P and Ujlaki, G and Sipos, A and Uray, K and Bai, P and Mikó, E}, title = {The bacterial metabolite, lithocholic acid, has antineoplastic effects in pancreatic adenocarcinoma.}, journal = {Cell death discovery}, volume = {10}, number = {1}, pages = {248}, pmid = {38782891}, issn = {2058-7716}, abstract = {Lithocholic acid (LCA) is a secondary bile acid. LCA enters the circulation after bacterial synthesis in the gastrointestinal tract, reaches distantly located cancer cells, and influences their behavior. LCA was considered carcinogenic, but recent studies demonstrated that LCA has antitumor effects. We assessed the possible role of LCA in pancreatic adenocarcinoma. At the serum reference concentration, LCA induced a multi-pronged antineoplastic program in pancreatic adenocarcinoma cells. LCA inhibited cancer cell proliferation and induced mesenchymal-to-epithelial (MET) transition that reduced cell invasion capacity. LCA induced oxidative/nitrosative stress by decreasing the expression of nuclear factor, erythroid 2-like 2 (NRF2) and inducing inducible nitric oxide synthase (iNOS). The oxidative/nitrosative stress increased protein nitration and lipid peroxidation. Suppression of oxidative stress by glutathione (GSH) or pegylated catalase (pegCAT) blunted LCA-induced MET. Antioxidant genes were overexpressed in pancreatic adenocarcinoma and decreased antioxidant levels correlated with better survival of pancreatic adenocarcinoma patients. Furthermore, LCA treatment decreased the proportions of cancer stem cells. Finally, LCA induced total and ATP-linked mitochondrial oxidation and fatty acid oxidation. LCA exerted effects through the farnesoid X receptor (FXR), vitamin D receptor (VDR), and constitutive androstane receptor (CAR). LCA did not interfere with cytostatic agents used in the chemotherapy of pancreatic adenocarcinoma. Taken together, LCA is a non-toxic compound and has antineoplastic effects in pancreatic adenocarcinoma.}, }
@article {pmid38777633, year = {2024}, author = {Leonard, A and ,  and Alberdi, A}, title = {A global initiative for ecological and evolutionary hologenomics.}, journal = {Trends in ecology &amp; evolution}, volume = {39}, number = {7}, pages = {616-620}, doi = {10.1016/j.tree.2024.03.005}, pmid = {38777633}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; Ecology ; Genomics ; Host Microbial Interactions ; *Microbiota ; }, abstract = {The Earth Hologenome Initiative (EHI) is a global collaboration to generate and analyse hologenomic data from wild animals and associated microorganisms using standardised methodologies underpinned by open and inclusive research principles. Initially focused on vertebrates, it aims to re-examine ecological and evolutionary questions by studying host-microbiota interactions from a systemic perspective.}, }
@article {pmid38777199, year = {2024}, author = {Yang, Q and Ling, J and Zhang, Y and Zhou, W and Wei, Z and Li, J and Zhang, Y and Dong, J and Qian, P}, title = {Microbial nitrogen removal in reef-building corals: A light-sensitive process.}, journal = {Chemosphere}, volume = {359}, number = {}, pages = {142394}, doi = {10.1016/j.chemosphere.2024.142394}, pmid = {38777199}, issn = {1879-1298}, mesh = {*Anthozoa/metabolism ; Animals ; *Coral Reefs ; *Nitrogen/metabolism ; *Denitrification ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Light ; Nitrogen Cycle ; Anaerobiosis ; Bacteria/metabolism ; Ecosystem ; }, abstract = {Scleractinian corals are the main framework-building groups in tropical coral reefs. In the coral holobiont, nitrogen-cycling mediated by microbes is fundamental for sustaining the coral reef ecosystems. However, little direct evidence characterizing the activities of microbial nitrogen removal via complete denitrification and anaerobic ammonium oxidation (anammox) in stony corals has been presented. In this study, multiple incubation experiments using [15]N-tracer were conducted to identify and characterize N2 production by denitrification and anammox in the stony coral Pocillopora damicornis. The rates of denitrification and anammox were recorded up to 0.765 ± 0.162 and 0.078 ± 0.009 nmol N2 cm[-2] h[-1] respectively. Denitrification contributed the majority (∼90%) of N2 production by microbial nitrogen removal in stony corals. The microbial nitrogen removal activities showed diel rhythms, which might correspond to photosynthetic oxygen production. The N2 production rates of anammox and denitrification increased with incubation time. To the authors' knowledge, this study is the first to confirm and characterize the activities of complete denitrification and anammox in stony corals via stable isotope techniques. This study extends the understanding on nitrogen-cycling in coral reefs and how it participates in corals' resilience to environmental stressors.}, }
@article {pmid38771026, year = {2024}, author = {Aires, T and Cúcio, C and Brakel, J and Weinberger, F and Wahl, M and Teles, A and Muyzer, G and Engelen, AH}, title = {Impact of persistently high sea surface temperatures on the rhizobiomes of Zostera marina in a Baltic Sea benthocosms.}, journal = {Global change biology}, volume = {30}, number = {5}, pages = {e17337}, doi = {10.1111/gcb.17337}, pmid = {38771026}, issn = {1365-2486}, support = {//Deutsche Bundesstiftung Umwelt/ ; //Deutsche Forschungsgemeinschaft/ ; CEECINST/00114/2018//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BPD/116774/2016//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04326/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04326/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0101/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; }, mesh = {*Zosteraceae/microbiology ; *Microbiota ; Plant Roots/microbiology ; Geologic Sediments/microbiology ; Hot Temperature ; Global Warming ; Oceans and Seas ; Bacteria/classification/isolation &amp; purification ; Seasons ; Climate Change ; }, abstract = {Persistently high marine temperatures are escalating and threating marine biodiversity. The Baltic Sea, warming faster than other seas, is a good model to study the impact of increasing sea surface temperatures. Zostera marina, a key player in the Baltic ecosystem, faces susceptibility to disturbances, especially under chronic high temperatures. Despite the increasing number of studies on the impact of global warming on seagrasses, little attention has been paid to the role of the holobiont. Using an outdoor benthocosm to replicate near-natural conditions, this study explores the repercussions of persistent warming on the microbiome of Z. marina and its implications for holobiont function. Results show that both seasonal warming and chronic warming, impact Z. marina roots and sediment microbiome. Compared with roots, sediments demonstrate higher diversity and stability throughout the study, but temperature effects manifest earlier in both compartments, possibly linked to premature Z. marina die-offs under chronic warming. Shifts in microbial composition, such as an increase in organic matter-degrading and sulfur-related bacteria, accompany chronic warming. A higher ratio of sulfate-reducing bacteria compared to sulfide oxidizers was found in the warming treatment which may result in the collapse of the seagrasses, due to toxic levels of sulfide. Differentiating predicted pathways for warmest temperatures were related to sulfur and nitrogen cycles, suggest an increase of the microbial metabolism, and possible seagrass protection strategies through the production of isoprene. These structural and compositional variations in the associated microbiome offer early insights into the ecological status of seagrasses. Certain taxa/genes/pathways may serve as markers for specific stresses. Monitoring programs should integrate this aspect to identify early indicators of seagrass health. Understanding microbiome changes under stress is crucial for the use of potential probiotic taxa to mitigate climate change effects. Broader-scale examination of seagrass-microorganism interactions is needed to leverage knowledge on host-microbe interactions in seagrasses.}, }
@article {pmid38770020, year = {2024}, author = {Li, Z}, title = {Editorial: Marine microbial symbioses: host-microbe interaction, holobiont's adaptation to niches and global climate change.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1416897}, pmid = {38770020}, issn = {1664-302X}, }
@article {pmid38767404, year = {2024}, author = {Sivaprakasam, S and Mohd Azim Khan, NA and Yee Fan, T and Kumarasan, Y and Sicheritz-Pontén, T and Petersen, B and Mohd Hata, E and Vadamalai, G and Parimannan, S and Rajandas, H}, title = {Complete genome sequence of potential plant growth-promoting Bacillus altitudinis strain AIMST-CREST03 isolated from paddy field bulk soil.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0026124}, pmid = {38767404}, issn = {2576-098X}, support = {T09C2-19//Collaborative Research in Engineering, Science and Technology Centre (CREST)/ ; }, abstract = {We present the complete genome of a potential plant growth-promoting bacteria Bacillus altitudinis AIMST-CREST03 isolated from a high-yielding paddy plot. The genome is 3,669,202 bp in size with a GC content of 41%. Annotation predicted 3,327 coding sequences, including several genes required for plant growth promotion.}, }
@article {pmid38759466, year = {2024}, author = {Galià-Camps, C and Junkin, L and Borrallo, X and Carreras, C and Pascual, M and Turon, X}, title = {Navigating spatio-temporal microbiome dynamics: Environmental factors and trace elements shape the symbiont community of an invasive marine species.}, journal = {Marine pollution bulletin}, volume = {203}, number = {}, pages = {116477}, doi = {10.1016/j.marpolbul.2024.116477}, pmid = {38759466}, issn = {1879-3363}, mesh = {*Microbiota ; Animals ; *Introduced Species ; *Trace Elements/analysis ; *Urochordata/microbiology ; *Seawater/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Symbiosis ; Seasons ; Gills/microbiology ; }, abstract = {The proliferation of marine invasive species is a mounting concern. While the role of microbial communities in invasive ascidian species is recognized, the role of seasonal shifts in microbiome composition remains largely unexplored. We sampled five individuals of the invasive ascidian Styela plicata quarterly from January 2020 to October 2021 in two harbours, examining gills, tunics, and surrounding water. By analysing Amplicon Sequence Variants (ASVs) and seawater trace elements, we found that compartment (seawater, tunic, or gills) was the primary differentiating factor, followed by harbour. Clear seasonal patterns were evident in seawater bacteria, less so in gills, and absent in tunics. We identified compartment-specific bacteria, as well as seasonal indicator ASVs and ASVs correlated with trace element concentrations. Among these bacteria, we found that Endozoicomonas, Hepatoplasma and Rhodobacteraceae species had reported functions which might be necessary for overcoming seasonality and trace element shifts. This study contributes to understanding microbiome dynamics in invasive holobiont systems, and the patterns found indicate a potential role in adaptation and invasiveness.}, }
@article {pmid38756985, year = {2024}, author = {Roughgarden, J}, title = {Lytic/Lysogenic Transition as a Life-History Switch.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae028}, pmid = {38756985}, issn = {2057-1577}, abstract = {The transition between lytic and lysogenic life cycles is the most important feature of the life-history of temperate viruses. To explain this transition, an optimal life-history model is offered based a discrete-time formulation of phage/bacteria population dynamics that features infection of bacteria by Poisson sampling of virions from the environment. The time step is the viral latency period. In this model, density-dependent viral absorption onto the bacterial surface produces virus/bacteria coexistence and density dependence in bacterial growth is not needed. The formula for the transition between lytic and lysogenic phases is termed the 'fitness switch'. According to the model, the virus switches from lytic to lysogenic when its population grows faster as prophage than as virions produced by lysis of the infected cells, and conversely for the switch from lysogenic to lytic. A prophage that benefits the bacterium it infects automatically incurs lower fitness upon exiting the bacterial genome, resulting in its becoming locked into the bacterial genome in what is termed here as a 'prophage lock'. The fitness switch qualitatively predicts the ecogeographic rule that environmental enrichment leads to microbialization with a concomitant increase in lysogeny, fluctuating environmental conditions promote virus-mediated horizontal gene transfer, and prophage-containing bacteria can integrate into the microbiome of a eukaryotic host forming a functionally integrated tripartite holobiont. These predictions accord more with the 'Piggyback-the-Winner' hypothesis than with the 'Kill-the-Winner' hypothesis in virus ecology.}, }
@article {pmid38750108, year = {2024}, author = {Standish, CD and Trend, J and Kleboe, J and Chalk, TB and Mahajan, S and Milton, JA and Page, TM and Robinson, LF and Stewart, JA and Foster, GL}, title = {Correlative geochemical imaging of Desmophyllum dianthus reveals biomineralisation strategy as a key coral vital effect.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {11121}, pmid = {38750108}, issn = {2045-2322}, support = {#884650/ERC_/European Research Council/International ; EP/N509747/1//University of Southampton/ ; NE/X00127X/1//NERC/ ; }, mesh = {*Anthozoa/metabolism ; Animals ; Calcification, Physiologic ; Biomineralization ; }, abstract = {The chemical and isotopic composition of stony coral skeletons form an important archive of past climate. However, these reconstructions are largely based on empirical relationships often complicated by "vital effects" arising from uncertain physiological processes of the coral holobiont. The skeletons of deep-sea corals, such as Desmophyllum dianthus, are characterised by micron-scale or larger geochemical heterogeneity associated with: (1) centres of calcification (COCs) where nucleation of new skeleton begins, and (2) fibres that thicken the skeleton. These features are difficult to sample cleanly using traditional techniques, resulting in uncertainty surrounding both the causes of geochemical differences and their influence on environmental signals. Here we combine optical, and in-situ chemical and isotopic, imaging tools across a range of spatial resolutions (~ 100 nm to 10 s of μm) in a correlative multimodal imaging (CMI) approach to isolate the microstructural geochemistry of each component. This reveals COCs are characterised by higher organic content, Mg, Li and Sr and lower U, B and δ[11]B compared to fibres, reflecting the contrasting biomineralisation mechanisms employed to construct each feature. CMI is rarely applied in Environmental/Earth Sciences, but here we illustrate the power of this approach to unpick the "vital effects" in D. dianthus, and by extension, other scleractinian corals.}, }
@article {pmid38740753, year = {2024}, author = {Nanes Sarfati, D and Xue, Y and Song, ES and Byrne, A and Le, D and Darmanis, S and Quake, SR and Burlacot, A and Sikes, J and Wang, B}, title = {Coordinated wound responses in a regenerative animal-algal holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {4032}, pmid = {38740753}, issn = {2041-1723}, support = {R35 GM138061/GM/NIGMS NIH HHS/United States ; 1R35GM138061//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Animals ; *Symbiosis ; *Regeneration/physiology ; *Photosynthesis ; Chlorophyta/genetics ; Transcription Factors/metabolism/genetics ; }, abstract = {Animal regeneration involves coordinated responses across cell types throughout the animal body. In endosymbiotic animals, whether and how symbionts react to host injury and how cellular responses are integrated across species remain unexplored. Here, we study the acoel Convolutriloba longifissura, which hosts symbiotic Tetraselmis sp. green algae and can regenerate entire bodies from tissue fragments. We show that animal injury causes a decline in the photosynthetic efficiency of the symbiotic algae, alongside two distinct, sequential waves of transcriptional responses in acoel and algal cells. The initial algal response is characterized by the upregulation of a cohort of photosynthesis-related genes, though photosynthesis is not necessary for regeneration. A conserved animal transcription factor, runt, is induced after injury and required for acoel regeneration. Knockdown of Cl-runt dampens transcriptional responses in both species and further reduces algal photosynthetic efficiency post-injury. Our results suggest that the holobiont functions as an integrated unit of biological organization by coordinating molecular networks across species through the runt-dependent animal regeneration program.}, }
@article {pmid38723604, year = {2024}, author = {Bogza, A and King, IL and Maurice, CF}, title = {Worming into infancy: Exploring helminth-microbiome interactions in early life.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {5}, pages = {639-650}, doi = {10.1016/j.chom.2024.04.009}, pmid = {38723604}, issn = {1934-6069}, mesh = {Animals ; Humans ; Infant ; *Gastrointestinal Microbiome ; *Helminthiasis/microbiology ; *Helminths/physiology ; Intestinal Diseases, Parasitic ; }, abstract = {There is rapidly growing awareness of microbiome assembly and function in early-life gut health. Although many factors, such as antibiotic use and highly processed diets, impinge on this process, most research has focused on people residing in high-income countries. However, much of the world's population lives in low- and middle-income countries (LMICs), where, in addition to erratic antibiotic use and suboptimal diets, these groups experience unique challenges. Indeed, many children in LMICs are infected with intestinal helminths. Although helminth infections are strongly associated with diverse developmental co-morbidities and induce profound microbiome changes, few studies have directly examined whether intersecting pathways between these components of the holobiont shape health outcomes in early life. Here, we summarize microbial colonization within the first years of human life, how helminth-mediated changes to the gut microbiome may affect postnatal growth, and why more research on this relationship may improve health across the lifespan.}, }
@article {pmid38719945, year = {2024}, author = {Zhang, Y and Chen, H and Lian, C and Cao, L and Guo, Y and Wang, M and Zhong, Z and Li, M and Zhang, H and Li, C}, title = {Insights into phage-bacteria interaction in cold seep Gigantidas platifrons through metagenomics and transcriptome analyses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {10540}, pmid = {38719945}, issn = {2045-2322}, support = {42030407//National Natural Science Foundation of China/ ; 2022QNLM030004//Laoshan Laboratory/ ; ZDBS-LY-DQC032//the Key Research Program of Frontier Sciences/ ; XDA22050303//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation &amp; purification ; *Gills/microbiology/virology/metabolism ; *Bivalvia/microbiology/virology/genetics ; Gene Expression Profiling ; Transcriptome ; Virome/genetics ; Bacteria/genetics/classification ; Symbiosis/genetics ; Metagenome ; }, abstract = {Viruses are crucial for regulating deep-sea microbial communities and biogeochemical cycles. However, their roles are still less characterized in deep-sea holobionts. Bathymodioline mussels are endemic species inhabiting cold seeps and harboring endosymbionts in gill epithelial cells for nutrition. This study unveiled a diverse array of viruses in the gill tissues of Gigantidas platifrons mussels and analyzed the viral metagenome and transcriptome from the gill tissues of Gigantidas platifrons mussels collected from a cold seep in the South Sea. The mussel gills contained various viruses including Baculoviridae, Rountreeviridae, Myoviridae and Siphovirdae, but the active viromes were Myoviridae, Siphoviridae, and Podoviridae belonging to the order Caudovirales. The overall viral community structure showed significant variation among environments with different methane concentrations. Transcriptome analysis indicated high expression of viral structural genes, integrase, and restriction endonuclease genes in a high methane concentration environment, suggesting frequent virus infection and replication. Furthermore, two viruses (GP-phage-contig14 and GP-phage-contig72) interacted with Gigantidas platifrons methanotrophic gill symbionts (bathymodiolin mussels host intracellular methanotrophic Gammaproteobacteria in their gills), showing high expression levels, and have huge different expression in different methane concentrations. Additionally, single-stranded DNA viruses may play a potential auxiliary role in the virus-host interaction using indirect bioinformatics methods. Moreover, the Cro and DNA methylase genes had phylogenetic similarity between the virus and Gigantidas platifrons methanotrophic gill symbionts. This study also explored a variety of viruses in the gill tissues of Gigantidas platifrons and revealed that bacteria interacted with the viruses during the symbiosis with Gigantidas platifrons. This study provides fundamental insights into the interplay of microorganisms within Gigantidas platifrons mussels in deep sea.}, }
@article {pmid38717896, year = {2024}, author = {Næsborg-Nielsen, C and Mounsey, K and Wilkinson, V and Eisenhofer, R and Burridge, CP and Carver, S}, title = {Changes in the Skin Microbiota in Two Bare-nosed Wombats (Vombatus ursinus) with Differing Recovery Trajectories following Treatment for Sarcoptic Mange.}, journal = {Journal of wildlife diseases}, volume = {60}, number = {3}, pages = {734-738}, doi = {10.7589/JWD-D-23-00136}, pmid = {38717896}, issn = {1943-3700}, mesh = {Animals ; *Scabies/veterinary/drug therapy ; *Skin/microbiology/parasitology ; *Microbiota ; Marsupialia/microbiology/parasitology ; Sarcoptes scabiei ; Male ; Female ; }, abstract = {We report tracking of bacterial skin microbiota for two bare-nosed wombats (Vombatus ursinus) following in situ treatment for sarcoptic mange. Sarcoptes scabiei, the etiologic agent, has dramatic effects on skin microbiota. Our case reports show differing disease trajectory and bacterial beta diversity between the two treated individuals.}, }
@article {pmid38713089, year = {2024}, author = {Tsang, CTT and Hui, TKL and Chung, NM and Yuen, WT and Tsang, LM}, title = {Comparative analysis of gut microbiome of mangrove brachyuran crabs revealed patterns of phylosymbiosis and codiversification.}, journal = {Molecular ecology}, volume = {33}, number = {12}, pages = {e17377}, doi = {10.1111/mec.17377}, pmid = {38713089}, issn = {1365-294X}, support = {CUHK14104623//General Research Fund of Research Grants Council, Hong Kong/ ; CUHK14119419//General Research Fund of Research Grants Council, Hong Kong/ ; }, mesh = {Animals ; *Brachyura/microbiology ; *Symbiosis ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Bacteria/classification/genetics ; Wetlands ; }, abstract = {The acquisition of microbial symbionts enables animals to rapidly adapt to and exploit novel ecological niches, thus significantly enhancing the evolutionary fitness and success of their hosts. However, the dynamics of host-microbe interactions and their evolutionary implications remain largely underexplored in marine invertebrates. Crabs of the family Sesarmidae (Crustacea: Brachyura) are dominant inhabitants of mangrove forests and are considered keystone species there. Their rapid diversification, particularly after adopting a plant-feeding lifestyle, is believed to have been facilitated by symbiotic gut microbes, enabling successful colonization of intertidal and terrestrial environments. To investigate the patterns and mechanisms shaping the microbial communities and the role of microbes in the evolution of Sesarmidae, we characterized and compared the gut microbiome compositions across 43 crab species from Sesarmidae and other mangrove-associated families using 16S metabarcoding. We found that the gut microbiome assemblages in crabs are primarily determined by host identity, with a secondary influence from environmental factors such as microhabitat and sampling location, and to a lesser extent influenced by biological factors such as sex and gut region. While patterns of phylosymbiosis (i.e. when microbial community relationships recapitulate the phylogeny of their hosts) were consistently observed in all beta-diversity metrics analysed, the strength of phylosymbiosis varied across crab families. This suggests that the bacterial assemblages in each family were differentially shaped by different degrees of host filtering and/or other evolutionary processes. Notably, Sesarmidae displayed signals of cophylogeny with its core gut bacterial genera, which likely play crucial functional roles in their hosts by providing lignocellulolytic enzymes, essential amino acids, and fatty acids supplementation. Our results support the hypothesis of microbial contribution to herbivory and terrestrialization in mangrove crabs, highlighting the tight association and codiversification of the crab holobiont.}, }
@article {pmid38709876, year = {2024}, author = {Zhao, J and Nair, S and Zhang, Z and Wang, Z and Jiao, N and Zhang, Y}, title = {Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38709876}, issn = {1751-7370}, support = {U1906216//Natural Science Foundation of China/ ; GZC20232809//Postdoctoral Fellowship Program of CPSF/ ; SDBX2022030//Shandong Province Postdoctoral Fund Project/ ; QN2022025001L//Ministry of Science and Technology Foreign Youth Expert Talent Project/ ; QDBSH20240102185//Qingdao Postdoctoral Fund Project/ ; //Ocean Negative Carbon Emissions (ONCE) Program/ ; }, mesh = {*Microbiota ; *Kelp/microbiology ; *Seawater/microbiology/virology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metagenomics ; Seaweed/microbiology/virology ; Geologic Sediments/microbiology/virology ; Prokaryotic Cells/virology/metabolism ; Bacteriophages/genetics/physiology/isolation &amp; purification ; Virome ; }, abstract = {The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.}, }
@article {pmid38707840, year = {2024}, author = {Maire, J and Collingro, A and Horn, M and van Oppen, MJH}, title = {Chlamydiae in corals: shared functional potential despite broad taxonomic diversity.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae054}, pmid = {38707840}, issn = {2730-6151}, support = {P 32112/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.}, }
@article {pmid38706829, year = {2024}, author = {Yang, K and Zheng, Y and Sun, K and Wu, X and Zhang, Z and He, C and Xiao, P}, title = {Rhizosphere microbial markers (micro-markers): A new physical examination indicator for traditional Chinese medicines.}, journal = {Chinese herbal medicines}, volume = {16}, number = {2}, pages = {180-189}, pmid = {38706829}, issn = {2589-3610}, abstract = {Rhizosphere microorganisms, as one of the most important components of the soil microbiota and plant holobiont, play a key role in the medicinal plant-soil ecosystem, which are closely related to the growth, adaptability, nutrient absorption, stress tolerance and pathogen resistance of host plants. In recent years, with the wide application of molecular biology and omics technologies, the outcomes of rhizosphere microorganisms on the health, biomass production and secondary metabolite biosynthesis of medicinal plants have received extensive attention. However, whether or to what extent rhizosphere microorganisms can contribute to the construction of the quality evaluation system of Chinese medicinal materials is still elusive. Based on the significant role of rhizosphere microbes in the survival and quality formation of medicinal plants, this paper proposed a new concept of rhizosphere microbial markers (micro-markers), expounded the relevant research methods and ideas of applying the new concept, highlighted the importance of micro-markers in the quality evaluation and control system of traditional Chinese medicines (TCMs), and introduced the potential value in soil environmental assessment, plant pest control and quality assessment of TCMs. It provides reference for developing ecological planting of TCMs and ensuring the production of high quality TCMs by regulating rhizosphere microbial communities.}, }
@article {pmid38702335, year = {2024}, author = {McGrath, AH and Lema, K and Egan, S and Wood, G and Gonzalez, SV and Kjelleberg, S and Steinberg, PD and Marzinelli, EM}, title = {Publisher Correction: Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {43}, doi = {10.1038/s41522-024-00515-7}, pmid = {38702335}, issn = {2055-5008}, }
@article {pmid38694748, year = {2024}, author = {Ranke, PS and Pepke, ML and Søraker, JS and David, G and Araya-Ajoy, YG and Wright, J and Nafstad, &#xc5;M and Rønning, B and Pärn, H and Ringsby, TH and Jensen, H and Sæther, BE}, title = {Long-distance dispersal in the short-distance dispersing house sparrow (Passer domesticus).}, journal = {Ecology and evolution}, volume = {14}, number = {5}, pages = {e11356}, pmid = {38694748}, issn = {2045-7758}, abstract = {The house sparrow (Passer domesticus) is a small passerine known to be highly sedentary. Throughout a 30-year capture-mark-recapture study, we have obtained occasional reports of recoveries far outside our main metapopulation study system, documenting unusually long dispersal distances. Our records constitute the highest occurrence of long-distance dispersal events recorded for this species in Scandinavia. Such long-distance dispersals radically change the predicted distribution of dispersal distances and connectedness for our study metapopulation. Moreover, it reveals a much greater potential for colonization than formerly recorded for the house sparrow, which is an invasive species across four continents. These rare and occasional long-distance dispersal events are challenging to document but may have important implications for the genetic composition of small and isolated populations and for our understanding of dispersal ecology and evolution.}, }
@article {pmid38693120, year = {2024}, author = {Moon, S and Han, S and Jang, IH and Ryu, J and Rha, MS and Cho, HJ and Yoon, SS and Nam, KT and Kim, CH and Park, MS and Seong, JK and Lee, WJ and Yoon, JH and Chung, YW and Ryu, JH}, title = {Airway epithelial CD47 plays a critical role in inducing influenza virus-mediated bacterial super-infection.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3666}, pmid = {38693120}, issn = {2041-1723}, support = {2019M3A9B6066971//National Research Foundation of Korea (NRF)/ ; 2016M3A9D5A01952415//National Research Foundation of Korea (NRF)/ ; 2013M3A9D5072550//National Research Foundation of Korea (NRF)/ ; 2021M3H9A1030260//National Research Foundation of Korea (NRF)/ ; RS-2023-00250400//National Research Foundation of Korea (NRF)/ ; 2015R1A3A2033475//National Research Foundation of Korea (NRF)/ ; }, mesh = {*CD47 Antigen/metabolism/genetics ; Humans ; *Staphylococcus aureus ; Animals ; *Superinfection/microbiology ; Mice ; *Epithelial Cells/metabolism/microbiology/virology ; *Staphylococcal Infections/immunology/metabolism/microbiology ; Influenza, Human/metabolism/immunology/virology ; Bacterial Adhesion ; Respiratory Mucosa/metabolism/microbiology/virology ; Mice, Inbred C57BL ; Bronchi/metabolism/cytology ; Bacterial Proteins/metabolism/genetics ; Orthomyxoviridae Infections/immunology/metabolism/virology ; Mice, Knockout ; Influenza A Virus, H1N1 Subtype ; }, abstract = {Respiratory viral infection increases host susceptibility to secondary bacterial infections, yet the precise dynamics within airway epithelia remain elusive. Here, we elucidate the pivotal role of CD47 in the airway epithelium during bacterial super-infection. We demonstrated that upon influenza virus infection, CD47 expression was upregulated and localized on the apical surface of ciliated cells within primary human nasal or bronchial epithelial cells. This induced CD47 exposure provided attachment sites for Staphylococcus aureus, thereby compromising the epithelial barrier integrity. Through bacterial adhesion assays and in vitro pull-down assays, we identified fibronectin-binding proteins (FnBP) of S. aureus as a key component that binds to CD47. Furthermore, we found that ciliated cell-specific CD47 deficiency or neutralizing antibody-mediated CD47 inactivation enhanced in vivo survival rates. These findings suggest that interfering with the interaction between airway epithelial CD47 and pathogenic bacterial FnBP holds promise for alleviating the adverse effects of super-infection.}, }
@article {pmid38676557, year = {2024}, author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M}, title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38676557}, issn = {1751-7370}, support = {T 1218//Austrian Science Fund/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Symbiosis ; *Nitrification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Phylogeny ; *Ammonia/metabolism ; Nitrites/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Metagenome ; }, abstract = {Ammonia-oxidizing archaea and nitrite-oxidizing bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification-the aerobic oxidation of ammonia to nitrite and further to nitrate-and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterize two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualization, and physiological rate measurements. Both represent a new genus in the ammonia-oxidizing archaeal class Nitrososphaeria and the nitrite-oxidizing bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonized by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidizing archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e. ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidizing bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidizers with ammonia via the utilization of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.}, }
@article {pmid38670883, year = {2024}, author = {Tan, W and Nian, H and Tran, LP and Jin, J and Lian, T}, title = {Small peptides: novel targets for modulating plant-rhizosphere microbe interactions.}, journal = {Trends in microbiology}, volume = {32}, number = {11}, pages = {1072-1083}, doi = {10.1016/j.tim.2024.03.011}, pmid = {38670883}, issn = {1878-4380}, mesh = {*Rhizosphere ; *Plants/microbiology ; *Peptides/metabolism ; *Plant Roots/microbiology ; Soil Microbiology ; Signal Transduction ; Plant Development ; Bacteria/metabolism ; Microbiota/physiology ; Symbiosis ; }, abstract = {The crucial role of rhizosphere microbes in plant growth and their resilience to environmental stresses underscores the intricate communication between microbes and plants. Plants are equipped with a diverse set of signaling molecules that facilitate communication across different biological kingdoms, although our comprehension of these mechanisms is still evolving. Small peptides produced by plants (SPPs) and microbes (SPMs) play a pivotal role in intracellular signaling and are essential in orchestrating various plant development stages. In this review, we posit that SPPs and SPMs serve as crucial signaling agents for the bidirectional cross-kingdom communication between plants and rhizosphere microbes. We explore several potential mechanistic pathways through which this communication occurs. Additionally, we propose that leveraging small peptides, inspired by plant-rhizosphere microbe interactions, represents an innovative approach in the field of holobiont engineering.}, }
@article {pmid38653719, year = {2024}, author = {Williams, A}, title = {Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {5}, pages = {}, pmid = {38653719}, issn = {1574-6941}, mesh = {*Anthozoa/genetics/microbiology ; Animals ; *Symbiosis ; Genomics ; Metabolomics ; Stress, Physiological ; Proteomics ; Computational Biology/methods ; Multiomics ; }, abstract = {Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.}, }
@article {pmid38651923, year = {2024}, author = {Michelle JiaMin, L and Karthikeyan, P and Kumaresan, R and Millard, A and Parimannan, S and Rajandas, H}, title = {Complete genome sequence of Enterococcus faecalis phage EF_RCK.}, journal = {Microbiology resource announcements}, volume = {13}, number = {6}, pages = {e0010924}, pmid = {38651923}, issn = {2576-098X}, support = {FRGS/1/2018/SKK14/AIMST/03/1//Ministry of Higher Education Malaysia/ ; }, abstract = {A lytic bacteriophage EF_RCK infecting Enterococcus faecalis was isolated from a water sample collected in a raw cockle storage container at Taman Ria market, Sungai Petani, Malaysia. The phage has a 57,848-bp double-stranded DNA genome harboring 107 protein-encoding genes and shares 90.9% nucleotide similarity with Enterococcus phage EFKL (Saphexavirus genus).}, }
@article {pmid38641475, year = {2024}, author = {Addison, SL and Rúa, MA and Smaill, SJ and Singh, BK and Wakelin, SA}, title = {Partner or perish: tree microbiomes and climate change.}, journal = {Trends in plant science}, volume = {29}, number = {9}, pages = {1029-1040}, doi = {10.1016/j.tplants.2024.03.008}, pmid = {38641475}, issn = {1878-4372}, mesh = {*Climate Change ; *Microbiota/physiology ; *Trees/microbiology/growth &amp; development/physiology ; }, abstract = {Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.}, }
@article {pmid38627822, year = {2024}, author = {Williams, J and Pettorelli, N and Hartmann, AC and Quinn, RA and Plaisance, L and O'Mahoney, M and Meyer, CP and Fabricius, KE and Knowlton, N and Ransome, E}, title = {Decline of a distinct coral reef holobiont community under ocean acidification.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {75}, pmid = {38627822}, issn = {2049-2618}, support = {NE/R012229/1//Natural Environment Research Council/ ; 2022717//National Science Foundation/ ; 1558868//National Science Foundation/ ; 1558868//National Science Foundation/ ; }, mesh = {Animals ; Coral Reefs ; Ecosystem ; Hydrogen-Ion Concentration ; Ocean Acidification ; Seawater ; *Anthozoa/physiology ; *Microbiota ; }, abstract = {BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome.<br><br>RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation.<br><br>CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings&#xa0;suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.}, }
@article {pmid38607980, year = {2024}, author = {Partida-Martínez, LP}, title = {Fungal holobionts as blueprints for synthetic endosymbiotic systems.}, journal = {PLoS biology}, volume = {22}, number = {4}, pages = {e3002587}, pmid = {38607980}, issn = {1545-7885}, mesh = {*Reproduction ; *Symbiosis ; }, abstract = {Rhizopus microsporus is an example of a fungal holobiont. Strains of this species can harbor bacterial and viral endosymbionts inherited by the next generation. These microbial allies increase pathogenicity and defense and control asexual and sexual reproduction.}, }
@article {pmid38606974, year = {2024}, author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS}, title = {Localization and symbiotic status of probiotics in the coral holobiont.}, journal = {mSystems}, volume = {9}, number = {5}, pages = {e0026124}, pmid = {38606974}, issn = {2379-5077}, support = {FCC/1/1976-40-01,BAS/1/1095-01-0//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Anthozoa/microbiology/physiology ; *Symbiosis/physiology ; Animals ; *Probiotics/pharmacology ; In Situ Hybridization, Fluorescence ; Halomonas/physiology ; Microbiota/physiology ; }, abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.<br><br>IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.}, }
@article {pmid38605712, year = {2024}, author = {Garrido, M and Minard, G and Veiga, J and Martínez-de la Puente, J}, title = {Editorial: Ecological interactions between mosquitoes and their microbiota: implications for pathogen transmission.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1395348}, pmid = {38605712}, issn = {1664-302X}, }
@article {pmid38602593, year = {2024}, author = {Maslin, M and Paix, B and van der Windt, N and Ambo-Rappe, R and Debitus, C and Gaertner-Mazouni, N and Ho, R and de Voogd, NJ}, title = {Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {65}, pmid = {38602593}, issn = {1572-9699}, support = {08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 3299/MTF//Government of French Polynesia/ ; 3299/MTF//Government of French Polynesia/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, mesh = {Animals ; *Porifera ; Aquaculture ; Agriculture ; *Microbiota ; Polynesia ; }, abstract = {Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.}, }
@article {pmid38601888, year = {2024}, author = {Sherwani, MK and Gopalakrishnan, S}, title = {A systematic literature review: deep learning techniques for synthetic medical image generation and their applications in radiotherapy.}, journal = {Frontiers in radiology}, volume = {4}, number = {}, pages = {1385742}, pmid = {38601888}, issn = {2673-8740}, abstract = {The aim of this systematic review is to determine whether Deep Learning (DL) algorithms can provide a clinically feasible alternative to classic algorithms for synthetic Computer Tomography (sCT). The following categories are presented in this study: ∙ MR-based treatment planning and synthetic CT generation techniques. ∙ Generation of synthetic CT images based on Cone Beam CT images. ∙ Low-dose CT to High-dose CT generation. ∙ Attenuation correction for PET images. To perform appropriate database searches, we reviewed journal articles published between January 2018 and June 2023. Current methodology, study strategies, and results with relevant clinical applications were analyzed as we outlined the state-of-the-art of deep learning based approaches to inter-modality and intra-modality image synthesis. This was accomplished by contrasting the provided methodologies with traditional research approaches. The key contributions of each category were highlighted, specific challenges were identified, and accomplishments were summarized. As a final step, the statistics of all the cited works from various aspects were analyzed, which revealed that DL-based sCTs have achieved considerable popularity, while also showing the potential of this technology. In order to assess the clinical readiness of the presented methods, we examined the current status of DL-based sCT generation.}, }
@article {pmid38589941, year = {2024}, author = {Liu, F and Ryu, T and Ravasi, T and Wang, X and Wang, G and Li, Z}, title = {Niche-dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge Mycale Grandis.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {22}, pmid = {38589941}, issn = {2524-6372}, support = {31861143020, 41776138//This work was supported by the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Most researches on sponge holobionts focus primarily on symbiotic microbes, yet data at the level of the sponge hologenome are still relatively scarce. Understanding of the sponge host and its microbial gene expression profiles and the host-microbes interplay in different niches represents a key aspect of sponge hologenome. Using the Hawaiian demosponge Mycale grandis in different niches as a model, i.e. on rocks, on the surface of coral Porites compressa, under alga Gracilaria salicornia, we compared the bacterial and fungal community structure, functional gene diversity, expression pattern and the host transcriptome by integrating open-format (deep sequencing) and closed-format (GeoChip microarray) high-throughput techniques.<br><br>RESULTS: Little inter-niche variation in bacterial and fungal phylogenetic diversity was detected for M. grandis in different niches, but a clear niche-dependent variability in the functional gene diversity and expression pattern of M. grandis host and its symbiotic microbiota was uncovered by GeoChip microarray and transcriptome analyses. Particularly, sponge host genes related to innate immunity and microbial recognition showed a strong correlation with the microbial symbionts' functional gene diversity and transcriptional richness in different niches. The cross-niche variability with respect to the symbiont functional gene diversity and the transcriptional richness of M. grandis holobiont putatively reflects the interplay of niche-specific selective pressure and the symbiont functional diversity.<br><br>CONCLUSIONS: Niche-dependent gene expression profiles of M. grandis hologenome and the host-microbes interplay were suggested though little inter-niche variation in bacterial and fungal diversity was detected, particularly the sponge innate immunity was found to be closely related to the symbiotic microbes. Altogether, these findings provide novel insights into the black box of one sponge holobiont in different niches at the hologenome level.}, }
@article {pmid38589605, year = {2024}, author = {Mazzella, V and Dell'Anno, A and Etxebarría, N and González-Gaya, B and Nuzzo, G and Fontana, A and Núñez-Pons, L}, title = {High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {422}, pmid = {38589605}, issn = {2399-3642}, mesh = {Phylogeny ; *Microbiota ; Biological Evolution ; *Cyanobacteria/genetics ; Metabolome ; }, abstract = {Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.}, }
@article {pmid38587594, year = {2024}, author = {Van Gerrewey, T and Chung, HS}, title = {MAPK Cascades in Plant Microbiota Structure and Functioning.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {62}, number = {3}, pages = {231-248}, pmid = {38587594}, issn = {1976-3794}, support = {2021R1F1A1048959//Ministry of Science and ICT, South Korea/ ; BOF/STA/202002/007//Bijzonder Onderzoeksfonds UGent/ ; }, mesh = {*Microbiota/physiology ; *Plants/microbiology ; *Plant Roots/microbiology ; MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/metabolism/genetics ; Symbiosis ; Plant Immunity ; }, abstract = {Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules that coordinate diverse biological processes such as plant innate immunity and development. Recently, MAPK cascades have emerged as pivotal regulators of the plant holobiont, influencing the assembly of normal plant microbiota, essential for maintaining optimal plant growth and health. In this review, we provide an overview of current knowledge on MAPK cascades, from upstream perception of microbial stimuli to downstream host responses. Synthesizing recent findings, we explore the intricate connections between MAPK signaling and the assembly and functioning of plant microbiota. Additionally, the role of MAPK activation in orchestrating dynamic changes in root exudation to shape microbiota composition is discussed. Finally, our review concludes by emphasizing the necessity for more sophisticated techniques to accurately decipher the role of MAPK signaling in establishing the plant holobiont relationship.}, }
@article {pmid38575584, year = {2024}, author = {Messer, LF and Bourne, DG and Robbins, SJ and Clay, M and Bell, SC and McIlroy, SJ and Tyson, GW}, title = {A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2902}, pmid = {38575584}, issn = {2041-1723}, mesh = {Animals ; *Anthozoa/genetics/microbiology ; *Resilience, Psychological ; *Microbiota/genetics ; Metagenome/genetics ; Nitrogen ; Coral Reefs ; Symbiosis/genetics ; }, abstract = {Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.}, }
@article {pmid38564842, year = {2024}, author = {Chatterjee, S and Leach, ST and Lui, K and Mishra, A}, title = {Symbiotic symphony: Understanding host-microbiota dialogues in a spatial context.}, journal = {Seminars in cell &amp; developmental biology}, volume = {161-162}, number = {}, pages = {22-30}, doi = {10.1016/j.semcdb.2024.03.001}, pmid = {38564842}, issn = {1096-3634}, mesh = {Humans ; *Symbiosis ; Bacteria/genetics ; *Microbiota/genetics ; Microbial Interactions ; }, abstract = {Modern precision sequencing techniques have established humans as a holobiont that live in symbiosis with the microbiome. Microbes play an active role throughout the life of a human ranging from metabolism and immunity to disease tolerance. Hence, it is of utmost significance to study the eukaryotic host in conjunction with the microbial antigens to obtain a complete picture of the host-microbiome crosstalk. Previous attempts at profiling host-microbiome interactions have been either superficial or been attempted to catalogue eukaryotic transcriptomic profile and microbial communities in isolation. Additionally, the nature of such immune-microbial interactions is not random but spatially organised. Hence, for a holistic clinical understanding of the interplay between hosts and microbiota, it's imperative to concurrently analyze both microbial and host genetic information, ensuring the preservation of their spatial integrity. Capturing these interactions as a snapshot in time at their site of action has the potential to transform our understanding of how microbes impact human health. In examining early-life microbial impacts, the limited presence of communities compels analysis within reduced biomass frameworks. However, with the advent of spatial transcriptomics we can address this challenge and expand our horizons of understanding these interactions in detail. In the long run, simultaneous spatial profiling of host-microbiome dialogues can have enormous clinical implications especially in gaining mechanistic insights into the disease prognosis of localised infections and inflammation. This review addresses the lacunae in host-microbiome research and highlights the importance of profiling them together to map their interactions while preserving their spatial context.}, }
@article {pmid38560995, year = {2024}, author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, MF and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G}, title = {Complexity of avian evolution revealed by family-level genomes.}, journal = {Nature}, volume = {629}, number = {8013}, pages = {851-860}, pmid = {38560995}, issn = {1476-4687}, mesh = {Animals ; *Birds/genetics/classification/anatomy &amp; histology ; Brain/anatomy &amp; histology ; *Evolution, Molecular ; Extinction, Biological ; *Genome/genetics ; Genomics ; *Phylogeny ; Population Density ; Male ; Female ; }, abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions[1-3]. Here we address these issues by analysing the genomes of 363 bird species[4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.}, }
@article {pmid38560465, year = {2024}, author = {Auclert, LZ and Chhanda, MS and Derome, N}, title = {Interwoven processes in fish development: microbial community succession and immune maturation.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17051}, pmid = {38560465}, issn = {2167-8359}, mesh = {Animals ; *Zebrafish ; *Microbiota ; Bacteria ; Inflammation ; Anti-Bacterial Agents ; }, abstract = {Fishes are hosts for many microorganisms that provide them with beneficial effects on growth, immune system development, nutrition and protection against pathogens. In order to avoid spreading of infectious diseases in aquaculture, prevention includes vaccinations and routine disinfection of eggs and equipment, while curative treatments consist in the administration of antibiotics. Vaccination processes can stress the fish and require substantial farmer's investment. Additionally, disinfection and antibiotics are not specific, and while they may be effective in the short term, they have major drawbacks in the long term. Indeed, they eliminate beneficial bacteria which are useful for the host and promote the raising of antibiotic resistance in beneficial, commensal but also in pathogenic bacterial strains. Numerous publications highlight the importance that plays the diversified microbial community colonizing fish (i.e., microbiota) in the development, health and ultimately survival of their host. This review targets the current knowledge on the bidirectional communication between the microbiota and the fish immune system during fish development. It explores the extent of this mutualistic relationship: on one hand, the effect that microbes exert on the immune system ontogeny of fishes, and on the other hand, the impact of critical steps in immune system development on the microbial recruitment and succession throughout their life. We will first describe the immune system and its ontogeny and gene expression steps in the immune system development of fishes. Secondly, the plurality of the microbiotas (depending on host organism, organ, and development stage) will be reviewed. Then, a description of the constant interactions between microbiota and immune system throughout the fish's life stages will be discussed. Healthy microbiotas allow immune system maturation and modulation of inflammation, both of which contribute to immune homeostasis. Thus, immune equilibrium is closely linked to microbiota stability and to the stages of microbial community succession during the host development. We will provide examples from several fish species and describe more extensively the mechanisms occurring in zebrafish model because immune system ontogeny is much more finely described for this species, thanks to the many existing zebrafish mutants which allow more precise investigations. We will conclude on how the conceptual framework associated to the research on the immune system will benefit from considering the relations between microbiota and immune system maturation. More precisely, the development of active tolerance of the microbiota from the earliest stages of life enables the sustainable establishment of a complex healthy microbial community in the adult host. Establishing a balanced host-microbiota interaction avoids triggering deleterious inflammation, and maintains immunological and microbiological homeostasis.}, }
@article {pmid38553475, year = {2024}, author = {McGrath, AH and Lema, K and Egan, S and Wood, G and Gonzalez, SV and Kjelleberg, S and Steinberg, PD and Marzinelli, EM}, title = {Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {33}, pmid = {38553475}, issn = {2055-5008}, support = {Holsworth Wildlife Endowment//Ecological Society of Australia (ESA)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; DP180104041//Department of Education and Training | Australian Research Council (ARC)/ ; }, mesh = {*Microbiota/physiology ; Bacteria/genetics ; Host Microbial Interactions ; Anti-Bacterial Agents ; }, abstract = {Host-associated microbiota are critical for eukaryotic host functioning, to the extent that hosts and their associated microbial communities are often considered "holobionts". Most studies of holobionts have focused on descriptive approaches or have used model systems, usually in the laboratory, to understand host-microbiome interactions. To advance our understanding of host-microbiota interactions and their wider ecological impacts, we need experimental frameworks that can explore causation in non-model hosts, which often have highly diverse microbiota, and in their natural ecological setting (i.e. in the field). We used a dominant habitat-forming seaweed, Hormosira banksii, to explore these issues and to experimentally test host-microbiota interactions in a non-model holobiont. The experimental protocols were aimed at trying to disentangle microbially mediated effects on hosts from direct effects on hosts associated with the methods employed to manipulate host-microbiota. This was done by disrupting the microbiome, either through removal/disruption using a combination of antimicrobial treatments, or additions of specific taxa via inoculations, or a combination of thew two. The experiments were done in mesocosms and in the field. Three different antibiotic treatments were used to disrupt seaweed-associated microbiota to test whether disturbances of microbiota, particularly bacteria, would negatively affect host performance. Responses of bacteria to these disturbances were complex and differed substantially among treatments, with some antibacterial treatments having little discernible effect. However, the temporal sequence of responses antibiotic treatments, changes in bacterial diversity and subsequent decreases in host performance, strongly suggested an effect of the microbiota on host performance in some treatments, as opposed to direct effects of the antibiotics. To further test these effects, we used 16S-rRNA-gene sequencing to identify bacterial taxa that were either correlated, or uncorrelated, with poor host performance following antibiotic treatment. These were then isolated and used in inoculation experiments, independently or in combination with the previously used antibiotic treatments. Negative effects on host performance were strongest where specific microbial antimicrobials treatments were combined with inoculations of strains that were correlated with poor host performance. For these treatments, negative host effects persisted the entire experimental period (12 days), even though treatments were only applied at the beginning of the experiment. Host performance recovered in all other treatments. These experiments provide a framework for exploring causation and disentangling microbially mediated vs. direct effects on hosts for ecologically important, non-model holobionts in the field. This should allow for better predictions of how these systems will respond to, and potentially mitigate, environmental disturbances in their natural context.}, }
@article {pmid38548931, year = {2024}, author = {Friedländer, MR and Gilbert, MTP}, title = {How ancient RNA survives and what we can learn from it.}, journal = {Nature reviews. Molecular cell biology}, volume = {25}, number = {6}, pages = {417-418}, pmid = {38548931}, issn = {1471-0080}, }
@article {pmid38543670, year = {2024}, author = {Tosado-Rodríguez, E and Alvarado-Vélez, I and Romaguera, J and Godoy-Vitorino, F}, title = {Vaginal Microbiota and HPV in Latin America: A Narrative Review.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, pmid = {38543670}, issn = {2076-2607}, support = {U54 CA096297/CA/NCI NIH HHS/United States ; U54 MD007587/MD/NIMHD NIH HHS/United States ; U54MD007600/MD/NIMHD NIH HHS/United States ; P20GM103475/GM/NIGMS NIH HHS/United States ; U54 MD007600/MD/NIMHD NIH HHS/United States ; CA096297/CA/NCI NIH HHS/United States ; U54MD007587/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal microbiota is a specific case within the human microbiome where diversity is lower to maintain a chemical barrier of protection against infections. This narrative review focuses on the vaginal microbiome. It summarizes key findings on how native bacteria protect women from disease or predispose them to damaging inflammatory processes with an emphasis on the role of HPV infections in Latin America, one of the world's regions with the highest cervical cancer prevalence.}, }
@article {pmid38537113, year = {2024}, author = {Beza-Beza, CF and Wiegmann, BM and Ware, JA and Petersen, M and Gunter, N and Cole, ME and Schwarz, M and Bertone, MA and Young, D and Mikaelyan, A}, title = {Chewing through challenges: Exploring the evolutionary pathways to wood-feeding in insects.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {46}, number = {5}, pages = {e2300241}, doi = {10.1002/bies.202300241}, pmid = {38537113}, issn = {1521-1878}, mesh = {Animals ; *Biological Evolution ; Feeding Behavior/physiology ; *Gastrointestinal Microbiome ; *Insecta/classification/microbiology/physiology ; Mastication ; Phylogeny ; *Wood ; }, abstract = {Decaying wood, while an abundant and stable resource, presents considerable nutritional challenges due to its structural rigidity, chemical recalcitrance, and low nitrogen content. Despite these challenges, certain insect lineages have successfully evolved saproxylophagy (consuming and deriving sustenance from decaying wood), impacting nutrient recycling in ecosystems and carbon sequestration dynamics. This study explores the uneven phylogenetic distribution of saproxylophagy across insects and delves into the evolutionary origins of this trait in disparate insect orders. Employing a comprehensive analysis of gut microbiome data, from both saproxylophagous insects and their non-saproxylophagous relatives, including new data from unexplored wood-feeding insects, this Hypothesis paper discusses the broader phylogenetic context and potential adaptations necessary for this dietary specialization. The study proposes the "Detritivore-First Hypothesis," suggesting an evolutionary pathway to saproxylophagy through detritivory, and highlights the critical role of symbiotic gut microbiomes in the digestion of decaying wood.}, }
@article {pmid38536705, year = {2024}, author = {Kriaa, A and Mariaule, V and De Rudder, C and Jablaoui, A and Sokol, H and Wilmes, P and Maguin, E and Rhimi, M}, title = {From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333434}, pmid = {38536705}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Models, Animal ; *Microbiota ; Host Microbial Interactions ; Dysbiosis ; }, abstract = {Chronic digestive disorders are of increasing incidence worldwide with expensive treatments and no available cure. Available therapeutic schemes mainly rely on symptom relief, with large degrees of variability in patients' response to such treatments, underlining the need for new therapeutic strategies. There are strong indications that the gut microbiota's contribution seems to be a key modulator of disease activity and patients' treatment responses. Hence, efforts have been devoted to understanding host-microbe interactions and the mechanisms underpinning such variability. Animal models, being the gold standard, provide valuable mechanistic insights into host-microbe interactions. However, they are not exempt from limitations prompting the development of alternative methods. Emerging microfluidic technologies and gut-on-chip models were shown to mirror the main features of gut physiology and disease state, reflect microbiota modification, and include functional readouts for studying host responses. In this commentary, we discuss the relevance of animal models in understanding host-microbe interactions and how gut-on-chip technology holds promises for addressing patient variability in responses to chronic digestive disease treatment.}, }
@article {pmid38535570, year = {2024}, author = {Arnholdt-Schmitt, B and Sircar, D and Aziz, S and Germano, TA and Thiers, KLL and Noceda, C and Bharadwaj, R and Mohanapriya, G and Costa, JH}, title = {Transcriptome Analyses in Adult Olive Trees Indicate Acetaldehyde Release and Cyanide-Mediated Respiration Traits as Critical for Tolerance against Xylella fastidiosa and Suggest AOX Gene Family as Marker for Multiple-Resilience.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38535570}, issn = {2076-0817}, mesh = {*Olea/microbiology/metabolism/genetics ; *Xylella/genetics/metabolism ; *Plant Diseases/microbiology/virology ; *Gene Expression Profiling ; *Plant Proteins/genetics/metabolism ; *Acetaldehyde/metabolism ; Cyanides/metabolism ; Mitochondrial Proteins/genetics/metabolism ; Oxidoreductases/genetics/metabolism ; Transcriptome ; SARS-CoV-2 ; COVID-19 ; Humans ; }, abstract = {Xylella fastidiosa (Xf) is a global bacterial threat for a diversity of plants, including olive trees. However, current understanding of host responses upon Xf-infection is limited to allow early disease prediction, diagnosis, and sustainable strategies for breeding on plant tolerance. Recently, we identified a major complex trait for early de novo programming, named CoV-MAC-TED, by comparing early transcriptome data during plant cell survival with SARS-CoV-2-infected human cells. This trait linked ROS/RNS balancing during first hours of stress perception with increased aerobic fermentation connected to alpha-tubulin-based cell restructuration and control of cell cycle progression. Furthermore, our group had advanced concepts and strategies for breeding on plant holobionts. Here, we studied tolerance against Xf-infection by applying a CoV-MAC-TED-related gene set to (1) progress proof-of-principles, (2) highlight the importance of individual host responses for knowledge gain, (3) benefit sustainable production of Xf-threatened olive, (4) stimulate new thinking on principle roles of secondary metabolite synthesis and microbiota for system equilibration and, (5) advance functional marker development for resilience prediction including tolerance to Xf-infections. We performed hypothesis-driven complex analyses in an open access transcriptome of primary target xylem tissues of naturally Xf-infected olive trees of the Xf-tolerant cv. Leccino and the Xf-susceptible cv. Ogliarola. The results indicated that cyanide-mediated equilibration of oxygen-dependent respiration and carbon-stress alleviation by the help of increased glycolysis-driven aerobic fermentation paths and phenolic metabolism associate to tolerance against Xf. Furthermore, enhanced alternative oxidase (AOX) transcript levels through transcription Gleichschaltung linked to quinic acid synthesis appeared as promising trait for functional marker development. Moreover, the results support the idea that fungal endophytes strengthen Xf-susceptible genotypes, which lack efficient AOX functionality. Overall, this proof-of-principles approach supports the idea that efficient regulation of the multi-functional AOX gene family can assist selection on multiple-resilience, which integrates Xf-tolerance, and stimulates future validation across diverse systems.}, }
@article {pmid38535568, year = {2024}, author = {Fan, MZ and Kim, SW}, title = {Modulation of Porcine Gut Microbiota and Microbiome: Hologenomic, Dietary, and Endogenous Factors.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, pmid = {38535568}, issn = {2076-0817}, support = {na//the Natural Science and Engineering Research Council (NSERC) of Canada; Agriculture, Agri-Food Canada (AAFC) Swine Innovation Porc (SIP) Swine Cluster Program; and the Metagen Enzyme Corporation. North Carolina Agricultural Foundation (Raleigh, NC, USA) a/ ; }, mesh = {Animals ; Swine/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Animal Feed/microbiology ; }, abstract = {Global pig production contributes to about 35% of the world's meat production and consumption [...].}, }
@article {pmid38534358, year = {2024}, author = {Andrews, K and Landeryou, T and Sicheritz-Pontén, T and Nale, JY}, title = {Diverse Prophage Elements of Salmonella enterica Serovars Show Potential Roles in Bacterial Pathogenicity.}, journal = {Cells}, volume = {13}, number = {6}, pages = {}, pmid = {38534358}, issn = {2073-4409}, mesh = {*Salmonella enterica/genetics ; Virulence/genetics ; Prophages/genetics ; Serogroup ; Salmonella ; }, abstract = {Nontyphoidal salmonellosis is an important foodborne and zoonotic infection that causes significant global public health concern. Diverse serovars are multidrug-resistant and encode several virulence indicators; however, little is known on the role prophages play in driving these traits. Here, we extracted prophages from seventy-five Salmonella genomes which represent the fifteen important serovars in the United Kingdom. We analyzed the intact prophages for the presence of virulence genes and established their genomic relationships. We identified 615 prophages from the Salmonella strains, from which 195 prophages are intact, 332 are incomplete, while 88 are questionable. The average prophage carriage was found to be 'extreme' in S. Heidelberg, S. Inverness, and S. Newport (10.2-11.6 prophages/strain), 'high' in S. Infantis, S. Stanley, S. Typhimurium, and S. Virchow (8.2-9.0 prophages/strain), 'moderate' in S. Agona, S. Braenderup, S. Bovismorbificans, S. Choleraesuis, S. Dublin, and S. Java (6.0-7.8 prophages/strain), and 'low' in S. Javiana and S. Enteritidis (5.8 prophages/strain). Cumulatively, 61 virulence genes (1500 gene copies) were detected from representative intact prophages and linked to Salmonella delivery/secretion system (42.62%), adherence (32.7%), magnesium uptake (3.88%), regulation (5%), stress/survival (1.6%), toxins (10%), and antivirulence (1.6%). Diverse clusters were formed among the intact prophages and with bacteriophages of other enterobacteria, suggesting different lineages and associations. Our work provides a strong body of data to support the contributions diverse prophages make to the pathogenicity of Salmonella, including thirteen previously unexplored serovars.}, }
@article {pmid38529721, year = {2024}, author = {Pankey, MS and Gochfeld, DJ and Gastaldi, M and Macartney, KJ and Clayshulte Abraham, A and Slattery, M and Lesser, MP}, title = {Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin.}, journal = {Molecular ecology}, volume = {33}, number = {8}, pages = {e17321}, doi = {10.1111/mec.17321}, pmid = {38529721}, issn = {1365-294X}, support = {1632333//Division of Ocean Sciences/ ; 1632348//Division of Ocean Sciences/ ; 1638289//Division of Ocean Sciences/ ; 1638296//Division of Ocean Sciences/ ; }, mesh = {Animals ; Phylogeny ; *Agelas ; Caribbean Region ; West Indies ; Coral Reefs ; *Porifera/genetics ; }, abstract = {Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.}, }
@article {pmid38526019, year = {2024}, author = {Duchêne, DA and Duchêne, S and Stiller, J and Heller, R and Ho, SYW}, title = {ClockstaRX: Testing Molecular Clock Hypotheses With Genomic Data.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38526019}, issn = {1759-6653}, support = {H2020-MSCA-IF-2019-883832/ERC_/European Research Council/International ; APP1157586/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Evolution, Molecular ; *Models, Genetic ; Genomics ; Genome ; Biological Evolution ; Phylogeny ; }, abstract = {Phylogenomic data provide valuable opportunities for studying evolutionary rates and timescales. These analyses require theoretical and statistical tools based on molecular clocks. We present ClockstaRX, a flexible platform for exploring and testing evolutionary rate signals in phylogenomic data. Here, information about evolutionary rates in branches across gene trees is placed in Euclidean space, allowing data transformation, visualization, and hypothesis testing. ClockstaRX implements formal tests for identifying groups of loci and branches that make a large contribution to patterns of rate variation. This information can then be used to test for drivers of genomic evolutionary rates or to inform models for molecular dating. Drawing on the results of a simulation study, we recommend forms of data exploration and filtering that might be useful prior to molecular-clock analyses.}, }
@article {pmid38525076, year = {2024}, author = {Pineda-Mendoza, RM and Gutiérrez-Ávila, JL and Salazar, KF and Rivera-Orduña, FN and Davis, TS and Zúñiga, G}, title = {Comparative metabarcoding and biodiversity of gut-associated fungal assemblages of Dendroctonus species (Curculionidae: Scolytinae).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1360488}, pmid = {38525076}, issn = {1664-302X}, abstract = {The genus Dendroctonus is a Holarctic taxon composed of 21 nominal species; some of these species are well known in the world as disturbance agents of forest ecosystems. Under the bark of the host tree, these insects are involved in complex and dynamic associations with phoretic ectosymbiotic and endosymbiotic communities. Unlike filamentous fungi and bacteria, the ecological role of yeasts in the bark beetle holobiont is poorly understood, though yeasts were the first group to be recorded as microbial symbionts of these beetles. Our aim was characterize and compare the gut fungal assemblages associated to 14 species of Dendroctonus using the internal transcribed spacer 2 (ITS2) region. A total of 615,542 sequences were recovered yielding 248 fungal amplicon sequence variants (ASVs). The fungal diversity was represented by 4 phyla, 16 classes, 34 orders, 54 families, and 71 genera with different relative abundances among Dendroctonus species. The α-diversity consisted of 32 genera of yeasts and 39 genera of filamentous fungi. An analysis of β-diversity indicated differences in the composition of the gut fungal assemblages among bark beetle species, with differences in species and phylogenetic diversity. A common core mycobiome was recognized at the genus level, integrated mainly by Candida present in all bark beetles, Nakazawaea, Cladosporium, Ogataea, and Yamadazyma. The bipartite networks confirmed that these fungal genera showed a strong association between beetle species and dominant fungi, which are key to maintaining the structure and stability of the fungal community. The functional variation in the trophic structure was identified among libraries and species, with pathotroph-saprotroph-symbiotroph represented at the highest frequency, followed by saprotroph-symbiotroph, and saprotroph only. The overall network suggested that yeast and fungal ASVs in the gut of these beetles showed positive and negative associations among them. This study outlines a mycobiome associated with Dendroctonus nutrition and provides a starting point for future in vitro and omics approaches addressing potential ecological functions and interactions among fungal assemblages and beetle hosts.}, }
@article {pmid38517169, year = {2024}, author = {Paulay, A and Grimaud, GM and Caballero, R and Laroche, B and Leclerc, M and Labarthe, S and Maguin, E}, title = {Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae.}, journal = {mSystems}, volume = {9}, number = {4}, pages = {e0015324}, pmid = {38517169}, issn = {2379-5077}, support = {2019/0659//Agence Nationale de la Recherche (ANR)/ ; //Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (INRAE)/ ; //Biomathematica/ ; }, mesh = {Humans ; Proteolysis ; *Bacteria/genetics ; *Fatty Acids, Volatile/metabolism ; Peptide Hydrolases/metabolism ; *Bacteroides ; }, abstract = {The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R[2] = 0.92 for the training set and R[2] = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.}, }
@article {pmid38506531, year = {2024}, author = {Sivaprakasam, S and Mohd Azim Khan, NA and Yee Fan, T and Kumarasan, Y and Sicheritz-Pontén, T and Petersen, B and Mohd Hata, E and Vadamalai, G and Parimannan, S and Rajandas, H}, title = {Complete genome sequence of plant growth-promoting Bacillus stratosphericus AIMST-CREST02 isolated from bulk soil of a paddy field.}, journal = {Microbiology resource announcements}, volume = {13}, number = {4}, pages = {e0113723}, pmid = {38506531}, issn = {2576-098X}, support = {T09C2-19//Collaborative Research in Engineering, Science and Technology Centre (CREST)/ ; }, abstract = {Here, we present the complete genome of a plant growth-promoting strain, Bacillus stratosphericus AIMST-CREST02 isolated from the bulk soil of a high-yielding paddy plot. The genome is 3,840,451 bp in size with a GC content of 41.25%. Annotation predicted the presence of 3,907 coding sequences, including genes involved in auxin biosynthesis regulation and gamma-aminobutyric acid (GABA) metabolism.}, }
@article {pmid38505556, year = {2024}, author = {Chakraborty, N}, title = {Metabolites: a converging node of host and microbe to explain meta-organism.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1337368}, pmid = {38505556}, issn = {1664-302X}, abstract = {Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.}, }
@article {pmid38500001, year = {2024}, author = {Jiang, W and Cheng, Z and Zhai, W and Ma, X and Gao, J and Liu, X and Liu, D and Zhou, Z and Wang, P}, title = {Oxytetracycline Increases the Residual Risk of Imidacloprid in Radish (Raphanus sativus) and Disturbs the Plant-Rhizosphere Microbiome Holobiont Homeostasis.}, journal = {Journal of agricultural and food chemistry}, volume = {72}, number = {12}, pages = {6167-6177}, doi = {10.1021/acs.jafc.4c00271}, pmid = {38500001}, issn = {1520-5118}, mesh = {*Raphanus/chemistry ; *Oxytetracycline/metabolism/pharmacology ; Rhizosphere ; *Microbiota ; Soil/chemistry ; *Neonicotinoids ; *Nitro Compounds ; }, abstract = {Antibiotics can be accidentally introduced into farmland by wastewater irrigation, and the environmental effects are still unclear. In this study, the effects of oxytetracycline on the residue of imidacloprid in soil and radishes were investigated. Besides, the rhizosphere microbiome and radish metabolome were analyzed. It showed that the persistence of imidacloprid in soil was unchanged, but the content of olefin-imidacloprid was increased by oxytetracycline. The residue of imidacloprid in radishes was increased by nearly 1.5 times, and the hazard index of imidacloprid was significantly raised by 1.5-4 times. Oxytetracycline remodeled the rhizosphere microbiome, including Actinobe, Elusimic, and Firmicutes, and influenced the metabolome of radishes. Especially, some amino acid metabolic pathways in radish were downregulated, which might be involved in imidacloprid degradation. It can be assumed that oxytetracycline increased the imidacloprid residue in radish through disturbing the plant-rhizosphere microbiome holobiont and, thus, increased the pesticide dietary risk.}, }
@article {pmid38499447, year = {2024}, author = {Piccini, C and Martínez de la Escalera, G and Segura, AM and Croci, C and Kruk, C}, title = {The Microcystis-microbiome interactions: origins of the colonial lifestyle.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {4}, pages = {}, pmid = {38499447}, issn = {1574-6941}, support = {FCE_1_2019_1_156308//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, mesh = {*Microcystis/genetics ; *Cyanobacteria ; Biomass ; Ecology ; *Microbiota ; }, abstract = {Species of the Microcystis genus are the most common bloom-forming toxic cyanobacteria worldwide. They belong to a clade of unicellular cyanobacteria whose ability to reach high biomasses during blooms is linked to the formation of colonies. Colonial lifestyle provides several advantages under stressing conditions of light intensity, ultraviolet light, toxic substances and grazing. The progression from a single-celled organism to multicellularity in Microcystis has usually been interpreted as individual phenotypic responses of the cyanobacterial cells to the environment. Here, we synthesize current knowledge about Microcystis colonial lifestyle and its role in the organism ecology. We then briefly review the available information on Microcystis microbiome and propose that changes leading from single cells to colonies are the consequence of specific and tightly regulated signals between the cyanobacterium and its microbiome through a biofilm-like mechanism. The resulting colony is a multi-specific community of interdependent microorganisms.}, }
@article {pmid38497271, year = {2024}, author = {Destoumieux-Garzón, D and Montagnani, C and Dantan, L and Nicolas, NS and Travers, MA and Duperret, L and Charrière, GM and Toulza, E and Mitta, G and Cosseau, C and Escoubas, JM}, title = {Cross-talk and mutual shaping between the immune system and the microbiota during an oyster's life.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1901}, pages = {20230065}, pmid = {38497271}, issn = {1471-2970}, mesh = {Animals ; *Crassostrea/genetics ; Immune System ; }, abstract = {The Pacific oyster Crassostrea gigas lives in microbe-rich marine coastal systems subjected to rapid environmental changes. It harbours a diversified and fluctuating microbiota that cohabits with immune cells expressing a diversified immune gene repertoire. In the early stages of oyster development, just after fertilization, the microbiota plays a key role in educating the immune system. Exposure to a rich microbial environment at the larval stage leads to an increase in immune competence throughout the life of the oyster, conferring a better protection against pathogenic infections at later juvenile/adult stages. This beneficial effect, which is intergenerational, is associated with epigenetic remodelling. At juvenile stages, the educated immune system participates in the control of the homeostasis. In particular, the microbiota is fine-tuned by oyster antimicrobial peptides acting through specific and synergistic effects. However, this balance is fragile, as illustrated by the Pacific Oyster Mortality Syndrome, a disease causing mass mortalities in oysters worldwide. In this disease, the weakening of oyster immune defences by OsHV-1 µVar virus induces a dysbiosis leading to fatal sepsis. This review illustrates the continuous interaction between the highly diversified oyster immune system and its dynamic microbiota throughout its life, and the importance of this cross-talk for oyster health. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.}, }
@article {pmid38497265, year = {2024}, author = {Klimovich, A and Bosch, TCG}, title = {Novel technologies uncover novel 'anti'-microbial peptides in Hydra shaping the species-specific microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1901}, pages = {20230058}, pmid = {38497265}, issn = {1471-2970}, mesh = {Humans ; Animals ; *Hydra/physiology ; Peptides ; *Microbiota ; Bacteria ; Epithelial Cells ; }, abstract = {The freshwater polyp Hydra uses an elaborate innate immune machinery to maintain its specific microbiome. Major components of this toolkit are conserved Toll-like receptor (TLR)-mediated immune pathways and species-specific antimicrobial peptides (AMPs). Our study harnesses advanced technologies, such as high-throughput sequencing and machine learning, to uncover a high complexity of the Hydra's AMPs repertoire. Functional analysis reveals that these AMPs are specific against diverse members of the Hydra microbiome and expressed in a spatially controlled pattern. Notably, in the outer epithelial layer, AMPs are produced mainly in the neurons. The neuron-derived AMPs are secreted directly into the glycocalyx, the habitat for symbiotic bacteria, and display high selectivity and spatial restriction of expression. In the endodermal layer, in contrast, endodermal epithelial cells produce an abundance of different AMPs including members of the arminin and hydramacin families, while gland cells secrete kazal-type protease inhibitors. Since the endodermal layer lines the gastric cavity devoid of symbiotic bacteria, we assume that endodermally secreted AMPs protect the gastric cavity from intruding pathogens. In conclusion, Hydra employs a complex set of AMPs expressed in distinct tissue layers and cell types to combat pathogens and to maintain a stable spatially organized microbiome. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.}, }
@article {pmid38497257, year = {2024}, author = {Maritan, E and Quagliariello, A and Frago, E and Patarnello, T and Martino, ME}, title = {The role of animal hosts in shaping gut microbiome variation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1901}, pages = {20230071}, pmid = {38497257}, issn = {1471-2970}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Host Microbial Interactions ; Metagenomics ; }, abstract = {Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.}, }
@article {pmid38495510, year = {2024}, author = {Yang, L and Guo, Y and Yang, H and Li, S and Zhang, Y and Gao, C and Wei, T and Hao, L}, title = {Distinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1361883}, pmid = {38495510}, issn = {1664-302X}, abstract = {The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer, which contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia, a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase, were more abundant in the resistant variety. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas. Among all the metagenome-assembled genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as a promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.}, }
@article {pmid38493232, year = {2024}, author = {Moreno-Pino, M and Manrique-de-la-Cuba, MF and López-Rodríguez, M and Parada-Pozo, G and Rodríguez-Marconi, S and Ribeiro, CG and Flores-Herrera, P and Guajardo, M and Trefault, N}, title = {Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6371}, pmid = {38493232}, issn = {2045-2322}, support = {3210656//ANID FONDECYT Postdoctoral Grant/ ; 21211164//ANID Doctoral Fellowships/ ; 21192150//ANID Doctoral Fellowships/ ; 21190286//ANID Doctoral Fellowships/ ; DG_02-22//INACH Grants/ ; DG_15-20//INACH Grants/ ; DG_12-20//INACH Grants/ ; RT_34-17//INACH Grants/ ; 1230758//ANID FONDECYT Grant/ ; }, mesh = {Animals ; *Porifera/microbiology ; Antarctic Regions ; Ammonia ; Archaea/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.}, }
@article {pmid38491515, year = {2024}, author = {Wentzien, NM and Fernández-González, AJ and Valverde-Corredor, A and Lasa, AV and Villadas, PJ and Wicaksono, WA and Cernava, T and Berg, G and Fernández-López, M and Mercado-Blanco, J}, title = {Pitting the olive seed microbiome.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {17}, pmid = {38491515}, issn = {2524-6372}, abstract = {BACKGROUND: The complex and co-evolved interplay between plants and their microbiota is crucial for the health and fitness of the plant holobiont. However, the microbiota of the seeds is still relatively unexplored and no studies have been conducted with olive trees so far. In this study, we aimed to characterize the bacterial, fungal and archaeal communities present in seeds of ten olive genotypes growing in the same orchard through amplicon sequencing to test whether the olive genotype is a major driver in shaping the seed microbial community, and to identify the origin of the latter. Therefore, we have developed a methodology for obtaining samples from the olive seed's endosphere under sterile conditions.<br><br>RESULTS: A diverse microbiota was uncovered in olive seeds, the plant genotype being an important factor influencing the structure and composition of the microbial communities. The most abundant bacterial phylum was Actinobacteria, accounting for an average relative abundance of 41%. At genus level, Streptomyces stood out because of its potential influence on community structure. Within the fungal community, Basidiomycota and Ascomycota were the most abundant phyla, including the genera Malassezia, Cladosporium, and Mycosphaerella. The shared microbiome was composed of four bacterial (Stenotrophomonas, Streptomyces, Promicromonospora and Acidipropionibacterium) and three fungal (Malassezia, Cladosporium and Mycosphaerella) genera. Furthermore, a comparison between findings obtained here and earlier results from the root endosphere of the same trees indicated that genera such as Streptomyces and Malassezia were present in both olive compartments.<br><br>CONCLUSIONS: This study provides the first insights into the composition of the olive seed microbiota. The highly abundant fungal genus Malassezia and the bacterial genus Streptomyces reflect a unique signature of the olive seed microbiota. The genotype clearly shaped the composition of the seed's microbial community, although a shared microbiome was found. We identified genera that may translocate from the roots to the seeds, as they were present in both organs of the same trees. These findings set the stage for future research into potential vertical transmission of olive endophytes and the role of specific microbial taxa in seed germination, development, and seedling survival.}, }
@article {pmid38488860, year = {2024}, author = {Freddi, S and Rajabal, V and Tetu, SG and Gillings, MR and Penesyan, A}, title = {Microbial biofilms on macroalgae harbour diverse integron gene cassettes.}, journal = {Microbiology (Reading, England)}, volume = {170}, number = {3}, pages = {}, pmid = {38488860}, issn = {1465-2080}, mesh = {*Integrons/genetics ; *Bacteria/genetics/metabolism ; Genes, Bacterial/genetics ; Drug Resistance, Microbial ; Biofilms ; }, abstract = {Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.}, }
@article {pmid38478382, year = {2024}, author = {Zenteno-Alegría, CO and Yarzábal Rodríguez, LA and Ciancas Jiménez, J and Álvarez Gutiérrez, PE and Gunde-Cimerman, N and Batista-García, RA}, title = {Fungi beyond limits: The agricultural promise of extremophiles.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14439}, pmid = {38478382}, issn = {1751-7915}, support = {389616//National Council of Humanities, Sciences and Technologies (CONAHCyT)/ ; //Darwin Initiative UK/ ; DARPP220//Darwin Initiative Round 27/ ; DIR30S2/1004//Darwin Initiative Round 30/ ; I0-0022//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; P4-0432//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; P1-0198//Slovenian Research Agency to Infrastructural Centre Mycosmo/ ; RYC2022-037554-I//MCIN/AEI/ ; //FSE+/ ; }, mesh = {*Extremophiles ; *Mycorrhizae ; Symbiosis ; Fungi/genetics ; Agriculture/methods ; Crops, Agricultural/microbiology ; }, abstract = {Global climate changes threaten food security, necessitating urgent measures to enhance agricultural productivity and expand it into areas less for agronomy. This challenge is crucial in achieving Sustainable Development Goal 2 (Zero Hunger). Plant growth-promoting microorganisms (PGPM), bacteria and fungi, emerge as a promising solution to mitigate the impact of climate extremes on agriculture. The concept of the plant holobiont, encompassing the plant host and its symbiotic microbiota, underscores the intricate relationships with a diverse microbial community. PGPM, residing in the rhizosphere, phyllosphere, and endosphere, play vital roles in nutrient solubilization, nitrogen fixation, and biocontrol of pathogens. Novel ecological functions, including epigenetic modifications and suppression of virulence genes, extend our understanding of PGPM strategies. The diverse roles of PGPM as biofertilizers, biocontrollers, biomodulators, and more contribute to sustainable agriculture and environmental resilience. Despite fungi's remarkable plant growth-promoting functions, their potential is often overshadowed compared to bacteria. Arbuscular mycorrhizal fungi (AMF) form a mutualistic symbiosis with many terrestrial plants, enhancing plant nutrition, growth, and stress resistance. Other fungi, including filamentous, yeasts, and polymorphic, from endophytic, to saprophytic, offer unique attributes such as ubiquity, morphology, and endurance in harsh environments, positioning them as exceptional plant growth-promoting fungi (PGPF). Crops frequently face abiotic stresses like salinity, drought, high UV doses and extreme temperatures. Some extremotolerant fungi, including strains from genera like Trichoderma, Penicillium, Fusarium, and others, have been studied for their beneficial interactions with plants. Presented examples of their capabilities in alleviating salinity, drought, and other stresses underscore their potential applications in agriculture. In this context, extremotolerant and extremophilic fungi populating extreme natural environments are muchless investigated. They represent both new challenges and opportunities. As the global climate evolves, understanding and harnessing the intricate mechanisms of fungal-plant interactions, especially in extreme environments, is paramount for developing effective and safe plant probiotics and using fungi as biocontrollers against phytopathogens. Thorough assessments, comprehensive methodologies, and a cautious approach are crucial for leveraging the benefits of extremophilic fungi in the changing landscape of global agriculture, ensuring food security in the face of climate challenges.}, }
@article {pmid38470181, year = {2024}, author = {Xu, M and Cai, Z and Cheng, K and Chen, G and Zhou, J}, title = {Mitigation of Vibrio coralliilyticus-induced coral bleaching through bacterial dysbiosis prevention by Ruegeria profundi.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0227423}, pmid = {38470181}, issn = {1098-5336}, support = {42106096//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; Coral Bleaching ; Ecosystem ; Dysbiosis ; *Vibrio ; *Anthozoa/microbiology ; Coral Reefs ; *Rhodobacteraceae ; }, abstract = {Vibrio species are prevalent in ocean ecosystems, particularly Vibrio coralliilyticus, and pose a threat to corals and other marine organisms under global warming conditions. While microbiota manipulation is considered for coral disease management, understanding the role of commensal bacteria in stress resilience remains limited. Here, a single bacterial species (Ruegeria profundi) rather than a consortium of native was used to combat pathogenic V. coralliilyticus and protect corals from bleaching. R. profundi showed therapeutic activity in vivo, preventing a significant reduction in bacterial diversity in bleached corals. Notably, the structure of the bacterial community differed significantly among all the groups. In addition, compared with the bleached corals caused by V. coralliilyticus, the network analysis revealed that complex interactions and positive correlations in the bacterial community of the R. profundi protected non-bleached corals, indicating R. profundi's role in fostering synergistic associations. Many genera of bacteria significantly increased in abundance during V. coralliilyticus infection, including Vibrio, Alteromonas, Amphritea, and Nautella, contributing to the pathogenicity of the bacterial community. However, R. profundi effectively countered the proliferation of these genera, promoting potential probiotic Endozoicomonas and other taxa, while reducing the abundance of betaine lipids and the type VI section system of the bacterial community. These changes ultimately influenced the interactive relationships among symbionts and demonstrated that probiotic R. profundi intervention can modulate coral-associated bacterial community, alleviate pathogenic-induced dysbiosis, and preserve coral health. These findings elucidated the relationship between the behavior of the coral-associated bacterial community and the occurrence of pathological coral bleaching.IMPORTANCEChanges in the global climate and marine environment can influence coral host and pathogen repartition which refers to an increased likelihood of pathogen infection in hosts. The risk of Vibrio coralliilyticus-induced coral disease is significantly heightened, primarily due to its thermos-dependent expression of virulent and populations. This study investigates how coral-associated bacterial communities respond to bleaching induced by V. coralliilyticus. Our findings demonstrate that Ruegeria profundi exhibits clear evidence of defense against pathogenic bacterial infection, contributing to the maintenance of host health and symbiont homeostasis. This observation suggests that bacterial pathogens could cause dysbiosis in coral holobionts. Probiotic bacteria display an essential capability in restructuring and manipulating coral-associated bacterial communities. This restructuring effectively reduces bacterial community virulence and enhances the pathogenic resistance of holobionts. The study provides valuable insights into the correlation between the health status of corals and how coral-associated bacterial communities may respond to both pathogens and probiotics.}, }
@article {pmid38462458, year = {2023}, author = {Libertini, G}, title = {Phenoptosis and the Various Types of Natural Selection.}, journal = {Biochemistry. Biokhimiia}, volume = {88}, number = {12}, pages = {2007-2022}, doi = {10.1134/S0006297923120052}, pmid = {38462458}, issn = {1608-3040}, mesh = {Animals ; Bees ; *Aging/genetics ; Ecosystem ; Selection, Genetic ; *Ants ; Reproduction ; Biological Evolution ; }, abstract = {In the first description of evolution, the fundamental mechanism is the natural selection favoring the individuals best suited for survival and reproduction (selection at the individual level or classical Darwinian selection). However, this is a very reductive description of natural selection that does not consider or explain a long series of known phenomena, including those in which an individual sacrifices or jeopardizes his life on the basis of genetically determined mechanisms (i.e., phenoptosis). In fact, in addition to (i) selection at the individual level, it is essential to consider other types of natural selection such as those concerning: (ii) kin selection and some related forms of group selection; (iii) the interactions between the innumerable species that constitute a holobiont; (iv) the origin of the eukaryotic cell from prokaryotic organisms; (v) the origin of multicellular eukaryotic organisms from unicellular organisms; (vi) eusociality (e.g., in many species of ants, bees, termites); (vii) selection at the level of single genes, or groups of genes; (viii) the interactions between individuals (or more precisely their holobionts) of the innumerable species that make up an ecosystem. These forms of natural selection, which are all effects and not violations of the classical Darwinian selection, also show how concepts as life, species, individual, and phenoptosis are somewhat not entirely defined and somehow arbitrary. Furthermore, the idea of organisms selected on the basis of their survival and reproduction capabilities is intertwined with that of organisms also selected on the basis of their ability to cooperate and interact, even by losing their lives or their distinct identities.}, }
@article {pmid38454513, year = {2024}, author = {Lavecchia, A and Fosso, B and Engelen, AH and Borin, S and Manzari, C and Picardi, E and Pesole, G and Placido, A}, title = {Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {47}, pmid = {38454513}, issn = {2049-2618}, support = {UIDB/04326/2020//Portuguese national funds from FCT/ ; 634486//European Commission/ ; 634486//European Commission/ ; 634486//European Commission/ ; }, mesh = {*Rhodophyta/genetics/metabolism ; *Microbiota/genetics ; Bacteria/genetics/metabolism ; *Seaweed/genetics/metabolism ; Metagenome ; *Anti-Infective Agents ; Halogens/metabolism ; }, abstract = {BACKGROUND: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.<br><br>RESULTS: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.<br><br>CONCLUSION: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.}, }
@article {pmid38451230, year = {2024}, author = {Eisenhofer, R and Nesme, J and Santos-Bay, L and Koziol, A and Sørensen, SJ and Alberdi, A and Aizpurua, O}, title = {A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0359023}, pmid = {38451230}, issn = {2165-0497}, support = {DNRF143//Danish National Research Foundation award/ ; CF20-0460//The Carlsberg Foundation/ ; }, mesh = {Animals ; Mice ; Sequence Analysis, DNA/methods ; *Genome, Bacterial ; *Microbiota/genetics ; Metagenomics/methods ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.}, }
@article {pmid38445866, year = {2024}, author = {Chen, B and Wei, Y and Yu, K and Liang, Y and Yu, X and Liao, Z and Qin, Z and Xu, L and Bao, Z}, title = {The microbiome dynamics and interaction of endosymbiotic Symbiodiniaceae and fungi are associated with thermal bleaching susceptibility of coral holobionts.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {4}, pages = {e0193923}, pmid = {38445866}, issn = {1098-5336}, support = {42090041, 42030502//MOST | National Natural Science Foundation of China (NSFC)/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; GXLSCRSCS2021103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; PM-zx703-202105-176, PM-zx703-202004-143//Central Public-Interest Scientific Institution Basal Fund/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; *Dinoflagellida ; *Microbiota ; Symbiosis ; Fungi/genetics ; }, abstract = {The thermal bleaching percentage of coral holobionts shows interspecific differences under heat-stress conditions, which are closely related to the coral-associated microbiome. However, the ecological effects of community dynamics and interactions between Symbiodiniaceae and fungi on coral thermal bleaching susceptibility remain unclear. In this study, we analyzed the diversity, community structure, functions, and potential interaction of Symbiodiniaceae and fungi among 18 coral species from a high thermal bleaching risk atoll using next-generation sequencing. The results showed that heat-tolerant C3u sub-clade and Durusdinium dominated the Symbiodiniaceae community of corals and that there were no core amplicon sequence variants in the coral-associated fungal community. Fungal richness and the abundance of confirmed functional animal-plant pathogens were significantly positively correlated with the coral thermal bleaching percentage. Fungal indicators, including Didymellaceae, Chaetomiaceae, Schizophyllum, and Colletotrichum, were identified in corals. Each coral species had a complex Symbiodiniaceae-fungi interaction network (SFIN), which was driven by the dominant Symbiodiniaceae sub-clades. The SFINs of coral holobionts with low thermal bleaching susceptibility exhibited low complexity and high betweenness centrality. These results indicate that the extra heat tolerance of coral in Huangyan Island may be linked to the high abundance of heat-tolerant Symbiodiniaceae. Fungal communities have high interspecific flexibility, and the increase of fungal diversity and pathogen abundance was correlated with higher thermal bleaching susceptibility of corals. Moreover, fungal indicators were associated with the degrees of coral thermal bleaching susceptibility, including both high and intermediate levels. The topological properties of SFINs suggest that heat-tolerant coral have limited fungal parasitism and strong microbial network resilience.IMPORTANCEGlobal warming and enhanced marine heatwaves have led to a rapid decline in coral reef ecosystems worldwide. Several studies have focused on the impact of coral-associated microbiomes on thermal bleaching susceptibility in corals; however, the ecological functions and interactions between Symbiodiniaceae and fungi remain unclear. We investigated the microbiome dynamics and potential interactions of Symbiodiniaceae and fungi among 18 coral species in Huangyan Island. Our study found that the Symbiodiniaceae community of corals was mainly composed of heat-tolerant C3u sub-clade and Durusdinium. The increase in fungal diversity and pathogen abundance has close associations with higher coral thermal bleaching susceptibility. We first constructed an interaction network between Symbiodiniaceae and fungi in corals, which indicated that restricting fungal parasitism and strong interaction network resilience would promote heat acclimatization of corals. Accordingly, this study provides insights into the role of microorganisms and their interaction as drivers of interspecific differences in coral thermal bleaching.}, }
@article {pmid38443414, year = {2024}, author = {Iguchi, A and Iijima, M and Mizusawa, N and Ohno, Y and Yasumoto, K and Suzuki, A and Suga, S and Tanaka, K and Zaitsu, K}, title = {Single-polyp metabolomics for coral health assessment.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3369}, pmid = {38443414}, issn = {2045-2322}, support = {19K22938//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; Animals ; *Anthozoa ; Ecosystem ; Tandem Mass Spectrometry ; Coral Reefs ; *Dinoflagellida ; *Polyps ; }, abstract = {Coral reef ecosystems supported by environmentally sensitive reef-building corals face serious threats from human activities. Our understanding of these reef threats is hampered by the lack of sufficiently sensitive coral environmental impact assessment systems. In this study, we established a platform for metabolomic analysis at the single-coral-polyp level using state-of-the-art mass spectrometry (probe electrospray ionization/tandem mass spectrometry; PESI/MS/MS) capable of fine-scale analysis. We analyzed the impact of the organic UV filter, benzophenone (BP), which has a negative impact on corals. We also analyzed ammonium and nitrate samples, which affect the environmental sensitivity of coral-zooxanthella (Symbiodiniaceae) holobionts, to provide new insights into coral biology with a focus on metabolites. The method established in this study breaks new ground by combining PESI/MS/MS with a technique for coral polyps that can control the presence or absence of zooxanthellae in corals, enabling functions of zooxanthellae to be assessed on a polyp-by-polyp basis for the first time. This system will clarify biological mechanisms of corals and will become an important model system for environmental impact assessment using marine organisms.}, }
@article {pmid38441978, year = {2024}, author = {Schwob, G and Cabrol, L and Saucède, T and Gérard, K and Poulin, E and Orlando, J}, title = {Unveiling the co-phylogeny signal between plunderfish Harpagifer spp. and their gut microbiomes across the Southern Ocean.}, journal = {Microbiology spectrum}, volume = {12}, number = {4}, pages = {e0383023}, pmid = {38441978}, issn = {2165-0497}, support = {3200036//ANID FONDECYT Postdoctoral Project/ ; 1211672//ANID FONDECYT Regular Project/ ; ICN2021_002//ANID-Millenium Science Initiative Program/ ; }, mesh = {Animals ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Biological Evolution ; *Microbiota ; Fishes/genetics ; *Perciformes ; Bacteria/genetics ; Oceans and Seas ; RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: Understanding the factors that sculpt fish gut microbiome is challenging, especially in natural populations characterized by high environmental and host genomic complexity. However, closely related hosts are valuable models for deciphering the contribution of host evolutionary history to microbiome assembly, through the underscoring of phylosymbiosis and co-phylogeny patterns. Here, we propose that the recent diversification of several Harpagifer species across the Southern Ocean would allow the detection of robust phylogenetic congruence between the host and its microbiome. We characterized the gut mucosa microbiome of 77 individuals from four field-collected species of the plunderfish Harpagifer (Teleostei, Notothenioidei), distributed across three biogeographic regions of the Southern Ocean. We found that seawater physicochemical properties, host phylogeny, and geography collectively explained 35% of the variation in bacterial community composition in Harpagifer gut mucosa. The core microbiome of Harpagifer spp. gut mucosa was characterized by a low diversity, mostly driven by selective processes, and dominated by a single Aliivibrio Operational Taxonomic Unit (OTU) detected in more than 80% of the individuals. Nearly half of the core microbiome taxa, including Aliivibrio, harbored co-phylogeny signal at microdiversity resolution with host phylogeny, indicating an intimate symbiotic relationship and a shared evolutionary history with Harpagifer. The clear phylosymbiosis and co-phylogeny signals underscore the relevance of the Harpagifer model in understanding the role of fish evolutionary history in shaping the gut microbiome assembly. We propose that the recent diversification of Harpagifer may have led to the diversification of Aliivibrio, exhibiting patterns that mirror the host phylogeny.<br><br>IMPORTANCE: Although challenging to detect in wild populations, phylogenetic congruence between marine fish and its microbiome is critical, as it highlights intimate associations between hosts and ecologically relevant microbial symbionts. Our study leverages a natural system of closely related fish species in the Southern Ocean to unveil new insights into the contribution of host evolutionary trajectory on gut microbiome assembly, an underappreciated driver of the global marine fish holobiont. Notably, we unveiled striking evidence of co-diversification between Harpagifer and its microbiome, demonstrating both phylosymbiosis of gut bacterial communities and co-phylogeny of some specific bacterial symbionts, mirroring the host diversification patterns. Given Harpagifer's significance as a trophic resource in coastal areas and its vulnerability to climatic and anthropic pressures, understanding the potential evolutionary interdependence between the hosts and its microbiome provides valuable microbial candidates for future monitoring, as they may play a pivotal role in host species acclimatization to a rapidly changing environment.}, }
@article {pmid38438489, year = {2024}, author = {Voolstra, CR and Raina, JB and Dörr, M and Cárdenas, A and Pogoreutz, C and Silveira, CB and Mohamed, AR and Bourne, DG and Luo, H and Amin, SA and Peixoto, RS}, title = {The coral microbiome in sickness, in health and in a changing world.}, journal = {Nature reviews. Microbiology}, volume = {22}, number = {8}, pages = {460-475}, pmid = {38438489}, issn = {1740-1534}, mesh = {*Anthozoa/microbiology ; Animals ; *Microbiota/physiology ; *Climate Change ; *Symbiosis ; *Bacteria/classification/genetics/metabolism ; Coral Reefs ; }, abstract = {Stony corals, the engines and engineers of reef ecosystems, face unprecedented threats from anthropogenic environmental change. Corals are holobionts that comprise the cnidarian animal host and a diverse community of bacteria, archaea, viruses and eukaryotic microorganisms. Recent research shows that the bacterial microbiome has a pivotal role in coral biology. A healthy bacterial assemblage contributes to nutrient cycling and stress resilience, but pollution, overfishing and climate change can break down these symbiotic relationships, which results in disease, bleaching and, ultimately, coral death. Although progress has been made in characterizing the spatial-temporal diversity of bacteria, we are only beginning to appreciate their functional contribution. In this Review, we summarize the ecological and metabolic interactions between bacteria and other holobiont members, highlight the biotic and abiotic factors influencing the structure of bacterial communities and discuss the impact of climate change on these communities and their coral hosts. We emphasize how microbiome-based interventions can help to decipher key mechanisms underpinning coral health and promote reef resilience. Finally, we explore how recent technological developments may be harnessed to address some of the most pressing challenges in coral microbiology, providing a road map for future research in this field.}, }
@article {pmid38425799, year = {2024}, author = {Abd El-Daim, IA and Saad, MM}, title = {Editorial: Holobionts cross talks during microbial-mediated stress tolerance in plants.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1377919}, pmid = {38425799}, issn = {1664-462X}, }
@article {pmid38424629, year = {2024}, author = {Toullec, G and Rädecker, N and Pogoreutz, C and Banc-Prandi, G and Escrig, S and Genoud, C and Olmos, CM and Spangenberg, J and Meibom, A}, title = {Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {42}, pmid = {38424629}, issn = {2049-2618}, support = {200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 212614//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; 200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, mesh = {Animals ; Ecosystem ; Symbiosis/physiology ; *Cnidaria ; Heat-Shock Response ; Coral Reefs ; *Dinoflagellida/physiology ; *Anthozoa/physiology ; }, abstract = {BACKGROUND: Global warming is causing large-scale disruption of cnidarian-Symbiodiniaceae symbioses fundamental to major marine ecosystems, such as coral reefs. However, the mechanisms by which heat stress perturbs these symbiotic partnerships remain poorly understood. In this context, the upside-down jellyfish Cassiopea has emerged as a powerful experimental model system.<br><br>RESULTS: We combined a controlled heat stress experiment with isotope labeling and correlative SEM-NanoSIMS imaging to show that host starvation is a central component in the chain of events that ultimately leads to the collapse of the Cassiopea holobiont. Heat stress caused an increase in catabolic activity and a depletion of carbon reserves in the unfed host, concurrent with a reduction in the supply of photosynthates from its algal symbionts. This state of host starvation was accompanied by pronounced in hospite degradation of algal symbionts, which may be a distinct feature of the heat stress response of Cassiopea. Interestingly, this loss of symbionts by degradation was concealed by body shrinkage of the starving animals, resulting in what could be referred to as "invisible" bleaching.<br><br>CONCLUSIONS: Overall, our study highlights the importance of the nutritional status in the heat stress response of the Cassiopea holobiont. Compared with other symbiotic cnidarians, the large mesoglea of Cassiopea, with its structural sugar and protein content, may constitute an energy reservoir capable of delaying starvation. It seems plausible that this anatomical feature at least partly contributes to the relatively high stress tolerance of these animals in rapidly warming oceans. Video Abstract.}, }
@article {pmid38395103, year = {2024}, author = {Prathapan, P}, title = {Characterisation of the fig-fig wasp holobiont.}, journal = {Bio Systems}, volume = {237}, number = {}, pages = {105162}, doi = {10.1016/j.biosystems.2024.105162}, pmid = {38395103}, issn = {1872-8324}, mesh = {Animals ; *Wasps ; *Ficus ; Pollination ; Ecosystem ; Symbiosis ; }, abstract = {Plants and animals have long been considered distinct kingdoms, yet here a 'plant-animal' is described. An extraordinary symbiosis in which neither organism can reproduce without the other, the fig tree (Ficus) provides the habitat for its exclusive pollinator: the fig wasp (Agaonidae). Characterising the 'fig-fig wasp holobiont' acknowledges, for the first time, 'plant-animal symbiogenesis'.}, }
@article {pmid38390522, year = {2024}, author = {Bech, PK and Jarmusch, SA and Rasmussen, JA and Limborg, MT and Gram, L and Henriksen, NNSE}, title = {Succession of microbial community composition and secondary metabolism during marine biofilm development.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae006}, pmid = {38390522}, issn = {2730-6151}, abstract = {In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.}, }
@article {pmid38385710, year = {2024}, author = {Xiao, Y and Gao, L and Li, Z}, title = {Unique high-temperature tolerance mechanisms of zoochlorellae Symbiochlorum hainanensis derived from scleractinian coral Porites lutea.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0278023}, pmid = {38385710}, issn = {2150-7511}, support = {42176146//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Anthozoa ; Temperature ; Chlorophyll A ; Selenic Acid ; Antioxidants ; Thiamine ; Symbiosis/physiology ; }, abstract = {UNLABELLED: Global warming is a key issue that causes coral bleaching mainly because of the thermosensitivity of zooxanthellae. Compared with the well-studied zooxanthellae Symbiodiniaceae in coral holobionts, we rarely know about other coral symbiotic algae, let alone their thermal tolerance. In this study, a zoochlorellae, Symbiochlorum hainanensis, isolated from the coral Porites lutea, was proven to have a threshold temperature of 38°C. Meanwhile, unique high-temperature tolerance mechanisms were suggested by integrated transcriptomics and real-time quantitative PCR, physiological and biochemical analyses, and electron microscopy observation. Under heat stress, S. hainanensis shared some similar response strategies with zooxanthellae Effrenium sp., such as increased ascorbate peroxidase, glutathione peroxidase, superoxide dismutase activities and chlorophyll a, thiamine, and thiamine phosphate contents. In particular, more chloroplast internal layered structure, increased CAT activity, enhanced selenate reduction, and thylakoid assembly pathways were highlighted for S. hainanensis's high-temperature tolerance. Notably, it is the first time to reveal a whole selenate reduction pathway from SeO4[2-] to Se[2-] and its contribution to the high-temperature tolerance of S. hainanensis. These unique mechanisms, including antioxidation and maintaining photosynthesis homeostasis, efficiently ensure the high-temperature tolerance of S. hainanensis than Effrenium sp. Compared with the thermosensitivity of coral symbiotic zooxanthellae Symbiodiniaceae, this study provides novel insights into the high-temperature tolerance mechanisms of coral symbiotic zoochlorellae S. hainanensis, which will contribute to corals' survival in the warming oceans caused by global climate change.<br><br>IMPORTANCE: The increasing ocean temperature above 31&#xb0;C-32&#xb0;C might trigger a breakdown of the coral-Symbiodiniaceae symbioses or coral bleaching because of the thermosensitivity of Symbiodiniaceae; therefore, the exploration of alternative coral symbiotic algae with high-temperature tolerance is important for the corals' protection under warming oceans. This study proves that zoochlorellae Symbiochlorum hainanensis can tolerate 38&#xb0;C, which is the highest temperature tolerance known for coral symbiotic algae to date, with unique high-temperature tolerance mechanisms. Particularly, for the first time, an internal selenium antioxidant mechanism of coral symbiotic S. hainanensis to high temperature was suggested.}, }
@article {pmid38376185, year = {2024}, author = {Hassani, MA and Cui, Z and LaReau, J and Huntley, RB and Steven, B and Zeng, Q}, title = {Inter-species interactions between two bacterial flower commensals and a floral pathogen reduce disease incidence and alter pathogen activity.}, journal = {mBio}, volume = {15}, number = {3}, pages = {e0021324}, pmid = {38376185}, issn = {2150-7511}, support = {2023-51181-41319, 2023-51300-40727, 2020-67013-31794//U.S. Department of Agriculture (USDA)/ ; }, mesh = {Incidence ; Flowers/microbiology ; *Malus/genetics/microbiology ; *Erwinia amylovora/metabolism ; Plant Diseases/microbiology ; }, abstract = {UNLABELLED: Flowers are colonized by a diverse community of microorganisms that can alter plant health and interact with floral pathogens. Erwinia amylovora is a flower-inhabiting bacterium and a pathogen that infects different plant species, including Malus × domestica (apple). Previously, we showed that the co-inoculation of two bacterial strains, members of the genera Pseudomonas and Pantoea, isolated from apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between the two flower-associated bacteria and E. amylovora in field experimentation and in vitro co-cultures. The two flower commensal strains did not competitively exclude E. amylovora from the stigma habitat, as both bacteria and the pathogen co-existed on the stigma of apple flowers and in vitro. This suggests that plant protection might be mediated by other mechanisms than competitive niche exclusion. Using a synthetic stigma exudation medium, ternary co-culture of the bacterial strains led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Importantly, the gene expression profiles for the ternary co-culture were not just additive from binary co-cultures, suggesting that some functions only emerged in multipartite co-culture. Additionally, the ternary co-culture of the strains resulted in a stronger acidification of the growth milieu than mono- or binary co-cultures, pointing to another emergent property of co-inoculation. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their potential impact on plant health and pathogen behavior.<br><br>IMPORTANCE: Fire blight, caused by Erwinia amylovora, is one of the most important plant diseases of pome fruits. Previous work largely suggested plant microbiota commensals suppressed disease by antagonizing pathogen growth. However, inter-species interactions of multiple flower commensals and their influence on pathogen activity and behavior have not been well studied. Here, we show that co-inoculating two bacterial strains that naturally colonize the apple flowers reduces disease incidence. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen led to the emergence of new gene expression patterns and a strong alteration of the external pH, factors that may modify the pathogen's behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.}, }
@article {pmid38374916, year = {2024}, author = {McLaughlin, MS and Yurgel, SN and Abbasi, PA and Ali, S}, title = {The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1342407}, pmid = {38374916}, issn = {1664-302X}, abstract = {Epiphytic and endophytic micro-organisms associated with plants form complex communities on or in their host plant. These communities influence physiological traits, development, and host susceptibility to abiotic and biotic stresses, and these communities are theorized to have evolved alongside their hosts, forming a unit of selection known as the holobiont. The microbiome is highly variable and can be influenced by abiotic factors, including applied exogenous agents. In this study, we compared the impact of chemical fungicide and salicylic acid treatments on the fungal communities of "Honeycrisp" apples at harvest over two consecutive growing years. We demonstrated variations in fungal community structure and composition by tissue type, growing season, and treatment regimes and that fungicide treatments were associated with reduced network complexity. Finally, we show that the inclusion of salicylic acid with 50% less chemical fungicides in an integrated spray program allowed a reduction in fungicide use while maintaining effective control of disease at harvest and following storage.}, }
@article {pmid38371405, year = {2024}, author = {Ghitti, E and Rolli, E and Vergani, L and Borin, S}, title = {Flavonoids influence key rhizocompetence traits for early root colonization and PCB degradation potential of Paraburkholderia xenovorans LB400.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1325048}, pmid = {38371405}, issn = {1664-462X}, abstract = {INTRODUCTION: Flavonoids are among the main plant root exudation components, and, in addition to their role in symbiosis, they can broadly affect the functionality of plant-associated microbes: in polluted environments, for instance, flavonoids can induce the expression of the enzymatic degradative machinery to clean-up soils from xenobiotics like polychlorinated biphenyls (PCBs). However, their involvement in root community recruitment and assembly involving non-symbiotic beneficial interactions remains understudied and may be crucial to sustain the holobiont fitness under PCB stress.<br><br>METHODS: By using a set of model pure flavonoid molecules and a natural blend of root exudates (REs) with altered flavonoid composition produced by Arabidopsis mutant lines affected in flavonoid biosynthesis and abundance (null mutant tt4, flavonoid aglycones hyperproducer tt8, and flavonoid conjugates hyperaccumulator ttg), we investigated flavonoid contribution in stimulating rhizocompetence traits and the catabolic potential of the model bacterial strain for PCB degradation Paraburkholderia xenovorans LB400.<br><br>RESULTS: Flavonoids influenced the traits involved in bacterial recruitment in the rhizoplane by improving chemotaxis and motility responses, by increasing biofilm formation and by promoting the growth and activation of the PCB-degradative pathway of strain LB400, being thus potentially exploited as carbon sources, stimulating factors and chemoattractant molecules. Indeed, early rhizoplane colonization was favored in plantlets of the tt8 Arabidopsis mutant and reduced in the ttg line. Bacterial growth was promoted by the REs of mutant lines tt4 and tt8 under control conditions and reduced upon PCB-18 stress, showing no significant differences compared with the WT and ttg, indicating that unidentified plant metabolites could be involved. PCB stress presumably altered the Arabidopsis root exudation profile, although a sudden "cry-for-help" response to recruit strain LB400 was excluded and flavonoids appeared not to be the main determinants. In the in vitro plant-microbe interaction assays, plant growth promotion and PCB resistance promoted by strain LB400 seemed to act through flavonoid-independent mechanisms without altering bacterial colonization efficiency and root adhesion pattern.<br><br>DISCUSSIONS: This study further contributes to elucidate the vast array of functions provided by flavonoids in orchestrating the early events of PCB-degrading strain LB400 recruitment in the rhizosphere and to support the holobiont fitness by stimulating the catabolic machinery involved in xenobiotics decomposition and removal.}, }
@article {pmid38371393, year = {2024}, author = {Chuang, PS and Yu, SP and Liu, PY and Hsu, MT and Chiou, YJ and Lu, CY and Tang, SL}, title = {A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae001}, pmid = {38371393}, issn = {2730-6151}, abstract = {Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.}, }
@article {pmid38366712, year = {2024}, author = {Pillai, P and Gouhier, TC}, title = {Metamicrobiome diversity promotes the evolution of host-microbial mutualisms.}, journal = {Journal of evolutionary biology}, volume = {37}, number = {4}, pages = {414-428}, doi = {10.1093/jeb/voae019}, pmid = {38366712}, issn = {1420-9101}, support = {OCE-1458158//National Science Foundation/ ; }, mesh = {*Symbiosis/physiology ; Biological Evolution ; *Microbiota ; }, abstract = {Ecological theory suggests that a host organism's internal spatial structure can promote the persistence of mutualistic microbes by allowing for the turnover of tissue occupied by non-beneficial or cheating microbes. This type of regulation, whereby a host preferentially rewards tissue occupied by beneficial members of its microbiome but sanctions tissue occupied by non-beneficial cheaters, is expected to generate a competition-extinction trade-off by allowing beneficial microbes to experience a lower extinction rate than competitively dominant cheaters. Using an adaptive dynamics approach, we demonstrate that although ecologically stable, microbial regulation via sanctioning is not stable in any evolutionary sense, as each individual host will be under pressure to reduce the costs incurred from cheater suppression in order to maximize its own fitness at the expense of the rest of the host population. However, increasing the diversity of non-beneficial cheaters in the host population metamicrobiome can lead to an increase in the relative fitness of hosts that actively sanction non-performing tissue, thus facilitating the evolutionary emergence and persistence of such strategies in host-microbial systems. These counter-intuitive results demonstrate how diversity at multiple levels of biological organization and spatiotemporal scales can interact to facilitate the establishment and maintenance of mutualistic relationships.}, }
@article {pmid38365239, year = {2024}, author = {Maire, J and Tsang Min Ching, SJ and Damjanovic, K and Epstein, HE and Judd, LM and Blackall, LL and van Oppen, MJH}, title = {Tissue-associated and vertically transmitted bacterial symbiont in the coral Pocillopora acuta.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {38365239}, issn = {1751-7370}, support = {FL180100036//Australian Research Council/ ; //Native Australian Animals Trust/ ; //Paul G. Allen Philanthropies/ ; //James Cook University/ ; //Australian Institute of Marine Science/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Metagenome ; *Gammaproteobacteria/genetics ; Coral Reefs ; Symbiosis ; }, abstract = {Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were found in both adults and larval offspring, suggesting vertical transmission. In situ laser capture microdissection of CAMAs followed by 16S rRNA gene amplicon sequencing and shotgun metagenomics produced a near complete metagenome-assembled genome. We subsequently cultured the CAMA bacteria from Pocillopora acuta colonies, and sequenced and assembled their genomes. Phylogenetic analyses showed that the CAMA bacteria belong to an undescribed Endozoicomonadaceae genus and species, which we propose to name Candidatus Sororendozoicomonas aggregata gen. nov sp. nov. Metabolic pathway reconstruction from its genome sequence suggests this species can synthesize most amino acids, several B vitamins, and antioxidants, and participate in carbon cycling and prey digestion, which may be beneficial to its coral hosts. This study provides detailed insights into a new member of the widespread Endozoicomonadaceae family, thereby improving our understanding of coral holobiont functioning. Vertically transmitted, tissue-associated bacteria, such as Sororendozoicomonas aggregata may be key candidates for the development of microbiome manipulation approaches with long-term positive effects on the coral host.}, }
@article {pmid38364305, year = {2024}, author = {Berg, G and Dorador, C and Egamberdieva, D and Kostka, JE and Ryu, CM and Wassermann, B}, title = {Shared governance in the plant holobiont and implications for one health.}, journal = {FEMS microbiology ecology}, volume = {100}, number = {3}, pages = {}, pmid = {38364305}, issn = {1574-6941}, support = {DE-SC0023297//Department of Energy/ ; RS-2022-RD010288//Rural Development Administration/ ; //National Research Foundation/ ; }, mesh = {Humans ; Aged, 80 and over ; Symbiosis ; *One Health ; *Microbiota ; Plants ; }, abstract = {The holobiont Holobiont theory is more than 80 years old, while the importance of microbial communities for plant holobionts was already identified by Lorenz Hiltner more than a century ago. Both concepts are strongly supported by results from the new field of microbiome research. Here, we present ecological and genetic features of the plant holobiont that underpin principles of a shared governance between hosts and microbes and summarize the relevance of plant holobionts in the context of global change. Moreover, we uncover knowledge gaps that arise when integrating plant holobionts in the broader perspective of the holobiome as well as one and planetary health concepts. Action is needed to consider interacting holobionts at the holobiome scale, for prediction and control of microbiome function to improve human and environmental health outcomes.}, }
@article {pmid38360316, year = {2024}, author = {Linsmayer, LB and Noel, SK and Leray, M and Wangpraseurt, D and Hassibi, C and Kline, DI and Tresguerres, M}, title = {Effects of bleaching on oxygen dynamics and energy metabolism of two Caribbean coral species.}, journal = {The Science of the total environment}, volume = {919}, number = {}, pages = {170753}, doi = {10.1016/j.scitotenv.2024.170753}, pmid = {38360316}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Oxygen/metabolism ; Caribbean Region ; *Dinoflagellida ; Energy Metabolism ; Hypoxia ; Coral Reefs ; }, abstract = {As mass coral bleaching events become more frequent, it is increasingly important to elucidate the factors underlying coral susceptibility and survival. We measured photosynthesis, respiration, and O2 concentration at the coral tissue surface, Symbiodiniaceae genotypes, and energy metabolic enzyme activities in Agaricia agaricites and Orbicella franksi throughout experimentally-induced thermal bleaching (+3 °C). A. agaricites colonies started to bleach two days into the thermal treatment and were fully bleached between Days 19-31. In contrast, O. franksi colonies only started to bleach on Day 12 and five colonies fully bleached between Days 24-38 while the remining three colonies took up 55 days. Both species experienced decreased photosynthesis and respiration rates as bleaching progressed. As a result, daytime O2 concentration at the coral surface shifted from hyperoxia in unbleached corals to normoxia in partially bleached corals, and to near hypoxia in fully bleached corals. Additionally, nighttime tissue surface O2 concentration shifted from hypoxia to normoxia, likely resulting from decreased symbiotic algae density, respiration, and photosynthates that fuel coral aerobic respiration. Genetic profiling of internal transcribed spacer 2 (ITS2) revealed differences in Symbiodiniaceae clade proportions between control and bleached colonies. Activity levels of energy metabolic enzymes did not significantly vary between control and bleached A. agaricites, but malate dehydrogenase and strombine dehydrogenase activities were significantly higher in bleached O. franksi colonies compared to controls. These differences were driven by the three O. franksi colonies that took the longest to bleach and contained >98 % Durusdinium sp. D1. The shifts in O2 dynamics within the microhabitat of bleached corals may have important implications for the metabolism of the coral holobiont while the changes in Symbiodiniaceae ITS2 profile and the upregulation of energy metabolic enzymes identify a potential factor contributing to bleaching dynamics.}, }
@article {pmid38354884, year = {2024}, author = {Ju, H and Zhang, J and Zou, Y and Xie, F and Tang, X and Zhang, S and Li, J}, title = {Bacteria undergo significant shifts while archaea maintain stability in Pocillopora damicornis under sustained heat stress.}, journal = {Environmental research}, volume = {250}, number = {}, pages = {118469}, doi = {10.1016/j.envres.2024.118469}, pmid = {38354884}, issn = {1096-0953}, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Archaea/genetics/physiology ; *Bacteria/genetics/classification ; Heat-Shock Response ; Microbiota ; Hot Temperature ; Coral Reefs ; }, abstract = {Global warming reportedly poses a critical risk to coral reef ecosystems. Bacteria and archaea are crucial components of the coral holobiont. The response of archaea associated with warming is less well understood than that of the bacterial community in corals. Also, there have been few studies on the dynamics of the microbial community in the coral holobiont under long-term heat stress. In order to track the dynamic alternations in the microbial communities within the heat-stressed coral holobiont, three-week heat-stress monitoring was carried out on the coral Pocillopora damicornis. The findings demonstrate that the corals were stressed at 32 °C, and showed a gradual decrease in Symbiodiniaceae density with increasing duration of heat stress. The archaeal community in the coral holobiont remained relatively unaltered by the increasing temperature, whereas the bacterial community was considerably altered. Sustained heat stress exacerbated the dissimilarities among parallel samples of the bacterial community, confirming the Anna Karenina Principle in animal microbiomes. Heat stress leads to more complex and unstable microbial networks, characterized by an increased average degree and decreased modularity, respectively. With the extension of heat stress duration, the relative abundances of the gene (nifH) and genus (Tistlia) associated with nitrogen fixation increased in coral samples, as well as the potential pathogenic bacteria (Flavobacteriales) and opportunistic bacteria (Bacteroides). Hence, our findings suggest that coral hosts might recruit nitrogen-fixing bacteria during the initial stages of suffering heat stress. An environment that is conducive to the colonization and development of opportunistic and pathogenic bacteria when the coral host becomes more susceptible as heat stress duration increases.}, }
@article {pmid38350445, year = {2024}, author = {Laine, J and Mak, SST and Martins, NFG and Chen, X and Gilbert, MTP and Jones, FC and Pedersen, MW and Romundset, A and Foote, AD}, title = {Late Pleistocene stickleback environmental genomes reveal the chronology of freshwater adaptation.}, journal = {Current biology : CB}, volume = {34}, number = {5}, pages = {1142-1147.e6}, doi = {10.1016/j.cub.2024.01.056}, pmid = {38350445}, issn = {1879-0445}, mesh = {Animals ; *Ecosystem ; Adaptation, Physiological/genetics ; *Smegmamorpha/genetics ; Retrospective Studies ; Lakes ; }, abstract = {Directly observing the chronology and tempo of adaptation in response to ecological change is rarely possible in natural ecosystems. Sedimentary ancient DNA (sedaDNA) has been shown to be a tractable source of genome-scale data of long-dead organisms[1][,][2][,][3] and to thereby potentially provide an understanding of the evolutionary histories of past populations.[4][,][5] To date, time series of ecosystem biodiversity have been reconstructed from sedaDNA, typically using DNA metabarcoding or shotgun sequence data generated from less than 1 g of sediment.[6][,][7] Here, we maximize sequence coverage by extracting DNA from ∼50× more sediment per sample than the majority of previous studies[1][,][2][,][3] to achieve genotype resolution. From a time series of Late Pleistocene sediments spanning from a marine to freshwater ecosystem, we compare adaptive genotypes reconstructed from the environmental genomes of three-spined stickleback at key time points of this transition. We find a staggered temporal dynamic in which freshwater alleles at known loci of large effect in marine-freshwater divergence of three-spined stickleback (e.g., EDA)[8] were already established during the brackish phase of the formation of the isolation basin. However, marine alleles were still detected across the majority of marine-freshwater divergence-associated loci, even after the complete isolation of the lake from marine ingression. Our retrospective approach to studying adaptation from environmental genomes of three-spined sticklebacks at the end of the last glacial period complements contemporary experimental approaches[9][,][10][,][11] and highlights the untapped potential for retrospective "evolve and resequence" natural experiments using sedaDNA.}, }
@article {pmid38347271, year = {2024}, author = {Suárez, J}, title = {Scrutinizing microbiome determinism: why deterministic hypotheses about the microbiome are conceptually ungrounded.}, journal = {History and philosophy of the life sciences}, volume = {46}, number = {1}, pages = {12}, pmid = {38347271}, issn = {1742-6316}, support = {2019/35/B/HS1/01998//Narodowe Centrum Nauki/ ; SV-23-FBBVA-1//Fundaci&#xf3;n BBVA/ ; PID2022-137993NA-I00//Spanish National Plan for Scientific and Technical Research and Innovation/ ; }, mesh = {*Biological Evolution ; Symbiosis ; *Microbiota/genetics ; Phenotype ; }, abstract = {This paper addresses the topic of determinism in contemporary microbiome research. I distinguish two types of deterministic claims about the microbiome, and I show evidence that both types of claims are present in the contemporary literature. First, the idea that the host genetics determines the composition of the microbiome which I call "host-microbiome determinism". Second, the idea that the genetics of the holobiont (the individual unit composed by a host plus its microbiome) determines the expression of certain phenotypic traits, which I call "microbiome-phenotype determinism". Drawing on the stability of traits conception of individuality (Suárez in Hist Philos Life Sci 42:11, 2020) I argue that none of these deterministic hypotheses is grounded on our current knowledge of how the holobiont is transgenerationally assembled, nor how it expresses its phenotypic traits.}, }
@article {pmid38345665, year = {2024}, author = {Sasaki, S and Mori, T and Enomoto, H and Nakamura, S and Yokota, H and Yamashita, H and Goto-Inoue, N}, title = {Assessing Molecular Localization of Symbiont Microalgae in Coral Branches Through Mass Spectrometry Imaging.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {26}, number = {2}, pages = {223-229}, pmid = {38345665}, issn = {1436-2236}, support = {21H04742//Japan Society for the Promotion of Science/ ; }, mesh = {*Anthozoa/metabolism ; *Symbiosis ; Animals ; *Dinoflagellida ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Microalgae/metabolism ; Coral Reefs ; Molecular Imaging/methods ; }, abstract = {Reef-building corals are a fundamental pillar of coral reef ecosystems in tropical and subtropical shallow environments. Corals harbor symbiotic dinoflagellates belonging to the family Symbiodiniaceae, commonly known as zooxanthellae. Extensive research has been conducted on this symbiotic relationship, yet the fundamental information about the distribution and localization of Symbiodiniaceae cells in corals is still limited. This information is crucial to understanding the mechanism underlying the metabolite exchange between corals and their algal symbionts, as well as the metabolic flow within holobionts. To examine the distribution of Symbiodiniaceae cells within corals, in this study, we used fluorescence imaging and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MS-Imaging) on branches of the Acropora tenuis coral. We successfully prepared frozen sections of the coral for molecular imaging without fixing or decalcifying the coral branches. By combining the results of MS-Imaging with that of the fluorescence imaging, we determined that the algal Symbiodiniaceae symbionts were not only localized in the tentacle and surface region of the coral branches but also inhabited the in inner parts. Therefore, the molecular imaging technique used in this study could be valuable to further investigate the molecular dynamics between corals and their symbionts.}, }
@article {pmid38340371, year = {2024}, author = {Wang, S and Lu, C and Zhang, Q and He, X and Wang, W and Li, J and Su, H}, title = {Microbial community and transcriptional responses to V. coralliilyticus stress in coral Favites halicora and Pocillopora damicornis holobiont.}, journal = {Marine environmental research}, volume = {196}, number = {}, pages = {106394}, doi = {10.1016/j.marenvres.2024.106394}, pmid = {38340371}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/genetics ; *Vibrio/physiology ; Transcriptome ; *Microbiota ; Coral Reefs ; }, abstract = {Variability in coral hosts susceptibility to Vibrio coralliilyticus is well-documented; however, the comprehensive understanding of tolerance of response to pathogen among coral species is lacked. Herein, we investigated the microbial communities and transcriptome dynamics of two corals in response to Vibrio coralliilyticus. Favites halicora displayed greater resistance to Vibrio coralliilyticus challenge than Pocillopora damicornis. Furthermore, the relative abundances of Flavobacteriaceae, Vibrionacea, Rhodobacteraceae, and Roseobacteraceae increased significantly in Favites halicora following pathogen stress, whereas that of Akkermansiaceae increased significantly in Pocillopora damicornis, leading to bacterial community imbalance. In contrast to the previous results, pathogen infection did not have much effect on the community structures of Symbiodiniaceae and fungi, but led to a decrease in the density of Symbiodiniaceae. Transcriptome analysis indicated that Vibrio infection triggered a coral immune response, resulting in higher expression of immune-related genes, which appeared to have higher transcriptional plasticity in Favites halicora than in Pocillopora damicornis. Specifically, the upregulated genes of Favites halicora were predominantly involved in the apoptosis pathway, whereas Pocillopora damicornis were significantly enriched in the nucleotide excision repair and base excision repair pathways. These findings suggest that coral holobionts activate different mechanisms across species in response to pathogens through shifts in microbial communities and transcriptomes, which provides novel insight into assessing the future coral assemblages suffering from disease outbreaks.}, }
@article {pmid38339825, year = {2024}, author = {Welsh, BL and Eisenhofer, R}, title = {The prevalence of controls in phyllosphere microbiome research: a methodological review.}, journal = {The New phytologist}, volume = {242}, number = {1}, pages = {23-29}, doi = {10.1111/nph.19573}, pmid = {38339825}, issn = {1469-8137}, support = {//Wine Australia/ ; }, mesh = {Prevalence ; Systematic Reviews as Topic ; *Microbiota/genetics ; }, abstract = {DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.}, }
@article {pmid38334273, year = {2024}, author = {Olofsson, JK and Tyler, T and Dunning, LT and Hjertson, M and Rühling, &#xc5; and Hansen, AJ}, title = {Morphological and genetic evidence suggest gene flow among native and naturalized mint species.}, journal = {American journal of botany}, volume = {111}, number = {2}, pages = {e16280}, doi = {10.1002/ajb2.16280}, pmid = {38334273}, issn = {1537-2197}, support = {/ERC_/European Research Council/International ; }, mesh = {Humans ; *Mentha/genetics ; Gene Flow ; Phylogeny ; *Oils, Volatile/pharmacology ; Hybridization, Genetic ; }, abstract = {PREMISE: Cultivation and naturalization of plants beyond their natural range can bring previously geographically isolated taxa together, increasing the opportunity for hybridization, the outcomes of which are not predictable. Here, we explored the phenotypic and genomic effects of interspecific gene flow following the widespread cultivation of Mentha spicata (spearmint), M. longifolia, and M. suaveolens.<br><br>METHODS: We morphologically evaluated 155 herbarium specimens of three Mentha species and sequenced the genomes of a subset of 93 specimens. We analyzed the whole genomes in a population and the phylogenetic framework and associated genomic classifications in conjunction with the morphological assessments.<br><br>RESULTS: The allopolyploid M. spicata, which likely evolved in cultivation, had altered trichome characters, that is possibly a product of human selection for a more palatable plant or a byproduct of selection for essential oils. There were signs of genetic admixture between mints, including allopolyploids, indicating that the reproductive barriers between Mentha species with differences in ploidy are likely incomplete. Still, despite gene flow between species, we found that genetic variants associated with the cultivated trichome morphology continue to segregate.<br><br>CONCLUSIONS: Although hybridization, allopolyploidization, and human selection during cultivation can increase species richness (e.g., by forming hybrid taxa), we showed that unless reproductive barriers are strong, these processes can also result in mixing of genes between species and the potential loss of natural biodiversity.}, }
@article {pmid38322319, year = {2024}, author = {Czajkowski, R and Zhu, L and Kuo, CH and Li, Z}, title = {Editorial: Insights in microbial symbioses: 2022/2023.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1367452}, pmid = {38322319}, issn = {1664-302X}, }
@article {pmid38320428, year = {2024}, author = {Estaque, T and Basthard-Bogain, S and Bianchimani, O and Blondeaux, V and Cheminée, A and Fargetton, M and Richaume, J and Bally, M}, title = {Investigating the outcomes of a threatened gorgonian in situ transplantation: Survival and microbiome diversity in Paramuricea clavata (Risso, 1827).}, journal = {Marine environmental research}, volume = {196}, number = {}, pages = {106384}, doi = {10.1016/j.marenvres.2024.106384}, pmid = {38320428}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa ; *Microbiota ; }, abstract = {Gorgonian octocorals are threatened by global and local stressors that can act synergistically to affect their health. In recent years, mass mortality events triggered by marine heatwaves have caused demographic declines in Mediterranean gorgonian populations that may lead to their collapse. Potential changes in microbiome composition under stressful conditions may further increase the susceptibility of the gorgonian holobiont to disease. Given the low recovery capacity of gorgonians, restoration approaches using transplantation are becoming an increasingly attractive option to counteract their decline. Here, we compared the survival and microbiome diversity of Paramuricea clavata colonies transplanted to sites differing in depth and local environmental conditions. Gorgonians sampled at a greater depth than the transplantation site were more likely to suffer necrosis after 1 year of monitoring. Gorgonian transplantation into environments disturbed by an anthropogenic source of pollution resulted in an imbalance of the microbiome with potential consequences on the success of restoration initiatives.}, }
@article {pmid38308082, year = {2024}, author = {Reigel, AM and Easson, CG and Apprill, A and Freeman, CJ and Bartley, MM and Fiore, CL}, title = {Sponge-derived matter is assimilated by coral holobionts.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {146}, pmid = {38308082}, issn = {2399-3642}, support = {1924540//National Science Foundation (NSF)/ ; 1923962//National Science Foundation (NSF)/ ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Biodiversity ; Nutrients ; }, abstract = {Coral reef biodiversity is maintained by a complex network of nutrient recycling among organisms. Sponges assimilate nutrients produced by other organisms like coral and algae, releasing them as particulate and dissolved matter, but to date, only a single trophic link between sponge-derived dissolved matter and a macroalgae has been identified. We sought to determine if sponge-coral nutrient exchange is reciprocal using a stable isotope 'pulse-chase' experiment to trace the uptake of [13]C and [15]N sponge-derived matter by the coral holobiont for three coral species (Acropora cervicornis, Orbicella faveolata, and Eunicea flexuosa). Coral holobionts incorporated 2.3-26.8x more [15]N than [13]C from sponge-derived matter and A. cervicornis incorporated more of both C and N than the other corals. Differential isotopic incorporation among coral species aligns with their ecophysiological characteristics (e.g., morphology, Symbiodiniaceae density). Our results elucidate a recycling pathway on coral reefs that has implications for improving coral aquaculture and management approaches.}, }
@article {pmid38304271, year = {2024}, author = {Hartvig, I and Kosawang, C and Rasmussen, H and Kjær, ED and Nielsen, LR}, title = {Co-occurring orchid species associated with different low-abundance mycorrhizal fungi from the soil in a high-diversity conservation area in Denmark.}, journal = {Ecology and evolution}, volume = {14}, number = {2}, pages = {e10863}, pmid = {38304271}, issn = {2045-7758}, abstract = {Plant-fungal interactions are ubiquitous across ecosystems and contribute significantly to plant ecology and evolution. All orchids form obligate symbiotic relationships with specific fungi for germination and early growth, and the distribution of terrestrial orchid species has been linked to occurrence and abundance of specific orchid mycorrhizal fungi (OMF) in the soil. The availability of OMF can therefore be a habitat requirement that is relevant to consider when establishing management and conservation strategies for threatened orchid species, but knowledge on the spatial distribution of OMF in soil is limited. We here studied the mycorrhizal associations of three terrestrial orchid species (Anacamptis pyramidalis, Orchis purpurea and Platanthera chlorantha) found in a local orchid diversity hotspot in eastern Denmark, and investigated the abundance of the identified mycorrhizal fungi in the surrounding soil. We applied ITS metabarcoding to samples of orchid roots, rhizosphere soil and bulk soil collected at three localities, supplemented with standard barcoding of root samples with OMF specific primers, and detected 22 Operational Taxonomic Units (OTUs) putatively identified as OMF. The three orchid species displayed different patterns of OMF associations, supporting the theory that association with specific fungi constitutes part of an orchid's ecological niche allowing co-occurrence of many species in orchid-rich habitats. The identified mycorrhizal partners in the basidiomycete families Tulasnellaceae and Ceratobasidiaceae (Cantharallales) were detected in low abundance in rhizosphere soil, and appeared almost absent from bulk soil at the localities. This finding highlights our limited knowledge of the ecology and trophic mode of OMF outside orchid tissues, as well as challenges in the detection of specific OMF with standard methods. Potential implications for management and conservation strategies are discussed.}, }
@article {pmid38294254, year = {2024}, author = {Brealey, JC and Kodama, M and Rasmussen, JA and Hansen, SB and Santos-Bay, L and Lecaudey, LA and Hansen, M and Fjære, E and Myrmel, LS and Madsen, L and Bernhard, A and Sveier, H and Kristiansen, K and Gilbert, MTP and Martin, MD and Limborg, MT}, title = {Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon.}, journal = {mSystems}, volume = {9}, number = {2}, pages = {e0104323}, pmid = {38294254}, issn = {2379-5077}, support = {901436//Fiskeri - og havbruksn&#xe6;ringens forskningsfond (FHF)/ ; CEH-DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; 817729//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; 311913//EC | ERC | HORIZON EUROPE European Research Council (ERC)/ ; CF21-0356//Carlsbergfondet (Carlsberg Foundation)/ ; 325589//Norges Forskningsr&#xe5;d (Forskningsr&#xe5;det)/ ; }, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; *Salmo salar ; Aquaculture ; Dysbiosis/veterinary ; *Parasitic Diseases ; *Cestode Infections ; }, abstract = {Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.}, }
@article {pmid38289136, year = {2024}, author = {Vergani, L and Patania, J and Riva, V and Nerva, L and Nuzzo, F and Gambino, G and Borin, S and Mapelli, F}, title = {Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0207823}, pmid = {38289136}, issn = {1098-5336}, support = {20172TZHYX//Ministero dell'Istruzione, dell'Universit&#xe0; e della Ricerca (MIUR)/ ; }, mesh = {*Agricultural Inoculants ; Phylogeny ; Plant Roots/microbiology ; Bacteria/genetics ; Enterobacteriaceae ; Endophytes/physiology ; }, abstract = {Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.}, }
@article {pmid38287457, year = {2024}, author = {Nweze, JE and Šustr, V and Brune, A and Angel, R}, title = {Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {16}, pmid = {38287457}, issn = {2049-2618}, support = {19-24309Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 19-24309Y//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Bacteria ; *Arthropods/genetics ; Metagenome ; Bacteroidetes/genetics ; Proteobacteria/genetics ; Metagenomics ; Carbohydrates ; Nitrogen/metabolism ; Sulfates/metabolism ; }, abstract = {BACKGROUND: Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.<br><br>RESULTS: The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.<br><br>CONCLUSIONS: Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.}, }
@article {pmid38273492, year = {2024}, author = {Vompe, AD and Epstein, HE and Speare, KE and Schmeltzer, ER and Adam, TC and Burkepile, DE and Sharpton, TJ and Vega Thurber, R}, title = {Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17088}, doi = {10.1111/gcb.17088}, pmid = {38273492}, issn = {1365-2486}, support = {2006244//Directorate for Biological Sciences/ ; 1637396//Division of Ocean Sciences/ ; 2023424//Division of Ocean Sciences/ ; 2023701//Division of Ocean Sciences/ ; }, mesh = {Animals ; Coral Reefs ; Coral Bleaching ; *Anthozoa/physiology ; *Microbiota ; Heat-Shock Response ; }, abstract = {Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large-scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long-term (28 months, 2018-2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves in Acropora retusa, Porites lobata, and Pocillopora spp., which included: microbiome acclimatization in A. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave in Pocillopora spp. Moreover, observed microbiome dynamics significantly correlated with coral species-specific phenotypes. For example, bleaching and mortality in A. retusa both significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, while P. lobata colonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality in A. retusa. This study reveals evidence for coral species-specific microbial responses to repeated heatwaves and, importantly, suggests that host-dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.}, }
@article {pmid38265168, year = {2024}, author = {Huang, W and Meng, L and Xiao, Z and Tan, R and Yang, E and Wang, Y and Huang, X and Yu, K}, title = {Heat-tolerant intertidal rock pool coral Porites lutea can potentially adapt to future warming.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17273}, doi = {10.1111/mec.17273}, pmid = {38265168}, issn = {1365-294X}, support = {42090041//National Natural Science Foundation of China/ ; 41866006//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; 2023GXNSFAA026510//Natural Science Foundation of Guangxi Province/ ; }, mesh = {Animals ; *Anthozoa/physiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; *Rhodobacteraceae/genetics ; Symbiosis ; }, abstract = {The growing threat of global warming on coral reefs underscores the urgency of identifying heat-tolerant corals and discovering their adaptation mechanisms to high temperatures. Corals growing in intertidal rock pools that vary markedly in daily temperature may have improved heat tolerance. In this study, heat stress experiments were performed on scleractinian coral Porites lutea from subtidal habitat and intertidal rock pool of Weizhou Island in the northern South China Sea. Thermotolerance differences in corals from the two habitats and their mechanisms were explored through phenotype, physiological indicators, ITS2, 16S rRNA, and RNA sequencing. At the extremely high temperature of 34°C, rock pool P. lutea had a stronger heat tolerance than those in the subtidal habitat. The strong antioxidant capacity of the coral host and its microbial partners was important in the resistance of rock pool corals to high temperatures. The host of rock pool corals at 34°C had stronger immune and apoptotic regulation, downregulated host metabolism and disease-infection-related pathways compared to the subtidal habitat. P. lutea, in this habitat, upregulated Cladocopium C15 (Symbiodiniaceae) photosynthetic efficiency and photoprotection, and significantly increased bacterial diversity and coral probiotics, including ABY1, Ruegeria, and Alteromonas. These findings indicate that rock pool corals can tolerate high temperatures through the integrated response of coral holobionts. These corals may be 'touchstones' for future warming. Our research provides new insights into the complex mechanisms by which corals resist global warming and the theoretical basis for coral reef ecosystem restoration and selection of stress-resistant coral populations.}, }
@article {pmid38258023, year = {2024}, author = {Dor-Roterman, YR and Benayahu, Y and Reshef, L and Gophna, U}, title = {Host-Microbiome Interactions in a Changing Sea: The Gill Microbiome of an Invasive Oyster under Drastic Temperature Changes.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, pmid = {38258023}, issn = {2076-2607}, abstract = {The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to host health. Spondylus spinosus is an invasive Lessepsian oyster in the Eastern Mediterranean Sea that has become highly abundant while constantly expanding its range northwestward. Using 16S rRNA gene amplicon sequencing, we examined how temperature affects S. spinosus oysters and their gill microbiota in a series of experiments: exposing them to the current annual seawater temperature range, to the colder temperature of the Western Mediterranean Sea, and to the elevated temperature as predicted under global warming scenarios. The bacterial genus Endozoicomonas dominated the communities of the S. spinosus, mainly upon exposure to winter-like (16 °C) temperatures. Exposure to the elevated seawater temperature resulted in a significant change in the bacterial communities, while the oysters maintained normal functioning, suggesting that the oyster may survive a seawater warming scenario. Exposure to 11 °C led to the health deterioration of the oysters, the emergence of opportunistic pathogens, such as Arcobacter, Vibrio, Colwelliaceae, and Pseudoalteromonas, and a decline in the relative abundance of Endozoicomonas, suggesting that S. spinosus might not survive Western Mediterranean Sea winters. Both the host and its gill bacteria are thus greatly affected by temperature, which could consequently restrict the range of expansion of this and other invasive oysters.}, }
@article {pmid38246375, year = {2024}, author = {Efremova, J and Mazzella, V and Mirasole, A and Teixidó, N and Núñez-Pons, L}, title = {Divergent morphological and microbiome strategies of two neighbor sponges to cope with low pH in Mediterranean CO2 vents.}, journal = {The Science of the total environment}, volume = {916}, number = {}, pages = {170171}, doi = {10.1016/j.scitotenv.2024.170171}, pmid = {38246375}, issn = {1879-1026}, mesh = {Humans ; *Seawater/chemistry ; Carbon Dioxide ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Hydrogen-Ion Concentration ; *Microbiota/physiology ; Phylogeny ; }, abstract = {Ocean Acidification (OA) profoundly impacts marine biochemistry, resulting in a net loss of biodiversity. Porifera are often forecasted as winner taxa, yet the strategies to cope with OA can vary and may generate diverse fitness status. In this study, microbial shifts based on the V3-V4 16S rRNA gene marker were compared across neighboring Chondrosia reniformis sponges with high microbial abundance (HMA), and Spirastrella cunctatrix with low microbial abundance (LMA) microbiomes. Sponge holobionts co-occurred in a CO2 vent system with low pH (pHT ~ 7.65), and a control site with Ambient pH (pHT ~ 8.05) off Ischia Island, representing natural analogues to study future OA, and species' responses in the face of global environmental change. Microbial diversity and composition varied in both species across sites, yet at different levels. Increased numbers of core taxa were detected in S. cunctatrix, and a more diverse and flexible core microbiome was reported in C. reniformis under OA. Vent S. cunctatrix showed morphological impairment, along with signs of putative stress-induced dysbiosis, manifested by: 1) increases in alpha diversity, 2) shifts from sponge related microbes towards seawater microbes, and 3) high dysbiosis scores. Chondrosia reniformis in lieu, showed no morphological variation, low dysbiosis scores, and experienced a reduction in alpha diversity and less number of core taxa in vent specimens. Therefore, C. reniformis is hypothesized to maintain an state of normobiosis and acclimatize to OA, thanks to a more diverse, and likely metabolically versatile microbiome. A consortium of differentially abundant microbes was identified associated to either vent or control sponges, and chiefly related to carbon, nitrogen and sulfur-metabolisms for nutrient cycling and vitamin production, as well as probiotic symbionts in C. reniformis. Diversified symbiont associates supporting functional convergence could be the key behind resilience towards OA, yet specific acclimatization traits should be further investigated.}, }
@article {pmid38244627, year = {2024}, author = {Adomako, MO and Wu, J and Lu, Y and Adu, D and Seshie, VI and Yu, FH}, title = {Potential synergy of microplastics and nitrogen enrichment on plant holobionts in wetland ecosystems.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {170160}, doi = {10.1016/j.scitotenv.2024.170160}, pmid = {38244627}, issn = {1879-1026}, mesh = {*Ecosystem ; Wetlands ; Microplastics ; Plastics ; Nitrogen/metabolism ; Soil/chemistry ; *Microbiota ; }, abstract = {Wetland ecosystems are global hotspots for environmental contaminants, including microplastics (MPs) and nutrients such as nitrogen (N) and phosphorus (P). While MP and nutrient effects on host plants and their associated microbial communities at the individual level have been studied, their synergistic effects on a plant holobiont (i.e., a plant host plus its microbiota, such as bacteria and fungi) in wetland ecosystems are nearly unknown. As an ecological entity, plant holobionts play pivotal roles in biological nitrogen fixation, promote plant resilience and defense chemistry against pathogens, and enhance biogeochemical processes. We summarize evidence based on recent literature to elaborate on the potential synergy of MPs and nutrient enrichment on plant holobionts in wetland ecosystems. We provide a conceptual framework to explain the interplay of MPs, nutrients, and plant holobionts and discuss major pathways of MPs and nutrients into the wetland milieu. Moreover, we highlight the ecological consequences of loss of plant holobionts in wetland ecosystems and conclude with recommendations for pending questions that warrant urgent research. We found that nutrient enrichment promotes the recruitment of MPs-degraded microorganisms and accelerates microbially mediated degradation of MPs, modifying their distribution and toxicity impacts on plant holobionts in wetland ecosystems. Moreover, a loss of wetland plant holobionts via long-term MP-nutrient interactions may likely exacerbate the disruption of wetland ecosystems' capacity to offer nature-based solutions for climate change mitigation through soil organic C sequestration. In conclusion, MP and nutrient enrichment interactions represent a severe ecological risk that can disorganize plant holobionts and their taxonomic roles, leading to dysbiosis (i.e., the disintegration of a stable plant microbiome) and diminishing wetland ecosystems' integrity and multifunctionality.}, }
@article {pmid38238538, year = {2024}, author = {Allentoft, ME and Sikora, M and Refoyo-Martínez, A and Irving-Pease, EK and Fischer, A and Barrie, W and Ingason, A and Stenderup, J and Sjögren, KG and Pearson, A and Sousa da Mota, B and Schulz Paulsson, B and Halgren, A and Macleod, R and Jørkov, MLS and Demeter, F and Sørensen, L and Nielsen, PO and Henriksen, RA and Vimala, T and McColl, H and Margaryan, A and Ilardo, M and Vaughn, A and Fischer Mortensen, M and Nielsen, AB and Ulfeldt Hede, M and Johannsen, NN and Rasmussen, P and Vinner, L and Renaud, G and Stern, A and Jensen, TZT and Scorrano, G and Schroeder, H and Lysdahl, P and Ramsøe, AD and Skorobogatov, A and Schork, AJ and Rosengren, A and Ruter, A and Outram, A and Timoshenko, AA and Buzhilova, A and Coppa, A and Zubova, A and Silva, AM and Hansen, AJ and Gromov, A and Logvin, A and Gotfredsen, AB and Henning Nielsen, B and González-Rabanal, B and Lalueza-Fox, C and McKenzie, CJ and Gaunitz, C and Blasco, C and Liesau, C and Martinez-Labarga, C and Pozdnyakov, DV and Cuenca-Solana, D and Lordkipanidze, DO and En'shin, D and Salazar-García, DC and Price, TD and Borić, D and Kostyleva, E and Veselovskaya, EV and Usmanova, ER and Cappellini, E and Brinch Petersen, E and Kannegaard, E and Radina, F and Eylem Yediay, F and Duday, H and Gutiérrez-Zugasti, I and Merts, I and Potekhina, I and Shevnina, I and Altinkaya, I and Guilaine, J and Hansen, J and Aura Tortosa, JE and Zilhão, J and Vega, J and Buck Pedersen, K and Tunia, K and Zhao, L and Mylnikova, LN and Larsson, L and Metz, L and Yepiskoposyan, L and Pedersen, L and Sarti, L and Orlando, L and Slimak, L and Klassen, L and Blank, M and González-Morales, M and Silvestrini, M and Vretemark, M and Nesterova, MS and Rykun, M and Rolfo, MF and Szmyt, M and Przybyła, M and Calattini, M and Sablin, M and Dobisíková, M and Meldgaard, M and Johansen, M and Berezina, N and Card, N and Saveliev, NA and Poshekhonova, O and Rickards, O and Lozovskaya, OV and Gábor, O and Uldum, OC and Aurino, P and Kosintsev, P and Courtaud, P and Ríos, P and Mortensen, P and Lotz, P and Persson, P and Bangsgaard, P and de Barros Damgaard, P and Vang Petersen, P and Martinez, PP and Włodarczak, P and Smolyaninov, RV and Maring, R and Menduiña, R and Badalyan, R and Iversen, R and Turin, R and Vasilyev, S and Wåhlin, S and Borutskaya, S and Skochina, S and Sørensen, SA and Andersen, SH and Jørgensen, T and Serikov, YB and Molodin, VI and Smrcka, V and Merts, V and Appadurai, V and Moiseyev, V and Magnusson, Y and Kjær, KH and Lynnerup, N and Lawson, DJ and Sudmant, PH and Rasmussen, S and Korneliussen, TS and Durbin, R and Nielsen, R and Delaneau, O and Werge, T and Racimo, F and Kristiansen, K and Willerslev, E}, title = {Publisher Correction: Population genomics of post-glacial western Eurasia.}, journal = {Nature}, volume = {626}, number = {7997}, pages = {E3}, doi = {10.1038/s41586-024-07044-5}, pmid = {38238538}, issn = {1476-4687}, }
@article {pmid38233870, year = {2024}, author = {Tabassum, N and Ahmed, HI and Parween, S and Sheikh, AH and Saad, MM and Krattinger, SG and Hirt, H}, title = {Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {11}, pmid = {38233870}, issn = {2049-2618}, mesh = {*Soil/chemistry ; Genome-Wide Association Study ; Seeds/genetics/microbiology ; *Microbiota/genetics ; Plants ; Endophytes ; Genotype ; Bacteria/genetics ; }, abstract = {BACKGROUND: Fonio (Digitaria exilis), an orphan millet crop, is the oldest indigenous crop in West Africa. Although the yield is low due to pre-domestication characteristics, the quick maturation time, drought tolerance, and the ability to thrive on poor soils make fonio a climate-smart crop. Being holobionts, plants evolve in close interaction with microbial partners, which is crucial for plant phenology and fitness. As seeds are the bottleneck of vertically transmitting plant microbiota, we proposed to unravel the seed microbiome of the under-domesticated and resilient crop fonio. Our study investigated the bacterial seed endophyte diversity across 126 sequenced fonio accessions from distinct locations in West Africa. We conducted a correlation study of the structures and functions of the seed-associated microbiomes with the native geo-climate and soil structure data. We also performed Genome-wide association studies (GWAS) to identify genetic loci associated with seed endophyte diversity.<br><br>RESULT: We report that fonio millet has diverse heritable seed endophytic taxa. We analyzed the seed microbiomes of 126 fonio accessions and showed that despite the diversity of microbiomes from distinct geographical locations, all fonio genetic groups share a core microbiome. In addition, we observed that native soil composition, geo-climatic factors, and host genotype correlate with the seed microbiomes. GWAS analysis of genetic loci associated with endophyte seed bacterial diversity identified fonio SNPs associated with genes functioning in embryo development and stress/defense response.<br><br>CONCLUSION: Analysis of the seed endophyte of the climate-smart crop fonio indicated that despite possessing a heritable core microbiome, native conditions may shape the overall fonio seed microbiomes in different populations. These distinct microbiomes could play important roles in the adaptation of fonio to different environmental conditions. Our study identified the seed microbiome as a potential target for enhancing crop resilience to climate stress in a sustainable way. Video Abstract.}, }
@article {pmid38230446, year = {2024}, author = {Castro, LC and Vergés, A and Straub, SC and Campbell, AH and Coleman, MA and Wernberg, T and Steinberg, P and Thomas, T and Dworjanyn, S and Cetina-Heredia, P and Roughan, M and Marzinelli, EM}, title = {Effect of marine heatwaves and warming on kelp microbiota influence trophic interactions.}, journal = {Molecular ecology}, volume = {33}, number = {5}, pages = {e17267}, doi = {10.1111/mec.17267}, pmid = {38230446}, issn = {1365-294X}, support = {DP160100114//Australian Research Council/ ; DP170100023//Australian Research Council/ ; DP180104041//Australian Research Council/ ; LP150100064//Australian Research Council/ ; }, mesh = {*Kelp/physiology ; Ecosystem ; Climate Change ; Oceans and Seas ; *Seaweed ; *Microbiota ; }, abstract = {The range-expansion of tropical herbivores due to ocean warming can profoundly alter temperate reef communities by overgrazing the seaweed forests that underpin them. Such ecological interactions may be mediated by changes to seaweed-associated microbiota in response to warming, but empirical evidence demonstrating this is rare. We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp Ecklonia radiata's microbiota in sustained warming and MHW treatments was enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid Sargassum linearifolium's microbiota was unaffected by temperature. Consumption by the tropical sea-urchin Tripneustes gratilla was greater on Ecklonia where the microbiota had been altered by higher temperatures, while Sargassum's consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. Effects of warming and MHWs on seaweed holobionts (host plus its microbiota) are likely species-specific. The effect of increased temperature on Ecklonia's microbiota and subsequent increased consumption suggest that changes to kelp microbiota may underpin kelp-herbivore interactions, providing novel insights into potential mechanisms driving change in species' interactions in warming oceans.}, }
@article {pmid38228019, year = {2024}, author = {Li, J and Guo, A and Huang, S and Azam, F and Sun, X and Zhang, J and Long, L and Zhang, S}, title = {Outer membrane vesicles produced by coral-associated Vibrio coralliilyticus inhibit bacteriophage infection and its ecological implications.}, journal = {Microbiological research}, volume = {281}, number = {}, pages = {127607}, doi = {10.1016/j.micres.2024.127607}, pmid = {38228019}, issn = {1618-0623}, mesh = {Animals ; *Anthozoa/microbiology ; *Bacteriophages ; *Vibrio ; }, abstract = {The potential to produce and release outer membrane vesicles (OMVs) is evolutionarily conserved among bacteria, facilitating interactions between microbes. OMV release and its ecological significance have rarely been reported in coral holobionts. Here, via transmission electron microscopy (TEM), we discovered that the coral-associated strain Vibrio coralliilyticus DSM 19607 produced OMVs in culture. OMVs purified from V. coralliilyticus DSM 19607 inhibited the bacteriophage (phage) SBM1 infection of the V. coralliilyticus host, which was impaired by elevated temperature. Observation via TEM showed that sequestrating phages was a potential approach for V. coralliilyticus OMVs protection against phage infection. Furthermore, detection in coral mucus showed that interactions between membrane vesicles and phages potentially occurred in the natural environment. These results imply that OMVs regulate the coral microbiome and may have important implications for our mechanistic understanding of coral health and disease in the face of climate change.}, }
@article {pmid38216372, year = {2024}, author = {Pogoreutz, C and Ziegler, M}, title = {Frenemies on the reef? Resolving the coral-Endozoicomonas association.}, journal = {Trends in microbiology}, volume = {32}, number = {5}, pages = {422-434}, doi = {10.1016/j.tim.2023.11.006}, pmid = {38216372}, issn = {1878-4380}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Stony corals are poster child holobionts due to their intimate association with diverse microorganisms from all domains of life. We are only beginning to understand the diverse functions of most of these microbial associates, including potential main contributors to holobiont health and resilience. Among these, bacteria of the elusive genus Endozoicomonas are widely perceived as beneficial symbionts based on their genomic potential and their high prevalence and ubiquitous presence in coral tissues. Simultaneously, evidence of pathogenic and parasitic Endozoicomonas lineages in other marine animals is emerging. Synthesizing the current knowledge on the association of Endozoicomonas with marine holobionts, we challenge the perception of a purely mutualistic coral-Endozoicomonas relationship and propose directions to elucidate its role along the symbiotic spectrum.}, }
@article {pmid38200295, year = {2024}, author = {Allentoft, ME and Sikora, M and Refoyo-Martínez, A and Irving-Pease, EK and Fischer, A and Barrie, W and Ingason, A and Stenderup, J and Sjögren, KG and Pearson, A and Sousa da Mota, B and Schulz Paulsson, B and Halgren, A and Macleod, R and Jørkov, MLS and Demeter, F and Sørensen, L and Nielsen, PO and Henriksen, RA and Vimala, T and McColl, H and Margaryan, A and Ilardo, M and Vaughn, A and Fischer Mortensen, M and Nielsen, AB and Ulfeldt Hede, M and Johannsen, NN and Rasmussen, P and Vinner, L and Renaud, G and Stern, A and Jensen, TZT and Scorrano, G and Schroeder, H and Lysdahl, P and Ramsøe, AD and Skorobogatov, A and Schork, AJ and Rosengren, A and Ruter, A and Outram, A and Timoshenko, AA and Buzhilova, A and Coppa, A and Zubova, A and Silva, AM and Hansen, AJ and Gromov, A and Logvin, A and Gotfredsen, AB and Henning Nielsen, B and González-Rabanal, B and Lalueza-Fox, C and McKenzie, CJ and Gaunitz, C and Blasco, C and Liesau, C and Martinez-Labarga, C and Pozdnyakov, DV and Cuenca-Solana, D and Lordkipanidze, DO and En'shin, D and Salazar-García, DC and Price, TD and Borić, D and Kostyleva, E and Veselovskaya, EV and Usmanova, ER and Cappellini, E and Brinch Petersen, E and Kannegaard, E and Radina, F and Eylem Yediay, F and Duday, H and Gutiérrez-Zugasti, I and Merts, I and Potekhina, I and Shevnina, I and Altinkaya, I and Guilaine, J and Hansen, J and Aura Tortosa, JE and Zilhão, J and Vega, J and Buck Pedersen, K and Tunia, K and Zhao, L and Mylnikova, LN and Larsson, L and Metz, L and Yepiskoposyan, L and Pedersen, L and Sarti, L and Orlando, L and Slimak, L and Klassen, L and Blank, M and González-Morales, M and Silvestrini, M and Vretemark, M and Nesterova, MS and Rykun, M and Rolfo, MF and Szmyt, M and Przybyła, M and Calattini, M and Sablin, M and Dobisíková, M and Meldgaard, M and Johansen, M and Berezina, N and Card, N and Saveliev, NA and Poshekhonova, O and Rickards, O and Lozovskaya, OV and Gábor, O and Uldum, OC and Aurino, P and Kosintsev, P and Courtaud, P and Ríos, P and Mortensen, P and Lotz, P and Persson, P and Bangsgaard, P and de Barros Damgaard, P and Vang Petersen, P and Martinez, PP and Włodarczak, P and Smolyaninov, RV and Maring, R and Menduiña, R and Badalyan, R and Iversen, R and Turin, R and Vasilyev, S and Wåhlin, S and Borutskaya, S and Skochina, S and Sørensen, SA and Andersen, SH and Jørgensen, T and Serikov, YB and Molodin, VI and Smrcka, V and Merts, V and Appadurai, V and Moiseyev, V and Magnusson, Y and Kjær, KH and Lynnerup, N and Lawson, DJ and Sudmant, PH and Rasmussen, S and Korneliussen, TS and Durbin, R and Nielsen, R and Delaneau, O and Werge, T and Racimo, F and Kristiansen, K and Willerslev, E}, title = {Population genomics of post-glacial western Eurasia.}, journal = {Nature}, volume = {625}, number = {7994}, pages = {301-311}, pmid = {38200295}, issn = {1476-4687}, support = {207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; U19 AG023122/AG/NIA NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; UH2 AG064706/AG/NIA NIH HHS/United States ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 GM138634/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Agriculture/history ; Asia, Western ; Black Sea ; Diploidy ; Europe/ethnology ; *Genetics, Population ; *Genome, Human ; Genotype ; History, Ancient ; *Human Migration/history ; Hunting/history ; *Metagenomics ; Ice Cover ; }, abstract = {Western Eurasia witnessed several large-scale human migrations during the Holocene[1-5]. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.}, }
@article {pmid38198924, year = {2024}, author = {Cha, J and Kim, TG and Bhae, E and Gwak, HJ and Ju, Y and Choe, YH and Jang, IH and Jung, Y and Moon, S and Kim, T and Lee, W and Park, JS and Chung, YW and Yang, S and Kang, YK and Hyun, YM and Hwang, GS and Lee, WJ and Rho, M and Ryu, JH}, title = {Skin microbe-dependent TSLP-ILC2 priming axis in early life is co-opted in allergic inflammation.}, journal = {Cell host &amp; microbe}, volume = {32}, number = {2}, pages = {244-260.e11}, doi = {10.1016/j.chom.2023.12.006}, pmid = {38198924}, issn = {1934-6069}, mesh = {Humans ; Adult ; Infant, Newborn ; *Thymic Stromal Lymphopoietin ; Immunity, Innate ; Lymphocytes ; Cytokines/metabolism ; Skin/metabolism ; *Dermatitis, Atopic ; Inflammation ; }, abstract = {Although early life colonization of commensal microbes contributes to long-lasting immune imprinting in host tissues, little is known regarding the pathophysiological consequences of postnatal microbial tuning of cutaneous immunity. Here, we show that postnatal exposure to specific skin commensal Staphylococcus lentus (S. lentus) promotes the extent of atopic dermatitis (AD)-like inflammation in adults through priming of group 2 innate lymphoid cells (ILC2s). Early postnatal skin is dynamically populated by discrete subset of primed ILC2s driven by microbiota-dependent induction of thymic stromal lymphopoietin (TSLP) in keratinocytes. Specifically, the indole-3-aldehyde-producing tryptophan metabolic pathway, shared across Staphylococcus species, is involved in TSLP-mediated ILC2 priming. Furthermore, we demonstrate a critical contribution of the early postnatal S. lentus-TSLP-ILC2 priming axis in facilitating AD-like inflammation that is not replicated by later microbial exposure. Thus, our findings highlight the fundamental role of time-dependent neonatal microbial-skin crosstalk in shaping the threshold of innate type 2 immunity co-opted in adulthood.}, }
@article {pmid38196363, year = {2024}, author = {Howe, J and Cornwallis, CK and Griffin, AS}, title = {Conflict-reducing innovations in development enable increased multicellular complexity.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2014}, pages = {20232466}, pmid = {38196363}, issn = {1471-2954}, mesh = {Animals ; Phylogeny ; *Cognition ; Cell Division ; *Stem Cells ; }, abstract = {Obligately multicellular organisms, where cells can only reproduce as part of the group, have evolved multiple times across the tree of life. Obligate multicellularity has only evolved when clonal groups form by cell division, rather than by cells aggregating, as clonality prevents internal conflict. Yet obligately multicellular organisms still vary greatly in 'multicellular complexity' (the number of cells and cell types): some comprise a few cells and cell types, while others have billions of cells and thousands of types. Here, we test whether variation in multicellular complexity is explained by two conflict-suppressing mechanisms, namely a single-cell bottleneck at the start of development, and a strict separation of germline and somatic cells. Examining the life cycles of 129 lineages of plants, animals, fungi and algae, we show using phylogenetic comparative analyses that an early segregation of the germline stem-cell lineage is key to the evolution of more cell types, driven by a strong correlation in the Metazoa. By contrast, the presence of a strict single-cell bottleneck was not related to either the number of cells or the number of cell types, but was associated with early germline segregation. Our results suggest that segregating the germline earlier in development enabled greater evolutionary innovation, although whether this is a consequence of conflict reduction or other non-conflict effects, such as developmental flexibility, is unclear.}, }
@article {pmid38196068, year = {2024}, author = {Szeőcs, D and Vida, B and Petővári, G and Póliska, S and Janka, E and Sipos, A and Uray, K and Sebestyén, A and Krasznai, Z and Bai, P}, title = {Cell-free ascites from ovarian cancer patients induces Warburg metabolism and cell proliferation through TGFβ-ERK signaling.}, journal = {GeroScience}, volume = {46}, number = {4}, pages = {3581-3597}, pmid = {38196068}, issn = {2509-2723}, support = {K142141//NKFIH/ ; FK128387//NKFIH/ ; TKP2021-EGA-19//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; Bolyai Fellowship//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; NKM2022-30//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; POST-COVID2021-33//Magyar Tudom&#xe1;nyos Akad&#xe9;mia/ ; FK146852//Nemzeti Kutat&#xe1;si Fejleszt&#xe9;si &#xe9;s Innov&#xe1;ci&#xf3;s Hivatal/ ; }, mesh = {Humans ; Female ; *Ovarian Neoplasms/metabolism/pathology ; *Cell Proliferation ; *Ascites/metabolism ; *Transforming Growth Factor beta/metabolism ; Cell Line, Tumor ; MAP Kinase Signaling System/physiology ; Warburg Effect, Oncologic ; Middle Aged ; }, abstract = {Ascites plays a key role in supporting the metastatic potential of ovarian cancer cells. Shear stress and carry-over of cancer cells by ascites flow support carcinogenesis and metastasis formation. In addition, soluble factors may participate in the procarcinogenic effects of ascites in ovarian cancer. This study aimed to determine the biological effects of cell-free ascites on carcinogenesis in ovarian cancer cells. Cell-free ascites from ovarian cancer patients (ASC) non-selectively induced cell proliferation in multiple models of ovarian cancer and untransformed primary human dermal fibroblasts. Furthermore, ASC induced a Warburg-type rearrangement of cellular metabolism in A2780 ovarian cancer cells characterized by increases in cellular oxygen consumption and glycolytic flux; increases in glycolytic flux were dominant. ASC induced mitochondrial uncoupling and fundamentally reduced fatty acid oxidation. Ascites-elicited effects were uniform among ascites specimens. ASC-elicited transcriptomic changes in A2780 ovarian cancer cells included induction of the TGFβ-ERK/MEK pathway, which plays a key role in inducing cell proliferation and oncometabolism. ASC-induced gene expression changes, as well as the overexpression of members of the TGFβ signaling system, were associated with poor survival in ovarian cancer patients. We provided evidence that the activation of the autocrine/paracrine of TGFβ signaling system may be present in bladder urothelial carcinoma and stomach adenocarcinoma. Database analysis suggests that the TGFβ system may feed forward bladder urothelial carcinoma and stomach adenocarcinoma. Soluble components of ASC support the progression of ovarian cancer. These results suggest that reducing ascites production may play an essential role in the treatment of ovarian cancer by inhibiting the progression and reducing the severity of the disease.}, }
@article {pmid38186589, year = {2023}, author = {Pellissier, L and Gaudry, A and Vilette, S and Lecoultre, N and Rutz, A and Allard, PM and Marcourt, L and Ferreira Queiroz, E and Chave, J and Eparvier, V and Stien, D and Gindro, K and Wolfender, JL}, title = {Comparative metabolomic study of fungal foliar endophytes and their long-lived host Astrocaryum sciophilum: a model for exploring the chemodiversity of host-microbe interactions.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1278745}, pmid = {38186589}, issn = {1664-462X}, abstract = {INTRODUCTION: In contrast to the dynamics observed in plant/pathogen interactions, endophytic fungi have the capacity to establish enduring associations within their hosts, leading to the development of a mutually beneficial relationship that relies on specialized chemical interactions. Research indicates that the presence of endophytic fungi has the ability to significantly modify the chemical makeup of the host organism. Our hypothesis proposes the existence of a reciprocal exchange of chemical signals between plants and fungi, facilitated by specialized chemical processes that could potentially manifest within the tissues of the host. This research aimed to precisely quantify the portion of the cumulative fungal endophytic community's metabolome detectable within host leaves, and tentatively evaluate its relevance to the host-endophyte interplay. The understory palm Astrocaryum sciophilum (Miq.) Pulle was used as a interesting host plant because of its notable resilience and prolonged life cycle, in a tropical ecosystem.<br><br>METHOD: Using advanced metabolome characterization, including UHPLC-HRMS/MS and molecular networking, the study explored enriched metabolomes of both host leaves and 15 endophytic fungi. The intention was to capture a metabolomic "snapshot" of both host and endophytic community, to achieve a thorough and detailed analysis.<br><br>RESULTS AND DISCUSSION: This approach yielded an extended MS-based molecular network, integrating diverse metadata for identifying host- and endophyte-derived metabolites. The exploration of such data (>24000 features in positive ionization mode) enabled effective metabolome comparison, yielding insights into cultivable endophyte chemodiversity and occurrence of common metabolites between the holobiont and its fungal communities. Surprisingly, a minor subset of features overlapped between host leaf and fungal samples despite significant plant metabolome enrichment. This indicated that fungal metabolic signatures produced in vitro remain sparingly detectable in the leaf. Several classes of primary metabolites were possibly shared. Specific fungal metabolites and/or compounds of their chemical classes were only occasionally discernible in the leaf, highlighting endophytes partial contribution to the overall holobiont metabolome. To our knowledge, the metabolomic study of a plant host and its microbiome has rarely been performed in such a comprehensive manner. The general analytical strategy proposed in this paper seems well-adapted for any study in the field of microbial- or microbiome-related MS and can be applied to most host-microbe interactions.}, }
@article {pmid38174936, year = {2024}, author = {Wei, Y and Chen, B and Yu, K and Liao, Z and Yu, X and Qin, Z and Bao, Z and Xu, L and Wang, Y}, title = {Evolutionary radiation and microbial community dynamics shape the thermal tolerance of Fungiidae in the southern South China Sea.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0243623}, pmid = {38174936}, issn = {2165-0497}, support = {42030502, 42090041//MOST | National Natural Science Foundation of China (NSFC)/ ; GXLSCRSCS2021103//Self-Topic Project of Guangxi Laboratory on the Study of Coral Reefs in the South China Sea/ ; PM-zx703-202105-176, PM-zx703-202004-143//Central Public-interest Scientific Institution Basal Research Fund/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Coral Reefs ; Acclimatization ; Bacteria ; *Microbiota ; China ; *Dinoflagellida/physiology ; }, abstract = {Fungiidae have shown increased thermal adaptability in coral reef ecosystems under global warming. This study analyzes the evolutionary divergence and microbial communities of Fungiidae in the Sanjiao Reef of the southern South China Sea and explores the impact of coral evolution radiation and microbial dynamics on the heat tolerance of Fungiidae. The results found that Cycloseris was an ancient branch of Fungiidae, dating back approximately 147.8953 Mya, and Fungiidae differentiated into two ancestral clades (clades I and II) before 107.0312 Ma. Fungiidae exhibited specific symbioses with the Cladocopium C27 sub-clade. Notably, the Cladocopium C1 sub-clade has a high relative abundance in clade I, whereas the heat-tolerant Cladocopium C40 and C3u sub-clades subdominante in clade II. Regarding bacterial communities, Cycloseris costulata, the earliest divergent species, had higher bacterial β-diversity, while the latest divergent species, Lithophyllon scabra, displayed lower bacterial α-diversity and higher community stability. Beneficial bacteria dominante Fungiidae's bacterial community (54%). The co-occurrence network revealed that microbial networks in clade II exhibited lower complexity and greater resilience than those in clade I. Our study highlights that host evolutionary radiation and microbial communities shaped Fungiidae's thermal tolerance. The variability in subdominant Symbiodiniaceae populations may contribute to interspecific differences in thermal tolerance along the evolutionary branches of Fungiidae. The presence of abundant beneficial bacteria may further enhance the thermal ability of the Fungiidae. Furthermore, the later divergent species of Fungiidae have stronger heat tolerance, possibly driven by the increased regulation ability of the host on the bacterial community, greater microbial community stability, and interaction network resistance.IMPORTANCECoral reefs are facing significant threats due to global warming. The heat tolerance of coral holobionts depends on both the coral host and its microbiome. However, the association between coral evolutionary radiation and interspecific differences in microbial communities remains unclear. In this study, we investigated the role of evolutionary radiation and microbial community dynamics in shaping the thermal acclimation potential of Fungiidae in the Sanjiao Reef of the southern South China Sea. The study's results suggest that evolutionary radiation enhances the thermal tolerance of Fungiidae. Fungiidae species that have diverged more recently have exhibited a higher presence of heat-tolerant Symbiodiniaceae taxa, more stable bacterial communities, and a robust and resilient microbial interaction network, improving the thermal adaptability of Fungiidae. In summary, this study provides new insights into the thermal adaptation patterns of corals under global warming conditions.}, }
@article {pmid38153910, year = {2024}, author = {Khurana, MP and Scheidwasser-Clow, N and Penn, MJ and Bhatt, S and Duchêne, DA}, title = {The Limits of the Constant-rate Birth-Death Prior for Phylogenetic Tree Topology Inference.}, journal = {Systematic biology}, volume = {73}, number = {1}, pages = {235-246}, pmid = {38153910}, issn = {1076-836X}, support = {MR/R015600/1//MRC Centre for Global Infectious Disease Analysis/ ; /MRC_/Medical Research Council/United Kingdom ; //National Institute for Health Research/ ; NIHR200908//UK Health Security Agency/ ; G-22-63345//Schmidt Polymath Award/ ; H2020-MSCA-IF-2019-883832/ERC_/European Research Council/International ; }, mesh = {*Phylogeny ; *Classification/methods ; Models, Biological ; Models, Genetic ; Bayes Theorem ; Birth Rate ; }, abstract = {Birth-death models are stochastic processes describing speciation and extinction through time and across taxa and are widely used in biology for inference of evolutionary timescales. Previous research has highlighted how the expected trees under the constant-rate birth-death (crBD) model tend to differ from empirical trees, for example, with respect to the amount of phylogenetic imbalance. However, our understanding of how trees differ between the crBD model and the signal in empirical data remains incomplete. In this Point of View, we aim to expose the degree to which the crBD model differs from empirically inferred phylogenies and test the limits of the model in practice. Using a wide range of topology indices to compare crBD expectations against a comprehensive dataset of 1189 empirically estimated trees, we confirm that crBD model trees frequently differ topologically compared with empirical trees. To place this in the context of standard practice in the field, we conducted a meta-analysis for a subset of the empirical studies. When comparing studies that used Bayesian methods and crBD priors with those that used other non-crBD priors and non-Bayesian methods (i.e., maximum likelihood methods), we do not find any significant differences in tree topology inferences. To scrutinize this finding for the case of highly imbalanced trees, we selected the 100 trees with the greatest imbalance from our dataset, simulated sequence data for these tree topologies under various evolutionary rates, and re-inferred the trees under maximum likelihood and using the crBD model in a Bayesian setting. We find that when the substitution rate is low, the crBD prior results in overly balanced trees, but the tendency is negligible when substitution rates are sufficiently high. Overall, our findings demonstrate the general robustness of crBD priors across a broad range of phylogenetic inference scenarios but also highlight that empirically observed phylogenetic imbalance is highly improbable under the crBD model, leading to systematic bias in data sets with limited information content.}, }
@article {pmid38150785, year = {2024}, author = {Bauermeister, A and Furtado, LC and Ferreira, EG and Moreira, EA and Jimenez, PC and Lopes, NP and Araújo, WL and Olchanheski, LR and Monteiro da Cruz Lotufo, T and Costa-Lotufo, LV}, title = {Chemical and microbial diversity of a tropical intertidal ascidian holobiont.}, journal = {Marine environmental research}, volume = {194}, number = {}, pages = {106303}, doi = {10.1016/j.marenvres.2023.106303}, pmid = {38150785}, issn = {1879-0291}, mesh = {Animals ; Phylogeny ; *Urochordata ; RNA, Ribosomal, 16S/genetics ; Tandem Mass Spectrometry ; Bacteria/genetics ; }, abstract = {The tropical ascidian Eudistoma vannamei, endemic to the northeastern coast of Brazil, is considered a prolific source of secondary metabolites and hosts Actinomycetota that produce bioactive compounds. Herein, we used an omics approach to study the ascidian as a holobiont, including the microbial diversity through 16S rRNA gene sequencing and metabolite production using mass spectrometry-based metabolomics. Gene sequencing analysis revealed all samples of E. vannamei shared about 50% of the observed ASVs, and Pseudomonadota (50.7%), Planctomycetota (9.58%), Actinomycetota (10.34%), Bacteroidota (12.05%) were the most abundant bacterial phyla. Analysis of tandem mass spectrometry (MS/MS) data allowed annotation of compounds, including phospholipids, amino acids, and pyrimidine alkaloids, such as staurosporine, a member of a well-known chemical class recognized as a microbial metabolite. Isolated bacteria, mainly belonging to Streptomyces and Micromonospora genera, were cultivated and extracted with ethyl acetate. MS/MS analysis of bacterial extracts allowed annotation of compounds not detected in the ascidian tissue, including marineosin and dihydroergotamine, yielding about 30% overlapped ions between host and isolated bacteria. This study reveals E. vannamei as a rich source of microbial and chemical diversity and, furthermore, highlights the importance of omic tools for a comprehensive investigation of holobiont systems.}, }
@article {pmid38148332, year = {2023}, author = {Boonmak, C and Kettongruang, S and Buranathong, B and Morikawa, M and Duangmal, K}, title = {Duckweed-associated bacteria as plant growth-promotor to enhance growth of Spirodela polyrhiza in wastewater effluent from a poultry farm.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {43}, pmid = {38148332}, issn = {1432-072X}, support = {FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; }, mesh = {Animals ; *Araceae/microbiology ; Farms ; Poultry ; *Wastewater ; }, abstract = {Duckweed has been highlighted as an invaluable resource because of its abilities to remove nitrogen and phosphorus from wastewater coupling with the production of high starch/protein-containing plant biomass. Duckweed recruits microbes and particularly forms a stable "core" bacterial microbiota, which greatly reduces the colonization efficiency of plant growth-promoting bacteria (PGPB). In this study, natural duckweeds were enriched in a sterilized-partially treated wastewater effluent from a poultry farm. After 24 days of cultivation, the duckweed-associated bacteria (DAB) were isolated and evaluated for their plant growth-promoting (PGP) potentials by co-cultivation with axenic Spirodela polyrhiza. Ten species were found in more than one location and could be considered candidates for the stable "core" DAB. Among them, all isolates of Acinetobacter soli, Acidovorax kalamii, Brevundimonas vesicularis, Pseudomonas toyotomiensis, and Shinella curvata increased duckweed growth in Hoagland medium. The highest PGP ability was observed in Sh. curvata W12-8 (with EPG value of 208.72%), followed by Paracoccus marcusii W7-16 (171.31%), Novosphingobium subterraneum W5-13 (156.96%), and Ac. kalamii W7-18 (156.96%). However, the highest growth promotion in the wastewater was observed when co-cultured with W7-16, which was able to increase biomass dry weight and root length of duckweed by 3.17 and 2.26 folds, respectively.}, }
@article {pmid38144201, year = {2023}, author = {Clerissi, C and Huot, C and Portet, A and Gourbal, B and Toulza, E}, title = {Covariation between microeukaryotes and bacteria associated with Planorbidae snails.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16639}, pmid = {38144201}, issn = {2167-8359}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Eukaryota/genetics ; *Microbiota/genetics ; Snails/genetics ; }, abstract = {BACKGROUND: Microbial communities associated with macroorganisms might affect host physiology and homeostasis. Bacteria are well studied in this context, but the diversity of microeukaryotes, as well as covariations with bacterial communities, remains almost unknown.<br><br>METHODS: To study microeukaryotic communities associated with Planorbidae snails, we developed a blocking primer to reduce amplification of host DNA during metabarcoding analyses. Analyses of alpha and beta diversities were computed to describe microeukaryotes and bacteria using metabarcoding of 18S and 16S rRNA genes, respectively.<br><br>RESULTS: Only three phyla (Amoebozoa, Opisthokonta and Alveolata) were dominant for microeukaryotes. Bacteria were more diverse with five dominant phyla (Proteobacteria, Bacteroidetes, Tenericutes, Planctomycetes and Actinobacteria). The composition of microeukaryotes and bacteria were correlated for the Biomphalaria glabrata species, but not for Planorbarius metidjensis. Network analysis highlighted clusters of covarying taxa. Among them, several links might reflect top-down control of bacterial populations by microeukaryotes, but also possible competition between microeukaryotes having opposite distributions (Lobosa and Ichthyosporea). The role of these taxa remains unknown, but we believe that the blocking primer developed herein offers new possibilities to study the hidden diversity of microeukaryotes within snail microbiota, and to shed light on their underestimated interactions with bacteria and hosts.}, }
@article {pmid38140133, year = {2023}, author = {Machado, ACHR and Marinheiro, LJ and Benson, HAE and Grice, JE and Martins, TDS and Lan, A and Lopes, PS and Andreo-Filho, N and Leite-Silva, VR}, title = {A Novel Handrub Tablet Loaded with Pre- and Post-Biotic Solid Lipid Nanoparticles Combining Virucidal Activity and Maintenance of the Skin Barrier and Microbiome.}, journal = {Pharmaceutics}, volume = {15}, number = {12}, pages = {}, pmid = {38140133}, issn = {1999-4923}, support = {UNIFESP Process N&#xba; 23089.125507 / 2020-08, Project Code PFSP-2101.0005//Embrapii - Empresa Brasileira de Pesquisa e Inova&#xe7;&#xe3;o Industrial/ ; }, abstract = {OBJECTIVE: This study aimed to develop a holobiont tablet with rapid dispersibility to provide regulation of the microbiota, virucidal activity, and skin barrier protection.<br><br>METHODS: A 2[3] factorial experiment was planned to define the best formulation for the development of the base tablet, using average weight, hardness, dimensions, swelling rate, and disintegration time as parameters to be analyzed. To produce holobiont tablets, the chosen base formulation was fabricated by direct compression of prebiotics, postbiotics, and excipients. The tablets also incorporated solid lipid nanoparticles containing postbiotics that were obtained by high-pressure homogenization and freeze-drying. The in vitro virucidal activity against alpha-coronavirus particles (CCoV-VR809) was determined in VERO cell culture. In vitro analysis, using monolayer cells and human equivalent skin, was performed by rRTq-PCR to determine the expression of interleukins 1, 6, 8, and 17, aquaporin-3, involucrin, filaggrin, FoxO3, and SIRT-1. Antioxidant activity and collagen-1 synthesis were also performed in fibroblast cells. Metagenomic analysis of the skin microbiome was determined in vivo before and after application of the holobiont tablet, during one week of continuous use, and compared to the use of alcohol gel. Samples were analyzed by sequencing the V3-V4 region of the 16S rRNA gene.<br><br>RESULTS: A handrub tablet with rapid dispersibility was developed for topical use and rinse off. After being defined as safe, the virucidal activity was found to be equal to or greater than that of 70% alcohol, with a reduction in interleukins and maintenance or improvement of skin barrier gene markers, in addition to the reestablishment of the skin microbiota after use.<br><br>CONCLUSIONS: The holobiont tablets were able to improve the genetic markers related to the skin barrier and also its microbiota, thereby being more favorable for use as a hand sanitizer than 70% alcohol.}, }
@article {pmid38135048, year = {2024}, author = {Martinez Boggio, G and Monteiro, HF and Lima, FS and Figueiredo, CC and Bisinotto, RS and Santos, JEP and Mion, B and Schenkel, FS and Ribeiro, ES and Weigel, KA and Peñagaricano, F}, title = {Host and rumen microbiome contributions to feed efficiency traits in Holstein cows.}, journal = {Journal of dairy science}, volume = {107}, number = {5}, pages = {3090-3103}, doi = {10.3168/jds.2023-23869}, pmid = {38135048}, issn = {1525-3198}, mesh = {Female ; Cattle ; Animals ; *Lactation ; Rumen ; RNA, Ribosomal, 16S ; Milk ; Phenotype ; *Microbiota ; Animal Feed ; Diet/veterinary ; }, abstract = {It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h[2]) and microbiability (m[2]), respectively. However, if the genome and microbiome are included in the model, then the h[2] reflects only the contribution of the direct genetic effects quantified as direct heritability (hd[2]), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho[2]). The objectives of this study were to estimate h[2], hd[2],m[2], and ho[2] for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd[2] estimates were always 10% to 15% lower than h[2] estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m[2] estimates were moderate for all traits, and up to 26% for milk energy. The ho[2] was greater than the sum of hd[2] and m[2], suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.}, }
@article {pmid38132295, year = {2023}, author = {Barker, T and Bulling, M and Thomas, V and Sweet, M}, title = {The Effect of Pollen on Coral Health.}, journal = {Biology}, volume = {12}, number = {12}, pages = {}, pmid = {38132295}, issn = {2079-7737}, abstract = {Corals are facing a range of threats, including rises in sea surface temperature and ocean acidification. Some now argue that keeping corals ex situ (in aquaria), may be not only important but necessary to prevent local extinction, for example in the Florida Reef Tract. Such collections or are already becoming common place, especially in the Caribbean, and may act as an ark, preserving and growing rare or endangered species in years to come. However, corals housed in aquaria face their own unique set of threats. For example, hobbyists (who have housed corals for decades) have noticed seasonal mortality is commonplace, incidentally following months of peak pollen production. So, could corals suffer from hay fever? If so, what does the future hold? In short, the answer to the first question is simple, and it is no, corals cannot suffer from hay fever, primarily because corals lack an adaptive immune system, which is necessary for the diagnosis of such an allergy. However, the threat from pollen could still be real. In this review, we explore how such seasonal mortality could play out. We explore increases in reactive oxygen species, the role of additional nutrients and how the microbiome of the pollen may introduce disease or cause dysbiosis in the holobiont.}, }
@article {pmid38129884, year = {2023}, author = {Troitsky, TS and Laine, VN and Lilley, TM}, title = {When the host's away, the pathogen will play: the protective role of the skin microbiome during hibernation.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {66}, pmid = {38129884}, issn = {2524-4671}, support = {202300065//Maj ja Tor Nesslingin S&#xe4;&#xe4;ti&#xf6;/ ; 329250//Academy of Finland/ ; 329250//Academy of Finland/ ; }, abstract = {The skin of animals is enveloped by a symbiotic microscopic ecosystem known as the microbiome. The host and microbiome exhibit a mutualistic relationship, collectively forming a single evolutionary unit sometimes referred to as a holobiont. Although the holobiome theory highlights the importance of the microbiome, little is known about how the skin microbiome contributes to protecting the host. Existing studies focus on humans or captive animals, but research in wild animals is in its infancy. Specifically, the protective role of the skin microbiome in hibernating animals remains almost entirely overlooked. This is surprising, considering the massive population declines in hibernating North American bats caused by the fungal pathogen Pseudogymnoascus destructans, which causes white-nose syndrome. Hibernation offers a unique setting in which to study the function of the microbiome because, during torpor, the host's immune system becomes suppressed, making it susceptible to infection. We conducted a systematic review of peer-reviewed literature on the protective role of the skin microbiome in non-human animals. We selected 230 publications that mentioned pathogen inhibition by microbes residing on the skin of the host animal. We found that the majority of studies were conducted in North America and focused on the bacterial microbiome of amphibians infected by the chytrid fungus. Despite mentioning pathogen inhibition by the skin microbiome, only 30.4% of studies experimentally tested the actual antimicrobial activity of symbionts. Additionally, only 7.8% of all publications studied defensive cutaneous symbionts during hibernation. With this review, we want to highlight the knowledge gap surrounding skin microbiome research in hibernating animals. For instance, research looking to mitigate the effects of white-nose syndrome in bats should focus on the antifungal microbiome of Palearctic bats, as they survive exposure to the Pseudogymnoascus destructans -pathogen during hibernation. We also recommend future studies prioritize lesser-known microbial symbionts, such as fungi, and investigate the effects of a combination of anti-pathogen microbes, as both areas of research show promise as probiotic treatments. By incorporating the protective skin microbiome into disease mitigation strategies, conservation efforts can be made more effective.}, }
@article {pmid38123486, year = {2024}, author = {Lee, JH}, title = {Host-Microbe Interactions Regulate Intestinal Stem Cells and Tissue Turnover in Drosophila.}, journal = {International journal of stem cells}, volume = {17}, number = {1}, pages = {51-58}, pmid = {38123486}, issn = {2005-3606}, abstract = {With the activity of intestinal stem cells and continuous turnover, the gut epithelium is one of the most dynamic tissues in animals. Due to its simple yet conserved tissue structure and enteric cell composition as well as advanced genetic and histologic techniques, Drosophila serves as a valuable model system for investigating the regulation of intestinal stem cells. The Drosophila gut epithelium is in constant contact with indigenous microbiota and encounters externally introduced "non-self" substances, including foodborne pathogens. Therefore, in addition to its role in digestion and nutrient absorption, another essential function of the gut epithelium is to control the expansion of microbes while maintaining its structural integrity, necessitating a tissue turnover process involving intestinal stem cell activity. As a result, the microbiome and pathogens serve as important factors in regulating intestinal tissue turnover. In this manuscript, I discuss crucial discoveries revealing the interaction between gut microbes and the host's innate immune system, closely associated with the regulation of intestinal stem cell proliferation and differentiation, ultimately contributing to epithelial homeostasis.}, }
@article {pmid38096292, year = {2023}, author = {Lin, AT and Hammond-Kaarremaa, L and Liu, HL and Stantis, C and McKechnie, I and Pavel, M and Pavel, SSM and Wyss, SS&#xc1; and Sparrow, DQ and Carr, K and Aninta, SG and Perri, A and Hartt, J and Bergström, A and Carmagnini, A and Charlton, S and Dalén, L and Feuerborn, TR and France, CAM and Gopalakrishnan, S and Grimes, V and Harris, A and Kavich, G and Sacks, BN and Sinding, MS and Skoglund, P and Stanton, DWG and Ostrander, EA and Larson, G and Armstrong, CG and Frantz, LAF and Hawkins, MTR and Kistler, L}, title = {The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge.}, journal = {Science (New York, N.Y.)}, volume = {382}, number = {6676}, pages = {1303-1308}, pmid = {38096292}, issn = {1095-9203}, support = {CC2109/WT_/Wellcome Trust/United Kingdom ; CC2109/CRUK_/Cancer Research UK/United Kingdom ; 852558/ERC_/European Research Council/International ; 217223/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; CC2109/MRC_/Medical Research Council/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; }, mesh = {Animals ; *Dogs/anatomy &amp; histology/classification/genetics ; Genomics ; Northwestern United States ; Breeding ; *Wool ; *Selection, Genetic ; }, abstract = {Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.}, }
@article {pmid38088556, year = {2024}, author = {Toullec, G and Lyndby, NH and Banc-Prandi, G and Pogoreutz, C and Martin Olmos, C and Meibom, A and Rädecker, N}, title = {Symbiotic nutrient exchange enhances the long-term survival of cassiosomes, the autonomous stinging-cell structures of Cassiopea.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0032223}, pmid = {38088556}, issn = {2379-5042}, support = {200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; 212614//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (SNF)/ ; ANR-22-CPJ2-0113-01//French National Research Agency (ANR)/ ; }, mesh = {*Symbiosis ; Nitrogen/metabolism ; *Dinoflagellida ; Carbon/metabolism ; Photosynthesis ; }, abstract = {Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to "contactless" stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secondary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro. Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.IMPORTANCEThe upside-down jellyfish Cassiopea releases autonomous tissue structures, which are a major cause of contactless stinging incidents in (sub-) tropical coastal waters. These so-called cassiosomes frequently harbor algal symbionts, yet their role in cassiosome functioning and survival is unknown. Our results show that cassiosomes are metabolically active and supported by algal symbionts. Algal photosynthesis enhances the cassiosomes long-term survival in the light. This functional understanding of cassiosomes thereby contributes to explaining the prevalence of contactless stinging incidents and the ecological success of some Cassiopea species. Finally, we show that cassiosomes are miniaturized symbiotic holobionts that can be used to study host-microbe interactions in a simplified system.}, }
@article {pmid38087002, year = {2023}, author = {Montaño-Salazar, S and Quintanilla, E and Sánchez, JA}, title = {Microbial shifts associated to ENSO-derived thermal anomalies reveal coral acclimation at holobiont level.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22049}, pmid = {38087002}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/microbiology ; El Nino-Southern Oscillation ; Biodiversity ; Acclimatization ; Cold Temperature ; Bacteria ; Coral Reefs ; }, abstract = {The coral microbiome conforms a proxy to study effects of changing environmental conditions. However, scarce information exists regarding microbiome dynamics and host acclimation in response to environmental changes associated to global-scale disturbances. We assessed El Niño Southern Oscillation (ENSO)-derived thermal anomalies shifts in the bacterial microbiome of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) from the remote island of Malpelo in the Tropical Eastern Pacific. Malpelo is a hot spot of biodiversity and lacks direct coastal anthropogenic impacts. We evaluated the community composition and predicted functional profiles of the microbiome during 2015, 2017 and 2018, including different phases of ENSO cycle. The bacterial community diversity and composition between the warming and cooling phase were similar, but differed from the neutral phase. Relative abundances of different microbiome core members such as Endozoicomonas and Mycoplasma mainly drove these differences. An acclimated coral holobiont is suggested not just to warm but also to cold stress by embracing similar microbiome shifts and functional redundancy that allow maintaining coral's viability under thermal stress. Responses of the microbiome of unperturbed sea fans such as P. cairnsi in Malpelo could be acting as an extended phenotype facilitating the acclimation at the holobiont level.}, }
@article {pmid38085949, year = {2023}, author = {Penn, MJ and Scheidwasser, N and Penn, J and Donnelly, CA and Duchêne, DA and Bhatt, S}, title = {Leaping through Tree Space: Continuous Phylogenetic Inference for Rooted and Unrooted Trees.}, journal = {Genome biology and evolution}, volume = {15}, number = {12}, pages = {}, pmid = {38085949}, issn = {1759-6653}, support = {MR/X020258/1/MRC_/Medical Research Council/United Kingdom ; H2020-MSCA-IF-2019-883832/ERC_/European Research Council/International ; }, mesh = {Phylogeny ; *Models, Genetic ; Computer Simulation ; *Algorithms ; }, abstract = {Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains challenging. To address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. This continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. Our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. The approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. Indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. Optimization is possible via automatic differentiation and our method presents an effective way forward for exploring the most difficult, data-deficient phylogenetic questions.}, }
@article {pmid38081809, year = {2023}, author = {Reeve, AH and Kennedy, JD and Pujolar, JM and Petersen, B and Blom, MPK and Alström, P and Haryoko, T and Ericson, PGP and Irestedt, M and Nylander, JAA and Jønsson, KA}, title = {The formation of the Indo-Pacific montane avifauna.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8215}, pmid = {38081809}, issn = {2041-1723}, mesh = {Animals ; Phylogeny ; *Biodiversity ; Climate ; Genetics, Population ; *Passeriformes ; }, abstract = {The processes generating the earth's montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species' ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region's montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.}, }
@article {pmid38077513, year = {2023}, author = {Aguirre, EG and Fine, MJ and Kenkel, CD}, title = {Abundance of Oligoflexales bacteria is associated with algal symbiont density, independent of thermal stress in Aiptasia anemones.}, journal = {Ecology and evolution}, volume = {13}, number = {12}, pages = {e10805}, pmid = {38077513}, issn = {2045-7758}, abstract = {Many multicellular organisms, such as humans, plants, and invertebrates, depend on symbioses with microbes for metabolic cooperation and exchange. Reef-building corals, an ecologically important order of invertebrates, are particularly vulnerable to environmental stress in part because of their nutritive symbiosis with dinoflagellate algae, and yet also benefit from these and other microbial associations. While coral microbiomes remain difficult to study because of their complexity, the anemone Aiptasia is emerging as a simplified model. Research has demonstrated co-occurrences between microbiome composition and the abundance and type of algal symbionts in cnidarians. However, whether these patterns are the result of general stress-induced shifts or depletions of algal-associated bacteria remains unclear. Our study aimed to distinguish the effect of changes in symbiont density and thermal stress on the microbiome of symbiotic Aiptasia strain CC7 by comparing them with aposymbiotic anemones, depleted of their native symbiont, Symbiodinium linucheae. Our analysis indicated that overall thermal stress had the greatest impact on disrupting the microbiome. We found that three bacterial classes made up most of the relative abundance (60%-85%) in all samples, but the rare microbiome fluctuated between symbiotic states and following thermal stress. We also observed that S. linucheae density correlated with abundance of Oligoflexales, suggesting these bacteria may be primary symbionts of the dinoflagellate algae. The findings of this study help expand knowledge on prospective multipartite symbioses in the cnidarian holobiont and how they respond to environmental disturbance.}, }
@article {pmid38072824, year = {2024}, author = {Valadez-Cano, C and Olivares-Hernández, R and Espino-Vázquez, AN and Partida-Martínez, LP}, title = {Genome-Scale Model of Rhizopus microsporus: Metabolic integration of a fungal holobiont with its bacterial and viral endosymbionts.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16551}, doi = {10.1111/1462-2920.16551}, pmid = {38072824}, issn = {1462-2920}, support = {FOINS-2015-01-006//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; }, mesh = {*Macrolides/metabolism ; *Rhizopus/genetics/metabolism ; Bacteria/genetics/metabolism ; Nucleotides/metabolism ; Symbiosis/genetics ; }, abstract = {Rhizopus microsporus often lives in association with bacterial and viral symbionts that alter its biology. This fungal model represents an example of the complex interactions established among diverse organisms in functional holobionts. We constructed a Genome-Scale Model (GSM) of the fungal-bacterial-viral holobiont (iHol). We employed a constraint-based method to calculate the metabolic fluxes to decipher the metabolic interactions of the symbionts with their host. Our computational analyses of iHol simulate the holobiont's growth and the production of the toxin rhizoxin. Analyses of the calculated fluxes between R. microsporus in symbiotic (iHol) versus asymbiotic conditions suggest that changes in the lipid and nucleotide metabolism of the host are necessary for the functionality of the holobiont. Glycerol plays a pivotal role in the fungal-bacterial metabolic interaction, as its production does not compromise fungal growth, and Mycetohabitans bacteria can efficiently consume it. Narnavirus RmNV-20S and RmNV-23S affected the nucleotide metabolism without impacting the fungal-bacterial symbiosis. Our analyses highlighted the metabolic stability of Mycetohabitans throughout its co-evolution with the fungal host. We also predicted changes in reactions of the bacterial metabolism required for the active production of rhizoxin. This iHol is the first GSM of a fungal holobiont.}, }
@article {pmid38072822, year = {2024}, author = {Bonacolta, AM and Miravall, J and Gómez-Gras, D and Ledoux, JB and López-Sendino, P and Garrabou, J and Massana, R and Del Campo, J}, title = {Differential apicomplexan presence predicts thermal stress mortality in the Mediterranean coral Paramuricea clavata.}, journal = {Environmental microbiology}, volume = {26}, number = {1}, pages = {e16548}, doi = {10.1111/1462-2920.16548}, pmid = {38072822}, issn = {1462-2920}, support = {2021SGR00420//Centres de Recerca de Catalunya, PID2020- 118836GA-I00 financed by MCIN/AEI/10.13039/501100011033/ ; Futuremares SEP-210597628//European Union/ ; 2021.00855//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDP/04423/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 1MED15_3.2_M2_337//Interreg-Med Programme MPA-Engage/ ; PID2020-118836GA-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; //University of Miami, Rosenstiel School of Marine, Atmospheric and EarthSciences/ ; //Start-up Funds/ ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota/physiology ; Heat-Shock Response ; Global Warming ; Symbiosis/physiology ; }, abstract = {Paramuricea clavata is an ecosystem architect of the Mediterranean temperate reefs that is currently threatened by episodic mass mortality events related to global warming. The microbiome may play an active role in the thermal stress susceptibility of corals, potentially holding the answer as to why corals show differential sensitivity to heat stress. To investigate this, the prokaryotic and eukaryotic microbiome of P. clavata collected from around the Mediterranean was characterised before experimental heat stress to determine if its microbial composition influences the thermal response of the holobiont. We found that members of P. clavata's microeukaryotic community were significantly correlated with thermal stress sensitivity. Syndiniales from the Dino-Group I Clade 1 were significantly enriched in thermally resistant corals, while the apicomplexan corallicolids were significantly enriched in thermally susceptible corals. We hypothesise that P. clavata mortality following heat stress may be caused by a shift from apparent commensalism to parasitism in the corallicolid-coral host relationship driven by the added stress. Our results show the potential importance of corallicolids and the rest of the microeukaryotic community of corals to understanding thermal stress response in corals and provide a useful tool to guide conservation efforts and future research into coral-associated microeukaryotes.}, }
@article {pmid38062479, year = {2023}, author = {Dungan, AM and Geissler, L and Williams, AS and Gotze, CR and Flynn, EC and Blackall, LL and van Oppen, MJH}, title = {DNA from non-viable bacteria biases diversity estimates in the corals Acropora loripes and Pocillopora acuta.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {86}, pmid = {38062479}, issn = {2524-6372}, support = {2022ECR096//University of Melbourne/ ; DP210100630//Australian Research Council/ ; DP210100630//Australian Research Council/ ; }, abstract = {BACKGROUND: Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.<br><br>RESULTS: By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A.&#xa0;loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs,&#x2009;>&#x2009;30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A.&#xa0;loripes and P.&#xa0;acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.<br><br>CONCLUSIONS: Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.}, }
@article {pmid38054002, year = {2023}, author = {Sedney, CJ and Harvill, ET}, title = {Making friends: active selection of symbionts and rejection of pathogens by the neonatal immune system.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1287518}, pmid = {38054002}, issn = {1664-3224}, support = {P01 AI056293/AI/NIAID NIH HHS/United States ; R21 AI171346/AI/NIAID NIH HHS/United States ; }, mesh = {Infant, Newborn ; Humans ; *Friends ; Immune System ; *Microbiota ; Symbiosis ; Anti-Inflammatory Agents ; }, abstract = {The neonatal immune system is generally viewed as deficient compared to adults, often attributed to its incomplete development. This view is reinforced by the extraordinary sensitivity and susceptibility of neonates to certain pathogens. Examination of the basis for this susceptibility has characterized neonatal immunity as skewed strongly toward anti-inflammatory responses, which are interpreted as the lack of full development of the strong inflammatory responses observed in adults. Here we examine the alternative explanation that neonatal immune responses are generally complete in healthy newborns but evolved and adapted to very different functions than adult immunity. Adult immunity is primarily aimed at controlling pathogens that invade the holobiont, with substantial competition and protection conferred by resident microbiota. Rather than simply repelling new invaders, the immediate and critical challenge of the neonatal immune system during the sudden transition from near sterility to microbe-rich world is the assimilation of a complex microbiota to generate a stable and healthy holobiont. This alternative view of the role of the neonatal immune system both explains its strong anti-inflammatory bias and provides a different perspective on its other unique aspects. Here we discuss recent work exploring the initial contact of newborns with microbes and their interactions with neonatal immune responses, contrasting these alternative perspectives. Understanding how the need to rapidly acquire a highly complex and rich microbiota of commensals affects interactions between the neonatal immune system and both commensals and pathogens will allow more targeted and effective collaboration with this system to quickly achieve a more disease-resistant holobiont.}, }
@article {pmid38053218, year = {2023}, author = {Prioux, C and Tignat-Perrier, R and Gervais, O and Estaque, T and Schull, Q and Reynaud, S and Béraud, E and Mérigot, B and Beauvieux, A and Marcus, MI and Richaume, J and Bianchimani, O and Cheminée, A and Allemand, D and Ferrier-Pagès, C}, title = {Unveiling microbiome changes in Mediterranean octocorals during the 2022 marine heatwaves: quantifying key bacterial symbionts and potential pathogens.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {271}, pmid = {38053218}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Anthozoa/microbiology ; *Microbiota ; Temperature ; Forests ; Coral Reefs ; }, abstract = {BACKGROUND: Climate change has accelerated the occurrence and severity of heatwaves in the Mediterranean Sea and poses a significant threat to the octocoral species that form the foundation of marine animal forests (MAFs). As coral health intricately relies on the symbiotic relationships established between corals and microbial communities, our goal was to gain a deeper understanding of the role of bacteria in the observed tissue loss of key octocoral species following the unprecedented heatwaves in 2022.<br><br>RESULTS: Using amplicon sequencing and taxon-specific qPCR analyses, we unexpectedly found that the absolute abundance of the major bacterial symbionts, Spirochaetaceae (C. rubrum) and Endozoicomonas (P. clavata), remained, in most cases, unchanged between colonies with 0% and 90% tissue loss. These results suggest that the impairment of coral health was not due to the loss of the main bacterial symbionts. However, we observed a significant increase in the total abundance of bacterial opportunists, including putative pathogens such as Vibrio, which was not evident when only their relative abundance was considered. In addition, there was no clear relation between bacterial symbiont loss and the intensity of thermal stress, suggesting that factors other than temperature may have influenced the differential response of octocoral microbiomes at different sampling sites.<br><br>CONCLUSIONS: Our results indicate that tissue loss in octocorals is not directly caused by the decline of the main bacterial symbionts but by the proliferation of opportunistic and pathogenic bacteria. Our findings thus underscore the significance of considering both relative and absolute quantification approaches when evaluating the impact of stressors on coral microbiome as the relative quantification does not accurately depict the actual changes in the microbiome. Consequently, this research enhances our comprehension of the intricate interplay between host organisms, their microbiomes, and environmental stressors, while offering valuable insights into the ecological implications of heatwaves on marine animal forests. Video Abstract.}, }
@article {pmid38047504, year = {2024}, author = {Pepke, ML}, title = {Telomere length is not a useful tool for chronological age estimation in animals.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {46}, number = {2}, pages = {e2300187}, doi = {10.1002/bies.202300187}, pmid = {38047504}, issn = {1521-1878}, mesh = {Animals ; *Telomere Shortening/genetics ; *Vertebrates/genetics ; Cell Division ; Oxidative Stress ; Telomere/genetics ; }, abstract = {Telomeres are short repetitive DNA sequences capping the ends of chromosomes. Telomere shortening occurs during cell division and may be accelerated by oxidative damage or ameliorated by telomere maintenance mechanisms. Consequently, telomere length changes with age, which was recently confirmed in a large meta-analysis across vertebrates. However, based on the correlation between telomere length and age, it was concluded that telomere length can be used as a tool for chronological age estimation in animals. Correlation should not be confused with predictability, and the current data and studies suggest that telomeres cannot be used to reliably predict individual chronological age. There are biological reasons for why there is large individual variation in telomere dynamics, which is mainly due to high susceptibility to a wide range of environmental, but also genetic factors, rendering telomeres unfeasible as a tool for age estimation. The use of telomeres for chronological age estimation is largely a misguided effort, but its occasional reappearance in the literature raises concerns that it will mislead resources in wildlife conservation.}, }
@article {pmid38045720, year = {2023}, author = {Ghoul, M and Andersen, SB and Marvig, RL and Johansen, HK and Jelsbak, L and Molin, S and Perron, G and Griffin, AS}, title = {Long-term evolution of antibiotic tolerance in Pseudomonas aeruginosa lung infections.}, journal = {Evolution letters}, volume = {7}, number = {6}, pages = {389-400}, pmid = {38045720}, issn = {2056-3744}, abstract = {Pathogenic bacteria respond to antibiotic pressure with the evolution of resistance but survival can also depend on their ability to tolerate antibiotic treatment, known as tolerance. While a variety of resistance mechanisms and underlying genetics are well characterized in vitro and in vivo, an understanding of the evolution of tolerance, and how it interacts with resistance in situ is lacking. We assayed for tolerance and resistance in isolates of Pseudomonas aeruginosa from chronic cystic fibrosis lung infections spanning up to 40 years of evolution, with 3 clinically relevant antibiotics: meropenem, ciprofloxacin, and tobramycin. We present evidence that tolerance is under positive selection in the lung and that it can act as an evolutionary stepping stone to resistance. However, by examining evolutionary patterns across multiple patients in different clone types, a key result is that the potential for an association between the evolution of resistance and tolerance is not inevitable, and difficult to predict.}, }
@article {pmid38044555, year = {2024}, author = {Wang, L and George, TS and Feng, G}, title = {Concepts and consequences of the hyphosphere core microbiome for arbuscular mycorrhizal fungal fitness and function.}, journal = {The New phytologist}, volume = {242}, number = {4}, pages = {1529-1533}, doi = {10.1111/nph.19396}, pmid = {38044555}, issn = {1469-8137}, support = {32272807//National Natural Science Foundation of China/ ; }, mesh = {*Mycorrhizae/physiology/genetics ; Microbiota ; Plants/microbiology ; }, abstract = {Arbuscular mycorrhizal (AM) fungi-associated hyphosphere microbiomes can be considered as the second genome of the mycorrhizal phosphorus uptake pathway. Their composition can be thought of as a stably recurring component of a holobiont, defined by the hyphosphere core microbiome, which is thought to benefit AM fungal fitness. Here, we review evidence indicating the existence of the hyphosphere core microbiome, highlight its functions linked to those functions lacking in AM fungi, and further explore the mechanisms by which different core members ensure their stable coexistence. We conclude that deciphering and utilizing the hyphosphere core microbiome provides an entry point for understanding the complex interactions among plants, AM fungi, and bacteria.}, }
@article {pmid38033807, year = {2023}, author = {Mauduit, M and Derrien, M and Grenier, M and Greff, S and Molinari, S and Chevaldonné, P and Simmler, C and Pérez, T}, title = {In Situ Capture and Real-Time Enrichment of Marine Chemical Diversity.}, journal = {ACS central science}, volume = {9}, number = {11}, pages = {2084-2095}, pmid = {38033807}, issn = {2374-7943}, abstract = {Analyzing the chemical composition of seawater to understand its influence on ecosystem functions is a long-lasting challenge due to the inherent complexity and dynamic nature of marine environments. Describing the intricate chemistry of seawater requires optimal in situ sampling. Here is presented a novel underwater hand-held solid-phase extraction device, I-SMEL (In Situ Marine moleculELogger), which aims to concentrate diluted molecules from large volumes of seawater in a delimited zone targeting keystone benthic species. Marine benthic holobionts, such as sponges, can impact the chemical composition of their surroundings possibly through the production and release of their specialized metabolites, hence termed exometabolites (EMs). I-SMEL was deployed in a sponge-dominated Mediterranean ecosystem at a 15 m depth. Untargeted MS-based metabolomics was performed on enriched EM extracts and showed (1) the chemical diversity of enriched seawater metabolites and (2) reproducible recovery and enrichment of specialized sponge EMs such as aerothionin, demethylfurospongin-4, and longamide B methyl ester. These EMs constitute the chemical identity of each targeted species: Aplysina cavernicola, Spongia officinalis, and Agelas oroides, respectively. I-SMEL concentrated sponge EMs from 10 L of water in a 10 min sampling time. The present proof of concept with I-SMEL opens new research perspectives in marine chemical ecology and sets the stage for further sustainable efforts in natural product chemistry.}, }
@article {pmid38030702, year = {2023}, author = {Romanenko, SA and Kliver, SF and Serdyukova, NA and Perelman, PL and Trifonov, VA and Seluanov, A and Gorbunova, V and Azpurua, J and Pereira, JC and Ferguson-Smith, MA and Graphodatsky, AS}, title = {Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21055}, pmid = {38030702}, issn = {2045-2322}, support = {19-14-00034-&#x41f;//Russian Science Foundation/ ; R37 AG046320/AG/NIA NIH HHS/United States ; P01 AG047200/AG/NIA NIH HHS/United States ; R01 AG027237/AG/NIA NIH HHS/United States ; P01 AG051449/AG/NIA NIH HHS/United States ; R01 AG046320/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Guinea Pigs ; Animals ; Synteny ; In Situ Hybridization, Fluorescence ; *Genome ; Karyotype ; *Mole Rats/genetics ; }, abstract = {Descriptions of karyotypes of many animal species are currently available. In addition, there has been a significant increase in the number of sequenced genomes and an ever-improving quality of genome assembly. To close the gap between genomic and cytogenetic data we applied fluorescent in situ hybridization (FISH) and Hi-C technology to make the first full chromosome-level genome comparison of the guinea pig (Cavia porcellus), naked mole-rat (Heterocephalus glaber), and human. Comparative chromosome maps obtained by FISH with chromosome-specific probes link genomic scaffolds to individual chromosomes and orient them relative to centromeres and heterochromatic blocks. Hi-C assembly made it possible to close all gaps on the comparative maps and to reveal additional rearrangements that distinguish the karyotypes of the three species. As a result, we integrated the bioinformatic and cytogenetic data and adjusted the previous comparative maps and genome assemblies of the guinea pig, naked mole-rat, and human. Syntenic associations in the two hystricomorphs indicate features of their putative ancestral karyotype. We postulate that the two approaches applied in this study complement one another and provide complete information about the organization of these genomes at the chromosome level.}, }
@article {pmid38023867, year = {2023}, author = {Cardoni, M and Mercado-Blanco, J}, title = {Confronting stresses affecting olive cultivation from the holobiont perspective.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1261754}, pmid = {38023867}, issn = {1664-462X}, abstract = {The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.}, }
@article {pmid38014935, year = {2024}, author = {Shimpi, GG and De la Vega, P and Bentlage, B}, title = {Complete genome sequence of Brachybacterium sp. GU-2 (Actinomycetota), isolated from the massive coral Porites lobata.}, journal = {Microbiology resource announcements}, volume = {13}, number = {1}, pages = {e0085523}, pmid = {38014935}, issn = {2576-098X}, support = {OIA-1946352//National Science Foundation (NSF)/ ; }, abstract = {Brachybacterium sp. GU-2 was isolated from the hard coral Porites lobata found in Apra Harbor, Guam, Micronesia. This genome sequence will be beneficial to understand the role of actinomycetes in coral holobionts. The Brachybacterium genome contains several gene clusters for bioactive compounds, including antibiotics.}, }
@article {pmid38000749, year = {2024}, author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S}, title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.}, journal = {The Science of the total environment}, volume = {911}, number = {}, pages = {168794}, doi = {10.1016/j.scitotenv.2023.168794}, pmid = {38000749}, issn = {1879-1026}, mesh = {*Rhizosphere ; Edible Grain/chemistry ; Nitrates ; Fertilizers/analysis ; Nitrogen Cycle ; *Microbiota/physiology ; Soil/chemistry ; Crops, Agricultural ; Nitrogen/analysis ; Soil Microbiology ; }, abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.}, }
@article {pmid37996910, year = {2023}, author = {Li, J and Zou, Y and Li, Q and Zhang, J and Bourne, DG and Lyu, Y and Liu, C and Zhang, S}, title = {A coral-associated actinobacterium mitigates coral bleaching under heat stress.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {83}, pmid = {37996910}, issn = {2524-6372}, support = {42122045//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; GJTD-2020-12//K. C. Wong Education Foundation/ ; }, abstract = {BACKGROUND: The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress.<br><br>RESULTS: Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain.<br><br>CONCLUSIONS: Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.}, }
@article {pmid37995319, year = {2023}, author = {Femerling, G and van Oosterhout, C and Feng, S and Bristol, RM and Zhang, G and Groombridge, J and P Gilbert, MT and Morales, HE}, title = {Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {37995319}, issn = {1537-1719}, mesh = {Humans ; Animals ; *Genetic Variation ; *Endangered Species ; Genetic Load ; Inbreeding ; Birds/genetics ; }, abstract = {High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.}, }
@article {pmid37993882, year = {2023}, author = {Rice, ES and Alberdi, A and Alfieri, J and Athrey, G and Balacco, JR and Bardou, P and Blackmon, H and Charles, M and Cheng, HH and Fedrigo, O and Fiddaman, SR and Formenti, G and Frantz, LAF and Gilbert, MTP and Hearn, CJ and Jarvis, ED and Klopp, C and Marcos, S and Mason, AS and Velez-Irizarry, D and Xu, L and Warren, WC}, title = {A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {267}, pmid = {37993882}, issn = {1741-7007}, support = {2020-67015-31574//National Institute of Food and Agriculture/ ; 2022-67015-36218//National Institute of Food and Agriculture/ ; 817729//HORIZON EUROPE Research Infrastructures/ ; }, mesh = {Animals ; *Chickens/genetics ; Genotype ; *Genome ; Sequence Analysis, DNA ; Genomics ; }, abstract = {BACKGROUND: The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.<br><br>METHODS: We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.<br><br>RESULTS: We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.<br><br>CONCLUSIONS: We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.}, }
@article {pmid37992160, year = {2023}, author = {Coffroth, MA and Buccella, LA and Eaton, KM and Lasker, HR and Gooding, AT and Franklin, H}, title = {What makes a winner? Symbiont and host dynamics determine Caribbean octocoral resilience to bleaching.}, journal = {Science advances}, volume = {9}, number = {47}, pages = {eadj6788}, pmid = {37992160}, issn = {2375-2548}, mesh = {Animals ; Ecosystem ; Coral Reefs ; *Anthozoa/physiology ; Caribbean Region ; *Dinoflagellida/genetics ; Symbiosis ; }, abstract = {Unlike reef-building, scleractinian corals, Caribbean soft corals (octocorals) have not suffered marked declines in abundance associated with anthropogenic ocean warming. Both octocorals and reef-building scleractinians depend on a nutritional symbiosis with single-celled algae living within their tissues. In both groups, increased ocean temperatures can induce symbiont loss (bleaching) and coral death. Multiple heat waves from 2014 to 2016 resulted in widespread damage to reef ecosystems and provided an opportunity to examine the bleaching response of three Caribbean octocoral species. Symbiont densities declined during the heat waves but recovered quickly, and colony mortality was low. The dominant symbiont genotypes within a host generally did not change, and all colonies hosted symbiont species in the genus Breviolum. Their association with thermally tolerant symbionts likely contributes to the octocoral holobiont's resistance to mortality and the resilience of their symbiont populations. The resistance and resilience of Caribbean octocorals offer clues for the future of coral reefs.}, }
@article {pmid37991377, year = {2024}, author = {Šigutová, H and Pyszko, P and Šigut, M and Czajová, K and Kostovčík, M and Kolařík, M and Hařovská, D and Drozd, P}, title = {Concentration-dependent effect of plant secondary metabolites on bacterial and fungal microbiomes in caterpillar guts.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0299423}, pmid = {37991377}, issn = {2165-0497}, support = {GA22-29971S//Czech Science Foundation/ ; }, mesh = {*Mycobiome ; Bacteria/genetics ; *Microbiota ; Plants ; }, abstract = {The caterpillar gut is an excellent model system for studying host-microbiome interactions, as it represents an extreme environment for microbial life that usually has low diversity and considerable variability in community composition. Our study design combines feeding caterpillars on a natural and artificial diet with controlled levels of plant secondary metabolites and uses metabarcoding and quantitative PCR to simultaneously profile bacterial and fungal assemblages, which has never been performed. Moreover, we focus on multiple caterpillar species and consider diet breadth. Contrary to many previous studies, our study suggested the functional importance of certain microbial taxa, especially bacteria, and confirmed the previously proposed lower importance of fungi for caterpillar holobiont. Our study revealed the lack of differences between monophagous and polyphagous species in the responses of microbial assemblages to plant secondary metabolites, suggesting the limited role of the microbiome in the plasticity of the herbivore diet.}, }
@article {pmid37979302, year = {2024}, author = {Chai, G and Li, J and Li, Z}, title = {The interactive effects of ocean acidification and warming on bioeroding sponge Spheciospongia vesparium microbiome indicated by metatranscriptomics.}, journal = {Microbiological research}, volume = {278}, number = {}, pages = {127542}, doi = {10.1016/j.micres.2023.127542}, pmid = {37979302}, issn = {1618-0623}, mesh = {*Seawater/chemistry ; Hydrogen-Ion Concentration ; Ocean Acidification ; Coral Reefs ; *Microbiota/genetics ; Oceans and Seas ; }, abstract = {Global climate change will cause coral reefs decline and is expected to increase the reef erosion potential of bioeroding sponges. Microbial symbionts are essential for the overall fitness and survival of sponge holobionts in changing ocean environments. However, we rarely know about the impacts of ocean warming and acidification on bioeroding sponge microbiome. Here, the structural and functional changes of the bioeroding sponge Spheciospongia vesparium microbiome, as well as its recovery potential, were investigated at the RNA level in a laboratory system simulating 32 °C and pH 7.7. Based on metatranscriptome analysis, acidification showed no significant impact, while warming or simultaneous warming and acidification disrupted the sponge microbiome. Warming caused microbial dysbiosis and recruited potentially opportunistic and pathogenic members of Nesiotobacter, Oceanospirillaceae, Deltaproteobacteria, Epsilonproteobacteria, Bacteroidetes and Firmicutes. Moreover, warming disrupted nutrient exchange and molecular interactions in the sponge holobiont, accompanied by stimulation of virulence activity and anaerobic metabolism including denitrification and dissimilatory reduction of nitrate and sulfate to promote sponge necrosis. Particularly, the interaction between acidification and warming alleviated the negative effects of warming and enhanced the Rhodobacteraceae-driven ethylmalonyl-CoA pathway and sulfur-oxidizing multienzyme system. The microbiome could not recover during the experiment period after warming or combined stress was removed. This study suggests that warming or combined warming and acidification will irreversibly destabilize the S. vesparium microbial community structure and function, and provides insight into the molecular mechanisms of the interactive effects of acidification and warming on the sponge microbiome.}, }
@article {pmid37968499, year = {2023}, author = {Pfister, CA and Cardini, U and Mirasole, A and Montilla, LM and Veseli, I and Gattuso, JP and Teixido, N}, title = {Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19996}, pmid = {37968499}, issn = {2045-2322}, mesh = {*Seawater/chemistry ; Carbon Dioxide/metabolism ; Nitrogen/metabolism ; Hydrogen-Ion Concentration ; Ocean Acidification ; *Alismatales/metabolism ; Mediterranean Sea ; Water/metabolism ; Ecosystem ; }, abstract = {Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6-17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.}, }
@article {pmid37964575, year = {2023}, author = {Giesler, JK and Harder, T and Wohlrab, S}, title = {Microbiome and photoperiod interactively determine thermal sensitivity of polar and temperate diatoms.}, journal = {Biology letters}, volume = {19}, number = {11}, pages = {20230151}, pmid = {37964575}, issn = {1744-957X}, mesh = {*Diatoms ; Photoperiod ; *Microbiota ; Climate Change ; Temperature ; }, abstract = {The effect of temperature on ectothermic organisms in the context of climate change has long been considered in isolation (i.e. as a single driver). This is challenged by observations demonstrating that temperature-dependent growth is correlated to further factors. However, little is known how the chronobiological history of an organism reflected in its adaptation to re-occurring cyclic patterns in its environment (e.g. annual range of photoperiods in its habitat) and biotic interactions with its microbiome, contribute to shaping its realized niche. To address this, we conducted a full-factorial microcosm multi-stressor experiment with the marine diatoms Thalassiosira gravida (polar) and Thalassiosira rotula (temperate) across multiple levels of temperature (4°C; 9°C; 13.5°C) and photoperiod (4 h; 16 h; 24 h), both in the presence or absence of their microbiomes. While temperature-dependent growth of the temperate diatom was constrained by short and long photoperiods, the polar diatom coped with a 24 h photoperiod up to its thermal optimum (9°C). The algal microbiomes particularly supported host growth at the margins of their respective fundamental niches except for the combination of the warmest temperature tested at 24 h photoperiod. Overall, this study demonstrates that temperature tolerances may have evolved interactively and that the mutualistic effect of the microbiome can only be determined once the multifactorial abiotic niche is defined.}, }
@article {pmid37962344, year = {2023}, author = {Ramírez-Mendoza, R and Ángeles-Argáiz, R and Lozano Aguirre-Beltrán, LF and Almaraz-Suárez, JJ and Hernández-Oaxaca, D and Ortiz-Lopez, I and Perez-Moreno, J}, title = {Whole-genome sequence of Pseudomonas yamanorum OLsAu1 isolated from the edible wild ectomycorrhizal mushroom Lactarius sp. section Deliciosi.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0084323}, pmid = {37962344}, issn = {2576-098X}, support = {316198//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACYT)/ ; Analitek Life-RRM//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM)/ ; }, abstract = {We announce the genome sequencing, assembly, and annotation of the OLsAu1 strain and its taxonomic assignment to Pseudomonas yamanorum. The isolate comes from a wild edible ectomycorrhizal Lactarius sp. mushroom in the Abies forest. There is information regarding the strain's ability to promote plant growth, indicating its potential application in forestry.}, }
@article {pmid37950889, year = {2023}, author = {Hernández-Alonso, G and Ramos-Madrigal, J and van Grouw, H and Ciucani, MM and Cavill, EL and Sinding, MS and Gopalakrishnan, S and Pacheco, G and Gilbert, MTP}, title = {Redefining the Evolutionary History of the Rock Dove, Columba livia, Using Whole Genome Sequences.}, journal = {Molecular biology and evolution}, volume = {40}, number = {11}, pages = {}, pmid = {37950889}, issn = {1537-1719}, mesh = {Animals ; *Columbidae/genetics ; *Genome ; }, abstract = {The domestic pigeon's exceptional phenotypic diversity was key in developing Darwin's Theory of Evolution and establishing the concept of artificial selection. However, unlike its domestic counterpart, its wild progenitor, the rock dove Columba livia has received considerably less attention. Therefore, questions regarding its domestication, evolution, taxonomy, and conservation status remain unresolved. We generated whole-genome sequencing data from 65 historical rock doves that represent all currently recognized subspecies and span the species' original geographic distribution. Our dataset includes 3 specimens from Darwin's collection, and the type specimens of 5 different taxa. We characterized their population structure, genomic diversity, and gene-flow patterns. Our results show the West African subspecies C. l. gymnocyclus is basal to rock doves and domestic pigeons, and suggests gene-flow between the rock dove's sister species C. rupestris, and the ancestor of rock doves after its split from West African populations. These genomes allowed us to propose a model for the evolution of the rock dove in light of the refugia theory. We propose that rock dove genetic diversity and introgression patterns derive from a history of allopatric cycles and dispersion waves during the Quaternary glacial and interglacial periods. To explore the rock dove domestication history, we combined our new dataset with available genomes from domestic pigeons. Our results point to at least 1 domestication event in the Levant that gave rise to all domestic breeds analysed in this study. Finally, we propose a species-level taxonomic arrangement to reflect the evolutionary history of the West African rock dove populations.}, }
@article {pmid37941678, year = {2023}, author = {Li, T and Gao, J}, title = {Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1168760}, pmid = {37941678}, issn = {1664-462X}, abstract = {Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.}, }
@article {pmid40303765, year = {2023}, author = {Figueiredo, AM and Köster, PC and Dashti, A and Torres, RT and Fonseca, C and Mysterud, A and Bailo, B and Carvalho, J and Ferreira, E and Hipólito, D and Fernandes, J and Lino, A and Palmeira, JD and Sarmento, P and Neves, N and Carrapato, C and Calero-Bernal, R and Carmena, D}, title = {Molecular Detection and Distribution of Giardia duodenalis and Cryptosporidium spp. Infections in Wild and Domestic Animals in Portugal.}, journal = {Transboundary and emerging diseases}, volume = {2023}, number = {}, pages = {5849842}, pmid = {40303765}, issn = {1865-1682}, mesh = {Animals ; Portugal/epidemiology ; *Giardiasis/epidemiology/veterinary/parasitology ; *Cryptosporidium/isolation &amp; purification/genetics ; *Cryptosporidiosis/epidemiology/parasitology ; *Giardia lamblia/isolation &amp; purification/genetics ; *Animals, Wild/parasitology ; *Animals, Domestic/parasitology ; Feces/parasitology ; Zoonoses ; }, abstract = {Enteric protozoan parasites Giardia duodenalis, Cryptosporidium spp., and, to a lesser extent, the ciliate Balantioides coli are responsible for severe human and animal intestinal disorders globally. However, limited information is available on the occurrence and epidemiology of these parasites in domestic, but especially wild species in Portugal. To fill this gap of knowledge, we have investigated G. duodenalis, Cryptosporidium spp., and B. coli occurrence, distribution, genetic diversity, and zoonotic potential by analyzing 756 fecal samples from several wild carnivores (n = 288), wild ungulates (n = 242), and domestic species (n = 226) collected across different areas of mainland Portugal. Overall, infection rates were 16.1% (122/756; 95% CI: 13.59-18.96) for G. duodenalis and 2.7% (20/756; CI: 1.62-4.06) for Cryptosporidium spp., while no ungulate sample analyzed yielded positive results for B. coli. Giardia duodenalis was found across a wide range of hosts and sampling areas, being most prevalent in the Iberian lynx (26.7%), the Iberian wolf (24.0%), and the domestic dog (23.9%). Cryptosporidium spp. was only identified in wild boar (8.4%), red fox (3.4%), Iberian lynx (3.3%), red deer (3.1%), and Iberian wolf (2.5%). Sequence analysis of G. duodenalis determined zoonotic assemblage A (subassemblage AI) in one roe deer sample, canine-specific assemblages C and D in Iberian wolf, red fox, and domestic dog, and ungulate-specific assemblage E in wild boar, sheep, cattle, and horse. Six Cryptosporidium species were identified: C. scrofarum in wild boar, C. canis in the Iberian wolf and red fox, C. ubiquitum in red deer and wild boar, C. felis in the Iberian lynx, and both C. ryanae and C. occultus in red deer. Giardia duodenalis and Cryptosporidium spp. coinfections were observed in 0.7% (5/756) of the samples. This is the first, most comprehensive, and largest molecular-based epidemiology study of its kind carried out in Portugal, covering a wide range of wild and domestic hosts and sampling areas. The detection of zoonotic Cryptosporidium spp. and G. duodenalis subassemblage AI demonstrates the role of wild and domestic host species in the transmission of these agents while representing a potential source of environmental contamination for other animals and humans.}, }
@article {pmid37938763, year = {2022}, author = {Xiang, N and Rädecker, N and Pogoreutz, C and Cárdenas, A and Meibom, A and Wild, C and Gärdes, A and Voolstra, CR}, title = {Presence of algal symbionts affects denitrifying bacterial communities in the sea anemone Aiptasia coral model.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {105}, pmid = {37938763}, issn = {2730-6151}, support = {15902919 FP 029/19//Universit&#xe4;t Konstanz (University of Konstanz)/ ; 15902919 FP 029/19//Universit&#xe4;t Konstanz (University of Konstanz)/ ; 15902919 FP 029/19//Universit&#xe4;t Konstanz (University of Konstanz)/ ; 200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {The coral-algal symbiosis is maintained by a constant and limited nitrogen availability in the holobiont. Denitrifiers, i.e., prokaryotes reducing nitrate/nitrite to dinitrogen, could contribute to maintaining the nitrogen limitation in the coral holobiont, however the effect of host and algal identity on their community is still unknown. Using the coral model Aiptasia, we quantified and characterized the denitrifier community in a full-factorial design combining two hosts (CC7 and H2) and two strains of algal symbionts of the family Symbiodiniaceae (SSA01 and SSB01). Strikingly, relative abundance of denitrifiers increased by up to 22-fold in photosymbiotic Aiptasia compared to their aposymbiotic (i.e., algal-depleted) counterparts. In line with this, while the denitrifier community in aposymbiotic Aiptasia was largely dominated by diet-associated Halomonas, we observed an increasing relative abundance of an unclassified bacterium in photosymbiotic CC7, and Ketobacter in photosymbiotic H2, respectively. Pronounced changes in denitrifier communities of Aiptasia with Symbiodinium linucheae strain SSA01 aligned with the higher photosynthetic carbon availability of these holobionts compared to Aiptasia with Breviolum minutum strain SSB01. Our results reveal that the presence of algal symbionts increases abundance and alters community structure of denitrifiers in Aiptasia. Thereby, patterns in denitrifier community likely reflect the nutritional status of aposymbiotic vs. symbiotic holobionts. Such a passive regulation of denitrifiers may contribute to maintaining the nitrogen limitation required for the functioning of the cnidarian-algal symbiosis.}, }
@article {pmid37938762, year = {2022}, author = {Lesser, MP and Sabrina Pankey, M and Slattery, M and Macartney, KJ and Gochfeld, DJ}, title = {Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {112}, pmid = {37938762}, issn = {2730-6151}, support = {OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; }, abstract = {Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.}, }
@article {pmid37935117, year = {2023}, author = {Jamieson, A and Carmagnini, A and Howard-McCombe, J and Doherty, S and Hirons, A and Dimopoulos, E and Lin, AT and Allen, R and Anderson-Whymark, H and Barnett, R and Batey, C and Beglane, F and Bowden, W and Bratten, J and De Cupere, B and Drew, E and Foley, NM and Fowler, T and Fox, A and Geigl, EM and Gotfredsen, AB and Grange, T and Griffiths, D and Groß, D and Haruda, A and Hjermind, J and Knapp, Z and Lebrasseur, O and Librado, P and Lyons, LA and Mainland, I and McDonnell, C and Muñoz-Fuentes, V and Nowak, C and O'Connor, T and Peters, J and Russo, IM and Ryan, H and Sheridan, A and Sinding, MS and Skoglund, P and Swali, P and Symmons, R and Thomas, G and Trolle Jensen, TZ and Kitchener, AC and Senn, H and Lawson, D and Driscoll, C and Murphy, WJ and Beaumont, M and Ottoni, C and Sykes, N and Larson, G and Frantz, L}, title = {Limited historical admixture between European wildcats and domestic cats.}, journal = {Current biology : CB}, volume = {33}, number = {21}, pages = {4751-4760.e14}, doi = {10.1016/j.cub.2023.08.031}, pmid = {37935117}, issn = {1879-0445}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Cats/genetics ; Animals ; Cattle ; Bees ; Sheep ; Swine ; *Hybridization, Genetic ; Chickens ; *Felis/genetics ; Europe ; Gene Flow ; }, abstract = {Domestic cats were derived from the Near Eastern wildcat (Felis lybica), after which they dispersed with people into Europe. As they did so, it is possible that they interbred with the indigenous population of European wildcats (Felis silvestris). Gene flow between incoming domestic animals and closely related indigenous wild species has been previously demonstrated in other taxa, including pigs, sheep, goats, bees, chickens, and cattle. In the case of cats, a lack of nuclear, genome-wide data, particularly from Near Eastern wildcats, has made it difficult to either detect or quantify this possibility. To address these issues, we generated 75 ancient mitochondrial genomes, 14 ancient nuclear genomes, and 31 modern nuclear genomes from European and Near Eastern wildcats. Our results demonstrate that despite cohabitating for at least 2,000 years on the European mainland and in Britain, most modern domestic cats possessed less than 10% of their ancestry from European wildcats, and ancient European wildcats possessed little to no ancestry from domestic cats. The antiquity and strength of this reproductive isolation between introduced domestic cats and local wildcats was likely the result of behavioral and ecological differences. Intriguingly, this long-lasting reproductive isolation is currently being eroded in parts of the species' distribution as a result of anthropogenic activities.}, }
@article {pmid37933991, year = {2023}, author = {Isaac, P and Mutusamy, P and Su Yin, L and Jing Wei, Y and Mohd Salleh, F and Abu Bakar, MALb and Parimannan, S and Rajandas, H}, title = {Complete genome sequences of Lactococcus lactis D1_2, a bacterium with antimicrobial properties isolated from peat soil.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0068023}, pmid = {37933991}, issn = {2576-098X}, support = {JPT(BKPI)1000/016/018/25 (60)//Ministry of Higher Education, Malaysia (MOHE)/ ; }, abstract = {Lactococcus lactis is a beneficial lactic acid bacterium commonly studied for its probiotic properties and role in dairy production. Here, we present a complete genome of Lactococcus lactis D1_2, isolated from peat swamp forests. To discover the potential antimicrobial properties, the complete genome of the strain was sequenced and analyzed.}, }
@article {pmid37933583, year = {2024}, author = {Cortazar-Chinarro, M and Richter-Boix, A and Rödin-Mörch, P and Halvarsson, P and Logue, JB and Laurila, A and Höglund, J}, title = {Association between the skin microbiome and MHC class II diversity in an amphibian.}, journal = {Molecular ecology}, volume = {33}, number = {1}, pages = {e17198}, doi = {10.1111/mec.17198}, pmid = {37933583}, issn = {1365-294X}, support = {BS2018-0110//Kungliga Vetenskapsakademin/ ; FO2018-0540//Stiftelsen Lars Hiertas Minne/ ; DO2013-0013//Stiftelsen Oscar och Lili Lamms Minne/ ; //Stilftensen for zoologiska forskning/ ; 146400178//Svenska Forskningsr&#xe5;det Formas/ ; 621-2013-4503//Swedish research Council/ ; }, mesh = {Animals ; *Genetic Variation ; Selection, Genetic ; Genes, MHC Class II/genetics ; Histocompatibility Antigens Class II/genetics ; *Microbiota/genetics ; Amphibians/genetics ; Alleles ; }, abstract = {Microbiomes play an important role in determining the ecology and behaviour of their hosts. However, questions remain pertaining to how host genetics shape microbiomes, and how microbiome composition influences host fitness. We explored the effects of geography, evolutionary history and host genetics on the skin microbiome diversity and structure in a widespread amphibian. More specifically, we examined the association between bacterial diversity and composition and the major histocompatibility complex class II exon 2 diversity in 12 moor frog (Rana arvalis) populations belonging to two geographical clusters that show signatures of past and ongoing differential selection. We found that while bacterial alpha diversity did not differ between the two clusters, MHC alleles/supertypes and genetic diversity varied considerably depending on geography and evolutionary history. Bacterial alpha diversity was positively correlated with expected MHC heterozygosity and negatively with MHC nucleotide diversity. Furthermore, bacterial community composition showed significant variation between the two geographical clusters and between specific MHC alleles/supertypes. Our findings emphasize the importance of historical demographic events on hologenomic variation and provide new insights into how immunogenetic host variability and microbial diversity may jointly influence host fitness with consequences for disease susceptibility and population persistence.}, }
@article {pmid37919016, year = {2024}, author = {Kothe, CI and Rasmussen, JA and Mak, SST and Gilbert, MTP and Evans, J}, title = {Exploring the microbial diversity of novel misos with metagenomics.}, journal = {Food microbiology}, volume = {117}, number = {}, pages = {104372}, doi = {10.1016/j.fm.2023.104372}, pmid = {37919016}, issn = {1095-9998}, mesh = {*Fabaceae ; Glycine max ; *Soy Foods ; *Fermented Foods ; Metagenomics ; Flavoring Agents/analysis ; Fermentation ; }, abstract = {Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.}, }
@article {pmid37916820, year = {2023}, author = {Howard, RD and Schul, MD and Rodriguez Bravo, LM and Altieri, AH and Meyer, JL}, title = {Shifts in the coral microbiome in response to in situ experimental deoxygenation.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0057723}, pmid = {37916820}, issn = {1098-5336}, support = {OCE-2048914//National Science Foundation (NSF)/ ; }, mesh = {Humans ; Animals ; *Anthozoa/microbiology ; Coral Reefs ; *Microbiota ; Bacteria/genetics ; Hypoxia ; }, abstract = {Marine hypoxia is a threat for corals but has remained understudied in tropical regions where coral reefs are abundant. Though microbial symbioses can alleviate the effects of ecological stress, we do not yet understand the taxonomic or functional response of the coral microbiome to hypoxia. In this study, we experimentally lowered oxygen levels around Siderastrea siderea and Agaricia lamarcki colonies in situ to observe changes in the coral microbiome in response to deoxygenation. Our results show that hypoxia triggers a stochastic change of the microbiome overall, with some bacterial families changing deterministically after just 48 hours of exposure. These families represent an increase in anaerobic and opportunistic taxa in the microbiomes of both coral species. Thus, marine deoxygenation destabilizes the coral microbiome and increases bacterial opportunism. This work provides novel and fundamental knowledge of the microbial response in coral during hypoxia and may provide insight into holobiont function during stress.}, }
@article {pmid37914705, year = {2023}, author = {Rädecker, N and Escrig, S and Spangenberg, JE and Voolstra, CR and Meibom, A}, title = {Coupled carbon and nitrogen cycling regulates the cnidarian-algal symbiosis.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6948}, pmid = {37914705}, issn = {2041-1723}, mesh = {Animals ; Carbon/metabolism ; Symbiosis ; *Sea Anemones/metabolism ; Nitrogen/metabolism ; Photosynthesis ; *Dinoflagellida/metabolism ; }, abstract = {Efficient nutrient recycling underpins the ecological success of cnidarian-algal symbioses in oligotrophic waters. In these symbioses, nitrogen limitation restricts the growth of algal endosymbionts in hospite and stimulates their release of photosynthates to the cnidarian host. However, the mechanisms controlling nitrogen availability and their role in symbiosis regulation remain poorly understood. Here, we studied the metabolic regulation of symbiotic nitrogen cycling in the sea anemone Aiptasia by experimentally altering labile carbon availability in a series of experiments. Combining [13]C and [15]N stable isotope labeling experiments with physiological analyses and NanoSIMS imaging, we show that the competition for environmental ammonium between the host and its algal symbionts is regulated by labile carbon availability. Light regimes optimal for algal photosynthesis increase carbon availability in the holobiont and stimulate nitrogen assimilation in the host metabolism. Consequently, algal symbiont densities are lowest under optimal environmental conditions and increase toward the lower and upper light tolerance limits of the symbiosis. This metabolic regulation promotes efficient carbon recycling in a stable symbiosis across a wide range of environmental conditions. Yet, the dependence on resource competition may favor parasitic interactions, explaining the instability of the cnidarian-algal symbiosis as environmental conditions in the Anthropocene shift towards its tolerance limits.}, }
@article {pmid37905582, year = {2024}, author = {Radice, VZ and Martinez, A and Paytan, A and Potts, DC and Barshis, DJ}, title = {Complex dynamics of coral gene expression responses to low pH across species.}, journal = {Molecular ecology}, volume = {33}, number = {1}, pages = {e17186}, doi = {10.1111/mec.17186}, pmid = {37905582}, issn = {1365-294X}, support = {9915-16//The National Geographic Explorer grant/ ; //The National Park Foundation Science Fellowship/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; Ecosystem ; Hydrogen-Ion Concentration ; Seawater/chemistry ; Transcriptome/genetics ; }, abstract = {Coral capacity to tolerate low pH affects coral community composition and, ultimately, reef ecosystem function. Low pH submarine discharges ('Ojo'; Yucatán, México) represent a natural laboratory to study plasticity and acclimatization to low pH in relation to ocean acidification. A previous >2-year coral transplant experiment to ambient and low pH common garden sites revealed differential survivorship across species and sites, providing a framework to compare mechanistic responses to differential pH exposures. Here, we examined gene expression responses of transplants of three species of reef-building corals (Porites astreoides, Porites porites and Siderastrea siderea) and their algal endosymbiont communities (Symbiodiniaceae) originating from low pH (Ojo) and ambient pH native origins (Lagoon or Reef). Transplant pH environment had the greatest effect on gene expression of Porites astreoides hosts and symbionts and P. porites hosts. Host P. astreoides Ojo natives transplanted to ambient pH showed a similar gene expression profile to Lagoon natives remaining in ambient pH, providing evidence of plasticity in response to ambient pH conditions. Although origin had a larger effect on host S. siderea gene expression due to differences in symbiont genera within Reef and Lagoon/Ojo natives, subtle effects of low pH on all origins demonstrated acclimatization potential. All corals responded to low pH by differentially expressing genes related to pH regulation, ion transport, calcification, cell adhesion and stress/immune response. This study demonstrates that the magnitude of coral gene expression responses to pH varies considerably among populations, species and holobionts, which could differentially affect acclimatization to and impacts of ocean acidification.}, }
@article {pmid37902324, year = {2023}, author = {Matthews, JL and Bartels, N and Elahee Doomun, SN and Davy, SK and De Souza, DP}, title = {Gas Chromatography-Mass Spectrometry-Based Targeted Metabolomics of Hard Coral Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {200}, pages = {}, doi = {10.3791/65628}, pmid = {37902324}, issn = {1940-087X}, mesh = {Animals ; *Anthozoa/metabolism ; Gas Chromatography-Mass Spectrometry ; Metabolomics/methods ; Bacteria ; Temperature ; Symbiosis ; Coral Reefs ; }, abstract = {Gas chromatography-mass spectrometry (GC-MS)-based approaches have proven to be powerful for elucidating the metabolic basis of the cnidarian-dinoflagellate symbiosis and how coral responds to stress (i.e., during temperature-induced bleaching). Steady-state metabolite profiling of the coral holobiont, which comprises the cnidarian host and its associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi, and viruses), has been successfully applied under ambient and stress conditions to characterize the holistic metabolic status of the coral. However, to answer questions surrounding the symbiotic interactions, it is necessary to analyze the metabolite profiles of the coral host and its algal symbionts independently, which can only be achieved by physical separation and isolation of the tissues, followed by independent extraction and analysis. While the application of metabolomics is relatively new to the coral field, the sustained efforts of research groups have resulted in the development of robust methods for analyzing metabolites in corals, including the separation of the coral host tissue and algal symbionts. This paper presents a step-by-step guide for holobiont separation and the extraction of metabolites for GC-MS analysis, including key optimization steps for consideration. We demonstrate how, once analyzed independently, the combined metabolite profile of the two fractions (coral and Symbiodiniaceae) is similar to the profile of the whole (holobiont), but by separating the tissues, we can also obtain key information about the metabolism of and interactions between the two partners that cannot be obtained from the whole alone.}, }
@article {pmid37876012, year = {2023}, author = {Yu, J and Jiang, C and Yamano, R and Koike, S and Sakai, Y and Mino, S and Sawabe, T}, title = {Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {54}, pmid = {37876012}, issn = {2524-4671}, abstract = {BACKGROUND: Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth.<br><br>RESULTS: We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and >&#x2009;70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus.<br><br>CONCLUSION: Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.}, }
@article {pmid37872593, year = {2023}, author = {Zhao, W and Chen, X and Liu, R and Tian, P and Niu, W and Zhang, XH and Liu, J and Wang, X}, title = {Distinct coral environments shape the dynamic of planktonic Vibrio spp.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {77}, pmid = {37872593}, issn = {2524-6372}, support = {42006085//National Natural Science Foundation of China/ ; 2021J05094//Marine S&amp;T Fund of Fujian Province/ ; EPR2023001//Fund of Key Laboratory of Marine Ecological Conservation and Restoration, Ministry of Natural Resources/ Fujian Provincial Key Laboratory of Marine Ecological Conservation and Restoration/ ; 202312034//Fundamental Research Funds for the Central Universities/ ; 2020005//Scientific Research Foundation of the Third Institute of Oceanography, MNR/ ; }, abstract = {BACKGROUND: Coral reefs are one of the most biodiverse and productive ecosystems, providing habitat for a vast of species. Reef-building scleractinian corals with a symbiotic microbiome, including bacteria, archaea, viruses and eukaryotic microbes, are referred to coral holobionts. Among them, coral diseases, mainly caused by Vibrio spp., have significantly contributed to the loss of coral cover and diversity. Habitat filtering across the globe has led to a variety structure of marine bacterial communities. Coral species, quantity and characteristics are significant differences between the Xisha Islands and Daya Bay (Guangdong Province). Thus, the Vibrio communities may be distinct between coral rich and poor areas.<br><br>RESULTS: Through comparison of Vibrio dynamics between coral-rich (Xisha Islands) and coral-poor (Daya Bay) locations, we uncovered differences in Vibrio abundance, diversity, community composition and assembly mechanisms associated with corals. The higher abundance of Vibrio in coral rich areas may indicate a strong interaction between vibrios and corals. V. campbellii, Paraphotobacterium marinum and V. caribbeanicus were widely distributed in both coral rich and poor areas, likely indicating weak species specificity in the coral-stimulated growth of Vibrio. Random-forest prediction revealed Vibrio species and Photobacterium species as potential microbial indicators in the coral rich and coral poor areas, respectively. Ecological drift rather than selection governed the Vibrio community assembly in the Xisha Islands. Comparatively, homogenizing selection was more important for the Daya Bay community, which may reflect a role of habitat filtration.<br><br>CONCLUSION: This study revealed the different distribution pattern and assembly mechanism of Vibrio spp. between coral rich and poor areas, providing the background data for the research of Vibrio community in coral reef areas and may help the protection of coral reef at the biological level. The main reasons for the difference were different number and species of corals, environmental (e.g., temperature) and spatial factors. It reflected the strong interaction between Vibrio and corals, and provided a new perspective for the investigation of Vibrio in coral reef ecosystem.}, }
@article {pmid37860235, year = {2023}, author = {De-la-Vega-Camarillo, E and Hernández-García, JA and Villa-Tanaca, L and Hernández-Rodríguez, C}, title = {Unlocking the hidden potential of Mexican teosinte seeds: revealing plant growth-promoting bacterial and fungal biocontrol agents.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1247814}, pmid = {37860235}, issn = {1664-462X}, abstract = {The bacterial component of plant holobiont maintains valuable interactions that contribute to plants' growth, adaptation, stress tolerance, and antagonism to some phytopathogens. Teosinte is the grass plant recognized as the progenitor of modern maize, domesticated by pre-Hispanic civilizations around 9,000 years ago. Three teosinte species are recognized: Zea diploperennis, Zea perennis, and Zea mays. In this work, the bacterial diversity of three species of Mexican teosinte seeds was explored by massive sequencing of 16S rRNA amplicons. Streptomyces, Acinetobacter, Olivibacter, Erwinia, Bacillus, Pseudomonas, Cellvibrio, Achromobacter, Devosia, Lysobacter, Sphingopyxis, Stenotrophomonas, Ochrobactrum, Delftia, Lactobacillus, among others, were the bacterial genera mainly represented. The bacterial alpha diversity in the seeds of Z. diploperennis was the highest, while the alpha diversity in Z. mays subsp. mexicana race was the lowest observed among the species and races. The Mexican teosintes analyzed had a core bacteriome of 38 bacterial genera, including several recognized plant growth promoters or fungal biocontrol agents such as Agrobacterium, Burkholderia, Erwinia, Lactobacillus, Ochrobactrum, Paenibacillus, Pseudomonas, Sphingomonas, Streptomyces, among other. Metabolic inference analysis by PICRUSt2 of bacterial genera showed several pathways related to plant growth promotion (PGP), biological control, and environmental adaptation. The implications of these findings are far-reaching, as they highlight the existence of an exceptional bacterial germplasm reservoir teeming with potential plant growth promotion bacteria (PGPB). This reserve holds the key to cultivating innovative bioinoculants and formidable fungal antagonistic strains, thereby paving the way for a more sustainable and eco-friendly approach to agriculture. Embracing these novel NGS-based techniques and understanding the profound impact of the vertical transference of microorganisms from seeds could revolutionize the future of agriculture and develop a new era of symbiotic harmony between plants and microbes.}, }
@article {pmid37857885, year = {2023}, author = {Bertile, F and Matallana-Surget, S and Tholey, A and Cristobal, S and Armengaud, J}, title = {Diversifying the concept of model organisms in the age of -omics.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1062}, pmid = {37857885}, issn = {2399-3642}, mesh = {Humans ; *Biodiversity ; Genomics ; Genome ; *Microbiota ; }, abstract = {In today's post-genomic era, it is crucial to rethink the concept of model organisms. While a few historically well-established organisms, e.g. laboratory rodents, have enabled significant scientific breakthroughs, there is now a pressing need for broader inclusion. Indeed, new organisms and models, from complex microbial communities to holobionts, are essential to fully grasp the complexity of biological principles across the breadth of biodiversity. By fostering collaboration between biology, advanced molecular science and omics communities, we can collectively adopt new models, unraveling their molecular functioning, and uncovering fundamental mechanisms. This concerted effort will undoubtedly enhance human health, environmental quality, and biodiversity conservation.}, }
@article {pmid37848067, year = {2023}, author = {Sinotte, VM and Renelies-Hamilton, J and Andreu-Sánchez, S and Vasseur-Cognet, M and Poulsen, M}, title = {Selective enrichment of founding reproductive microbiomes allows extensive vertical transmission in a fungus-farming termite.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2009}, pages = {20231559}, pmid = {37848067}, issn = {1471-2954}, mesh = {Animals ; *Isoptera ; Biological Evolution ; *Microbiota ; Fungi ; Agriculture ; Symbiosis ; Phylogeny ; }, abstract = {Mutualistic coevolution can be mediated by vertical transmission of symbionts between host generations. Termites host complex gut bacterial communities with evolutionary histories indicative of mixed-mode transmission. Here, we document that vertical transmission of gut bacterial strains is congruent across parent to offspring colonies in four pedigrees of the fungus-farming termite Macrotermes natalensis. We show that 44% of the offspring colony microbiome, including more than 80 bacterial genera and pedigree-specific strains, are consistently inherited. We go on to demonstrate that this is achieved because colony-founding reproductives are selectively enriched with a set of non-random, environmentally sensitive and termite-specific gut microbes from their colonies of origin. These symbionts transfer to offspring colony workers with high fidelity, after which priority effects appear to influence the composition of the establishing microbiome. Termite reproductives thus secure transmission of complex communities of specific, co-evolved microbes that are critical to their offspring colonies. Extensive yet imperfect inheritance implies that the maturing colony benefits from acquiring environmental microbes to complement combinations of termite, fungus and vertically transmitted microbes; a mode of transmission that is emerging as a prevailing strategy for hosts to assemble complex adaptive microbiomes.}, }
@article {pmid37841893, year = {2023}, author = {Xiang, X and Vilar Gomez, AA and Blomberg, SP and Yuan, H and Degnan, BM and Degnan, SM}, title = {Potential for host-symbiont communication via neurotransmitters and neuromodulators in an aneural animal, the marine sponge Amphimedon queenslandica.}, journal = {Frontiers in neural circuits}, volume = {17}, number = {}, pages = {1250694}, pmid = {37841893}, issn = {1662-5110}, mesh = {Animals ; *Dopamine ; *Porifera/microbiology ; Amines ; Neurotransmitter Agents ; Communication ; }, abstract = {Interkingdom signalling within a holobiont allows host and symbionts to communicate and to regulate each other's physiological and developmental states. Here we show that a suite of signalling molecules that function as neurotransmitters and neuromodulators in most animals with nervous systems, specifically dopamine and trace amines, are produced exclusively by the bacterial symbionts of the demosponge Amphimedon queenslandica. Although sponges do not possess a nervous system, A. queenslandica expresses rhodopsin class G-protein-coupled receptors that are structurally similar to dopamine and trace amine receptors. When sponge larvae, which express these receptors, are exposed to agonists and antagonists of bilaterian dopamine and trace amine receptors, we observe marked changes in larval phototactic swimming behaviour, consistent with the sponge being competent to recognise and respond to symbiont-derived trace amine signals. These results indicate that monoamines synthesised by bacterial symbionts may be able to influence the physiology of the host sponge.}, }
@article {pmid37840369, year = {2024}, author = {Chrismas, N and Tindall-Jones, B and Jenkins, H and Harley, J and Bird, K and Cunliffe, M}, title = {Metatranscriptomics reveals diversity of symbiotic interaction and mechanisms of carbon exchange in the marine cyanolichen Lichina pygmaea.}, journal = {The New phytologist}, volume = {241}, number = {5}, pages = {2243-2257}, doi = {10.1111/nph.19320}, pmid = {37840369}, issn = {1469-8137}, support = {218328/WT_/Wellcome Trust/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Ascomycota/physiology ; *Lichens/genetics ; *Cyanobacteria/genetics ; Symbiosis ; Phylogeny ; }, abstract = {Lichens are exemplar symbioses based upon carbon exchange between photobionts and their mycobiont hosts. Historically considered a two-way relationship, some lichen symbioses have been shown to contain multiple photobiont partners; however, the way in which these photobiont communities react to environmental change is poorly understood. Lichina pygmaea is a marine cyanolichen that inhabits rocky seashores where it is submerged in seawater during every tidal cycle. Recent work has indicated that L. pygmaea has a complex photobiont community including the cyanobionts Rivularia and Pleurocapsa. We performed rRNA-based metabarcoding and mRNA metatranscriptomics of the L. pygmaea holobiont at high and low tide to investigate community response to immersion in seawater. Carbon exchange in L. pygmaea is a dynamic process, influenced by both tidal cycle and the biology of the individual symbiotic components. The mycobiont and two cyanobiont partners exhibit distinct transcriptional responses to seawater hydration. Sugar-based compatible solutes produced by Rivularia and Pleurocapsa in response to seawater are a potential source of carbon to the mycobiont. We propose that extracellular processing of photobiont-derived polysaccharides is a fundamental step in carbon acquisition by L. pygmaea and is analogous to uptake of plant-derived carbon in ectomycorrhizal symbioses.}, }
@article {pmid37833238, year = {2023}, author = {Karimi, E and Dittami, SM}, title = {Maintaining beneficial alga-associated bacterial communities under heat stress: insights from controlled co-culture experiments using antibiotic-resistant bacterial strains.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad130}, pmid = {37833238}, issn = {1574-6941}, support = {//Centre National de la Recherche Scientifique/ ; }, mesh = {Coculture Techniques ; *Bacteria ; *Microbiota ; Plants ; Heat-Shock Response ; }, abstract = {Brown algae, like many eukaryotes, possess diverse microbial communities. Ectocarpus-a model brown alga-relies on these communities for essential processes, such as growth development. Controlled laboratory systems are needed for functional studies of these algal-bacterial interactions. We selected bacterial strains based on their metabolic networks to provide optimal completion of the algal metabolism, rendered them resistant to two antibiotics, and inoculate them to establish controlled co-cultures with Ectocarpus under continuous antibiotic treatment. We then monitored the stability of the resulting associations under control conditions and heat stress using 16S metabarcoding. Antibiotics strongly reduced bacterial diversity both in terms of taxonomy and predicted metabolic functions. In the inoculated sample, 63%-69% of reads corresponded to the inoculated strains, and the communities remained stable during temperature stress. They also partially restored the predicted metabolic functions of the natural community. Overall, the development of antibiotic-resistant helper cultures offers a promising route to fully controlled laboratory experiments with algae and microbiota and thus represents an important step towards generating experimental evidence for specific host-microbe interactions in the systems studied. Further work will be required to achieve full control and progressively expand our repertoire of helper strains including those currently 'unculturable'.}, }
@article {pmid37810788, year = {2023}, author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Ramírez-Fenández, L and Eguiarte, LE and Souza, V}, title = {Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15978}, pmid = {37810788}, issn = {2167-8359}, mesh = {Animals ; *Eukaryota/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Fishes/genetics ; Aquatic Organisms/genetics ; Mammals/genetics ; }, abstract = {Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.}, }
@article {pmid37804485, year = {2024}, author = {Pearman, WS and Duffy, GA and Liu, XP and Gemmell, NJ and Morales, SE and Fraser, CI}, title = {Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance.}, journal = {Annals of botany}, volume = {133}, number = {1}, pages = {169-182}, pmid = {37804485}, issn = {1095-8290}, support = {MFP-20-UOO-173//Royal Society Te Ap&#x101;rangi/ ; RDF-UOO1803//Rutherford Discovery fellowship/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Geography ; }, abstract = {BACKGROUND AND AIMS: Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation.<br><br>METHODS: In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment.<br><br>KEY RESULTS: We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome.<br><br>CONCLUSIONS: Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.}, }
@article {pmid37799611, year = {2023}, author = {Buschi, E and Dell'Anno, A and Tangherlini, M and Stefanni, S and Lo Martire, M and Núñez-Pons, L and Avila, C and Corinaldesi, C}, title = {Rhodobacteraceae dominate the core microbiome of the sea star Odontaster validus (Koehler, 1906) in two opposite geographical sectors of the Antarctic Ocean.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1234725}, pmid = {37799611}, issn = {1664-302X}, abstract = {Microbiota plays essential roles in the health, physiology, and in adaptation of marine multi-cellular organisms to their environment. In Antarctica, marine organisms have a wide range of unique physiological functions and adaptive strategies, useful for coping with extremely cold conditions. However, the role of microbiota associated with Antarctic organisms in such adaptive strategies is underexplored. In the present study, we investigated the diversity and putative functions of the microbiome of the sea star Odontaster validus, one of the main keystone species of the Antarctic benthic ecosystems. We compared the whole-body bacterial microbiome of sea stars from different sites of the Antarctic Peninsula and Ross Sea, two areas located in two opposite geographical sectors of the Antarctic continent. The taxonomic composition of O. validus microbiomes changed both between and within the two Antarctic sectors, suggesting that environmental and biological factors acting both at large and local scales may influence microbiome diversity. Despite this, one bacterial family (Rhodobacteraceae) was shared among all sea star individuals from the two geographical sectors, representing up to 95% of the microbial core, and suggesting a key functional role of this taxon in holobiont metabolism and well-being. In addition, the genus Roseobacter belonging to this family was also present in the surrounding sediment, implying a potential horizontal acquisition of dominant bacterial core taxa via host-selection processes from the environment.}, }
@article {pmid37790518, year = {2023}, author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM}, title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37790518}, issn = {2693-5015}, support = {R01 GM117163/GM/NIGMS NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; }, abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.}, }
@article {pmid37789578, year = {2023}, author = {Embacher, J and Zeilinger, S and Kirchmair, M and Neuhauser, S}, title = {Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans.}, journal = {Environmental microbiology reports}, volume = {15}, number = {6}, pages = {642-655}, pmid = {37789578}, issn = {1758-2229}, support = {Y0801-B16//Austrian Science Fund/ ; 346314//Universit&#xe4;t Innsbruck/ ; }, mesh = {*Basidiomycota ; *Ascomycota ; Bacteria/genetics ; Prokaryotic Cells ; }, abstract = {The basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon-sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the 'background' community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.}, }
@article {pmid37781006, year = {2023}, author = {Liu, Y and Ge, W and Dong, C and Shao, Q and Zhang, Z and Zou, X and Hu, H and Han, Y}, title = {The Analysis of Microbial Community Characteristics Revealed that the Pathogens of Leaf Spot of Rosa roxburghii Originated from the Phyllosphere.}, journal = {Indian journal of microbiology}, volume = {63}, number = {3}, pages = {324-336}, pmid = {37781006}, issn = {0046-8991}, abstract = {Members of the plant mycobiota are all associated to varying degrees with the development of plant diseases. Although many reports on the plant mycobiota are well documented, the relationships between mycobiota of Rosa roxburghii and plant diseases are poorly understood. Mutual interactions and extent of the roles of microbial communities associated with R. roxburghii and the source of pathogens are still unclear, and more research is needed on the health benefits of this ecologically important population. Using high-throughput sequencing, we analyzed the mycobiota composition and ecological guilds of the rhizosphere, root, and phyllosphere of healthy and diseased R. roxburghii from the Tianfu R. roxburghii Industrial Park in Panzhou city, Guizhou province. Analysis of community composition showed that the relative abundance of pathogens of leaf spot, including Alternaria, Pestalotiopsis and Neofusicoccum in the phyllosphere of diseased plant (LD), were 1.15%, 0.15% and 0.06%, and the relative abundance of Alternaria and Pestalotiopsis were 0.96% and 0.58% in healthy plant (LH). The alpha diversity indices indicated that fungal diversity was higher in healthy plants compared to diseased plants in each compartment. The alpha diversity index of fungi in the phyllosphere (LH) of healthy R. roxburghii, including Shannon, Chao-1, and Faith-pd indices, was 1.02, 81.50 and 10.42 higher than that of the diseased (LD), respectively. The fungi in the rhizosphere of healthy was 1.03, 59.00 and 5.56 higher than the diseased, respectively. The Shannon index of fungi in the root of healthy was 0.29 higher than that of diseased. Principal Coordinate analysis and ANOSIM results showed that there were significant differences in mycobiota composition between healthy and diseased phyllospheres (P < 0.05), as well as rhizosphere fungal community, while there was no significant difference between healthy and diseased roots (P > 0.05). Linear discriminant analysis effect size revealed that, at different taxonomic levels, there were significantly different taxa between the healthy and diseased plants in each compartment. The ecological guilds differed between healthy and diseased plants according to the FUNGuild analysis. For example, of healthy compared to diseased plants, the percentages of "lichenized-undefined saprotroph" were increased by 2.34%, 0.44%, and 1.54% in the phyllosphere, root, and rhizosphere, respectively. In addition, the plant pathogens existed in each compartment of R. roxburghii, but the percentages of "plant pathogen" were increased by 1.16% in the phyllosphere of diseased compared to healthy plants. Together, the ecological guild and co-occurrence network indicated that the potential pathogens of leaf spot were mainly found in the phyllosphere. This study explained one of pathogen origin of leaf spots of R. roxburghii by the microbial community ecology, which will provide the new insights for identification of plant pathogens.}, }
@article {pmid37775014, year = {2023}, author = {Xu, M and Lyu, Y and Cheng, K and Zhang, B and Cai, Z and Chen, G and Zhou, J}, title = {Interactions between quorum sensing/quorum quenching and virulence genes may affect coral health by regulating symbiotic bacterial community.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117221}, doi = {10.1016/j.envres.2023.117221}, pmid = {37775014}, issn = {1096-0953}, mesh = {Animals ; *Quorum Sensing/genetics ; Virulence ; *Anthozoa ; Bacteria/metabolism ; Virulence Factors ; }, abstract = {Quorum sensing (QS) and quorum quenching (QQ) are two antagonistic processes that may regulate the composition, function and structure of bacterial community. In coral holobiont, autoinducers signaling mediate the communication pathways between interspecies and intraspecies bacteria, which regulate the expression of the virulence factors that can damage host health. However, under environmental stressors, the interaction between the QS/QQ gene and virulence factors and their role in the bacterial communities and coral bleaching is still not fully clear. To address this question, here, metagenomics method was used to examine the profile of QS/QQ and virulence genes from a deeply sequenced microbial database, obtained from three bleached and non-bleached corals species. The prediction of bacterial genes of bleached samples involved in functional metabolic pathways were remarkably decreased, and the bacterial community structure on bleached samples was significantly different compared to non-bleached samples. The distribution and significant difference in QS/QQ and virulence genes were also carried out. We found that Proteobacteria was dominant bacteria among all samples, and AI-1 system is widespread within this group of bacteria. The identified specific genes consistently exhibited a trend of increased pathogenicity in bleached corals relative to non-bleached corals. The abundance of pathogenicity-associated QS genes, including bapA, pfoA and dgcB genes, were significantly increased in bleached corals and can encode the protein of biofilm formation and the membrane damaging toxins promoting pathogenic adhesion and infection. Similarly, the virulence genes, such as superoxide dismutase (Mn-SOD gene), metalloproteinase (yme1, yydH and zmpB), glycosidases (malE, malF, malG, and malK) and LodAB (lodB) genes significantly increased. Conversely, QQ genes that inhibit QS activity and virulence factors to defense the pathogens, including blpA, lsrK, amiE, aprE and gmuG showed a significant decrease in bleached groups. Furthermore, the significant correlations were found among virulence, QS/QQ genes, and coral associated bacterial community, and the virulence genes interact with key QS/QQ genes, directly or indirectly influence symbiotic bacterial communities homeostasis, thereby impacting coral health. It suggested that the functional and structural divergence in the symbiont bacteria may be partially attribute to the interplay, involving interactions among the host, bacterial communication signal systems, and bacterial virulence factors. In conclusion, these data helped to reveal the characteristic behavior of coral symbiotic bacteria, and facilitated a better understanding of bleaching mechanism from a chemical ecological perspective.}, }
@article {pmid37755006, year = {2023}, author = {Ševčíková, H and Malysheva, EF and Antonín, V and Borovička, J and Dovana, F and Ferisin, G and Eyssartier, G and Grootmyers, D and Heilmann-Clausen, J and Kalichman, J and Kaygusuz, O and Lebeuf, R and Muñoz González, G and Minnis, AM and Russell, SD and Saar, I and Nielsen, IB and Frøslev, TG and Justo, A}, title = {Holarctic Species in the Pluteus podospileus Clade: Description of Six New Species and Reassessment of Old Names.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37755006}, issn = {2309-608X}, abstract = {We studied the taxonomy of Pluteus podospileus and similar species using morphological and molecular (nrITS, TEF1-α) data, including a detailed study of the type collections of P. inflatus var. alneus, Pluteus minutissimus f. major, and P. granulatus var. tenellus. Within the P. podospileus complex, we phylogenetically confirmed six species in Europe, five in Asia, and eight in North America. Based on our results, we recognize P. seticeps as a separate species occurring in North America, while P. podospileus is limited to Eurasia. We describe six new species and a new variety: P. absconditus, P. fuscodiscus, P. gausapatus, P. inexpectatus, P. millsii, and P. notabilis and its variety, P. notabilis var. insignis. We elevate Pluteus seticeps var. cystidiosus to species rank as Pluteus cystidiosus. Based on the holotype of P. inflatus var. alneus, collections of P. inflatus identified by Velenovský, and several modern collections, we resurrect the name P. inflatus. Based on molecular analyses of syntypes of Pluteus minutissimus f. major and a holotype of Pluteus granulatus var. tenellus, we synonymize them under P. inflatus. We also increase our knowledge about the morphology and distribution of P. cutefractus.}, }
@article {pmid37752841, year = {2023}, author = {Lyndby, NH and Murthy, S and Bessette, S and Jakobsen, SL and Meibom, A and Kühl, M}, title = {Non-invasive investigation of the morphology and optical properties of the upside-down jellyfish Cassiopea with optical coherence tomography.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2007}, pages = {20230127}, pmid = {37752841}, issn = {1471-2954}, mesh = {Animals ; Tomography, Optical Coherence ; *Scyphozoa ; *Cnidaria ; Light ; Carbon ; }, abstract = {The jellyfish Cassiopea largely cover their carbon demand via photosynthates produced by microalgal endosymbionts, but how holobiont morphology and tissue optical properties affect the light microclimate and symbiont photosynthesis in Cassiopea remain unexplored. Here, we use optical coherence tomography (OCT) to study the morphology of Cassiopea medusae at high spatial resolution. We include detailed 3D reconstructions of external micromorphology, and show the spatial distribution of endosymbionts and white granules in the bell tissue. Furthermore, we use OCT data to extract inherent optical properties from light-scattering white granules in Cassiopea, and show that granules enhance local light-availability for symbionts in close proximity. Individual granules had a scattering coefficient of µs = 200-300 cm[-1], and scattering anisotropy factor of g = 0.7, while large tissue-regions filled with white granules had a lower µs = 40-100 cm[-1], and g = 0.8-0.9. We combined OCT information with isotopic labelling experiments to investigate the effect of enhanced light-availability in whitish tissue regions. Endosymbionts located in whitish tissue exhibited significantly higher carbon fixation compared to symbionts in anastomosing tissue (i.e. tissue without light-scattering white granules). Our findings support previous suggestions that white granules in Cassiopea play an important role in the host modulation of the light-microenvironment.}, }
@article {pmid37752514, year = {2023}, author = {Wang, C and Zheng, X and Kvitt, H and Sheng, H and Sun, D and Niu, G and Tchernov, D and Shi, T}, title = {Lineage-specific symbionts mediate differential coral responses to thermal stress.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {211}, pmid = {37752514}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Symbiosis/physiology ; *Dinoflagellida ; Photosynthesis ; }, abstract = {BACKGROUND: Ocean warming is a leading cause of increasing episodes of coral bleaching, the dissociation between coral hosts and their dinoflagellate algal symbionts in the family Symbiodiniaceae. While the diversity and flexibility of Symbiodiniaceae is presumably responsible for variations in coral response to physical stressors such as elevated temperature, there is little data directly comparing physiological performance that accounts for symbiont identity associated with the same coral host species. Here, using Pocillopora damicornis harboring genotypically distinct Symbiodiniaceae strains, we examined the physiological responses of the coral holobiont and the dynamics of symbiont community change under thermal stress in a laboratory-controlled experiment.<br><br>RESULTS: We found that P. damicornis dominated with symbionts of metahaplotype D1-D4-D6 in the genus Durusdinium (i.e., PdD holobiont) was more robust to thermal stress than its counterpart with symbionts of metahaplotype C42-C1-C1b-C1c in the genus Cladocopium (i.e., PdC holobiont). Under ambient temperature, however, the thermally sensitive Cladocopium spp. exhibited higher photosynthetic efficiency and translocated more fixed carbon to the host, likely facilitating faster coral growth and calcification. Moreover, we observed a thermally induced increase in Durusdinium proportion in the PdC holobiont; however, this "symbiont shuffling" in the background was overwhelmed by the overall Cladocopium dominance, which coincided with faster coral bleaching and reduced calcification.<br><br>CONCLUSIONS: These findings support that lineage-specific symbiont dominance is a driver of distinct coral responses to thermal stress. In addition, we found that "symbiont shuffling" may begin with stress-forced, subtle changes in the rare biosphere to eventually trade off growth for increased resilience. Furthermore, the flexibility in corals' association with thermally tolerant symbiont lineages to adapt or acclimatize to future warming oceans should be viewed with conservative optimism as the current rate of environmental changes may outpace the evolutionary capabilities of corals. Video Abstract.}, }
@article {pmid37752236, year = {2023}, author = {Roach, TNF and Matsuda, SB and Martin, C and Huckeba, G and Huckeba, J and Kahkejian, V and Santoro, EP and van der Geer, A and Drury, C and Quinn, RA}, title = {Single-polyp metabolomics reveals biochemical structuring of the coral holobiont at multiple scales.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {984}, pmid = {37752236}, issn = {2399-3642}, mesh = {Animals ; *Anthozoa ; Ecosystem ; Metabolomics ; Coral Reefs ; Data Accuracy ; }, abstract = {All biology happens in space, and spatial structuring plays an important role in mediating biological processes at all scales from cells to ecosystems. However, the metabolomic structuring of the coral holobiont has yet to be fully explored. Here, we present a method to detect high-quality metabolomic data from individual coral polyps and apply this method to study the patterning of biochemicals across multiple spatial (~1 mm - ~100 m) and organizational scales (polyp to population). The data show a strong signature for individual coral colonies, a weaker signature of branches within colonies, and variation at the polyp level related to the polyps' location along a branch. Mapping metabolites to either the coral or algal components of the holobiont reveals that polyp-level variation along the length of a branch was largely driven by molecules associated with the cnidarian host as opposed to the algal symbiont, predominantly putative sulfur-containing metabolites. This work yields insights on the spatial structuring of biochemicals in the coral holobiont, which is critical for design, analysis, and interpretation of studies on coral reef biochemistry.}, }
@article {pmid37744040, year = {2023}, author = {Galià-Camps, C and Baños, E and Pascual, M and Carreras, C and Turon, X}, title = {Multidimensional variability of the microbiome of an invasive ascidian species.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107812}, pmid = {37744040}, issn = {2589-0042}, abstract = {Animals, including invasive species, are complex entities consisting of a host and its associated symbionts (holobiont). The interaction between the holobiont components is crucial for the host's survival. However, our understanding of how microbiomes of invasive species change across different tissues, localities, and ontogenetic stages, is limited. In the introduced ascidian Styela plicata, we found that its microbiome is highly distinct and specialized among compartments (tunic, gill, and gut). Smaller but significant differences were also found across harbors, suggesting local adaptation, and between juveniles and adults. Furthermore, we found a correlation between the microbiome and environmental trace element concentrations, especially in adults. Functional analyses showed that adult microbiomes possess specific metabolic pathways that may enhance fitness during the introduction process. These findings highlight the importance of integrated approaches in studying the interplay between animals and microbiomes, as a first step toward understanding how it can affect the species' invasive success.}, }
@article {pmid37731336, year = {2024}, author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A}, title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.}, journal = {Critical reviews in biotechnology}, volume = {44}, number = {6}, pages = {1164-1182}, doi = {10.1080/07388551.2023.2254933}, pmid = {37731336}, issn = {1549-7801}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; }, abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.}, }
@article {pmid37726938, year = {2023}, author = {Markussen Bjorbaekmo, MF and Brodie, J and Krabberød, AK and Logares, R and Fuss, J and Fredriksen, S and Wold-Dobbe, A and Shalchian-Tabrizi, K and Bass, D}, title = {18S rDNA gene metabarcoding of microeukaryotes and epi-endophytes in the holobiome of seven species of large brown algae.}, journal = {Journal of phycology}, volume = {59}, number = {5}, pages = {859-878}, doi = {10.1111/jpy.13377}, pmid = {37726938}, issn = {1529-8817}, support = {//Sunniva og Egil Baardseths legat/ ; }, abstract = {Brown algae (Phaeophyceae) are habitat-forming species in coastal ecosystems and include kelp forests and seaweed beds that support a wide diversity of marine life. Host-associated microbial communities are an integral part of phaeophyte biology, and whereas the bacterial microbial partners have received considerable attention, the microbial eukaryotes associated with brown algae have hardly been studied. Here, we used broadly targeted "pan-eukaryotic" primers (metabarcoding) to investigate brown algal-associated eukaryotes (the eukaryome). Using this approach, we aimed to investigate the eukaryome of seven large brown algae that are important and common species in coastal ecosystems. We also aimed to assess whether these macroalgae harbor novel eukaryotic diversity and to ascribe putative functional roles to the host-associated eukaryome based on taxonomic affiliation and phylogenetic placement. We detected a significant diversity of microeukaryotic and algal lineages associated with the brown algal species investigated. The operational taxonomic units (OTUs) were taxonomically assigned to 10 of the eukaryotic major supergroups, including taxonomic groups known to be associated with seaweeds as epibionts, endobionts, parasites, and commensals. Additionally, we revealed previously unrecorded sequence types, including novel phaeophyte OTUs, particularly in the Fucus spp. samples, that may represent fucoid genomic variants, sequencing artifacts, or undescribed epi-/endophytes. Our results provide baseline data and technical insights that will be useful for more comprehensive seaweed eukaryome studies investigating the evidently lineage-rich and functionally diverse symbionts of brown algae.}, }
@article {pmid37719127, year = {2023}, author = {Castañeda-Molina, Y and Marulanda-Moreno, SM and Saldamando-Benjumea, C and Junca, H and Moreno-Herrera, CX and Cadavid-Restrepo, G}, title = {Microbiome analysis of Spodoptera frugiperda (Lepidoptera, Noctuidae) larvae exposed to Bacillus thuringiensis (Bt) endotoxins.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15916}, pmid = {37719127}, issn = {2167-8359}, mesh = {Animals ; Spodoptera ; Larva ; *Bacillus thuringiensis/genetics ; Endotoxins ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Spodoptera frugiperda (or fall armyworm, FAW) is a polyphagous pest native to Western Hemisphere and recently discovered in the Eastern Hemisphere. In Colombia, S. frugiperda is recognized as a pest of economic importance in corn. The species has genetically differentiated into two host populations named "corn" and "rice" strains. In 2012, a study made in central Colombia demonstrated that the corn strain is less susceptible to Bacillus thuringiensis (Bt) endotoxins (Cry1Ac and Cry 1Ab) than the rice strain. In this country, Bt transgenic corn has been extensively produced over the last 15 years. Since gut microbiota plays a role in the physiology and immunity of insects, and has been implicated in promoting the insecticidal activity of Bt, in this study an analysis of the interaction between Bt endotoxins and FAW gut microbiota was made. Also, the detection of endosymbionts was performed here, as they might have important implications in the biological control of a pest.<br><br>METHODS: The composition and diversity of microbiomes associated with larval specimens of S. frugiperda(corn strain) was investigated in a bioassay based on six treatments in the presence/absence of Bt toxins and antibiotics (Ab) through bacterial isolate analyses and by high throughput sequencing of the bacterial 16S rRNA gene. Additionally, species specific primers were used, to detect endosymbionts from gonads in S. frugiperda corn strain.<br><br>RESULTS: Firmicutes, Proteobacteria and Bacteroidota were the most dominant bacterial phyla found in S. frugiperda corn strain. No significant differences in bacteria species diversity and richness among the six treatments were found. Two species of Enterococcus spp., E. mundtii and E. casseliflavus were detected in treatments with Bt and antibiotics, suggesting that they are less susceptible to both of them. Additionally, the endosymbiont Arsenophonus was also identified on treatments in presence of Bt and antibiotics. The results obtained here are important since little knowledge exists about the gut microbiota on this pest and its interaction with Bt endotoxins. Previous studies made in Lepidoptera suggest that alteration of gut microbiota can be used to improve the management of pest populations, demonstrating the relevance of the results obtained in this work.}, }
@article {pmid37702122, year = {2023}, author = {Rasmussen, L and Fontsere, C and Soto-Calderón, ID and Guillen, R and Savage, A and Hansen, AJ and Hvilsom, C and Gilbert, MTP}, title = {Assessing the genetic composition of cotton-top tamarins (Saguinus oedipus) before sweeping anthropogenic impact.}, journal = {Molecular ecology}, volume = {32}, number = {20}, pages = {5514-5527}, doi = {10.1111/mec.17130}, pmid = {37702122}, issn = {1365-294X}, support = {//Alfred Benzon Foundation/ ; 143//Danmarks Grundforskningsfond/ ; //Torben &amp; Alice Frimodts Fund/ ; }, abstract = {During the last century, the critically endangered cotton-top tamarin (Saguinus oedipus) has been threatened by multiple anthropogenic factors that drastically affected their habitat and population size. As the genetic impact of these pressures is largely unknown, this study aimed to establish a genetic baseline with the use of temporal sampling to determine the genetic makeup before detrimental anthropogenic impact. Genomes were resequenced from a combination of historical museum samples and modern wild samples at low-medium coverage, to unravel how the cotton-top tamarin population structure and genomic diversity may have changed during this period. Our data suggest two populations can be differentiated, probably separated historically by the mountain ranges of the Paramillo Massif in Colombia. Although this population structure persists in the current populations, modern samples exhibit genomic signals consistent with recent inbreeding, such as long runs of homozygosity and a reduction in genome-wide heterozygosity especially in the greater northeast population. This loss is likely the consequence of the population reduction following the mass exportation of cotton-top tamarins for biomedical research in the 1960s, coupled with the habitat loss this species continues to experience. However, current populations have not experienced an increase in genetic load. We propose that the historical genetic baseline established in this study can be used to provide insight into alteration in the modern population influenced by a drastic reduction in population size as well as providing background information to be used for future conservation decision-making for the species.}, }
@article {pmid37702036, year = {2023}, author = {Peng, L and Hoban, J and Joffe, J and Smith, AH and Carpenter, M and Marcelis, T and Patel, V and Lynn-Bell, N and Oliver, KM and Russell, JA}, title = {Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {12}, pages = {1712-1730}, doi = {10.1111/jeb.14216}, pmid = {37702036}, issn = {1420-9101}, support = {1050098//National Science Foundation/ ; 1050128//National Science Foundation/ ; 1754302//National Science Foundation/ ; 1754597//National Science Foundation/ ; }, mesh = {Animals ; *Aphids/genetics/microbiology ; Pisum sativum ; *Coinfection ; Biotin ; *Gammaproteobacteria ; *Coxiellaceae/genetics ; Symbiosis/genetics ; }, abstract = {Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.}, }
@article {pmid37694134, year = {2023}, author = {Williams, A and Stephens, TG and Shumaker, A and Bhattacharya, D}, title = {Peeling back the layers of coral holobiont multi-omics data.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107623}, pmid = {37694134}, issn = {2589-0042}, abstract = {The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge and resources, its application to non-model organisms, such as coral holobionts, is less clear-cut. We explore, in the emerging rice coral model Montipora capitata, the intersection of holobiont transcriptomic, proteomic, metabolomic, and microbiome amplicon data and investigate how well they correlate under high temperature treatment. Using a typical thermal stress regime, we show that transcriptomic and proteomic data broadly capture the stress response of the coral, whereas the metabolome and microbiome datasets show patterns that likely reflect stochastic and homeostatic processes associated with each sample. These results provide a framework for interpreting multi-omics data generated from non-model systems, particularly those with complex biotic interactions among microbial partners.}, }
@article {pmid37692426, year = {2023}, author = {Senizza, B and Araniti, F and Lewin, S and Wende, S and Kolb, S and Lucini, L}, title = {Trichoderma spp.-mediated mitigation of heat, drought, and their combination on the Arabidopsis thaliana holobiont: a metabolomics and metabarcoding approach.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1190304}, pmid = {37692426}, issn = {1664-462X}, abstract = {INTRODUCTION: The use of substances to increase productivity and resource use efficiency is now essential to face the challenge of feeding the rising global population with the less environmental impact on the ecosystems. Trichoderma-based products have been used as biopesticides, to inhibit pathogenic microorganisms, and as biostimulants for crop growth, nutrient uptake promotion, and resistance to abiotic stresses.<br><br>METHODS: In this work, plant metabolomics combined with roots and rhizosphere bacterial metabarcoding were exploited to inspect the performance of Trichoderma spp. biostimulants on Arabidopsis thaliana under drought, heat and their combination and its impact on plant holobiont.<br><br>RESULTS AND DISCUSSION: An overall modulation of N-containing compounds, phenylpropanoids, terpenes and hormones could be pointed out by metabolomics. Moreover, metabarcoding outlined an impact on alpha and beta-diversity with an abundance of Proteobacteria, Pseudomonadales, Burkholderiales, Enterobacteriales and Azospirillales. A holobiont approach was applied as an integrated analytical strategy to resolve the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria using Arabidopsis thaliana as a model host species.}, }
@article {pmid37670990, year = {2023}, author = {Pérez-Llano, Y and Yarzábal Rodríguez, LA and Martínez-Romero, E and Dobson, ADW and Gunde-Cimerman, N and Vasconcelos, V and Batista-García, RA}, title = {From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213340}, pmid = {37670990}, issn = {1664-302X}, }
@article {pmid37669892, year = {2023}, author = {Hellal, J and Lise, B and Annette, B and Aurélie, C and Giulia, C and Simon, C and Cristiana, CL and Caroline, C and Nicolas, G and Marina, H and Fabrice, ML and Jean, M and Soizic, M and Carmen, P and Stéphane, P and Agnès, R and Stéphane, V}, title = {Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {10}, pages = {}, pmid = {37669892}, issn = {1574-6941}, mesh = {Ecotoxicology ; *Environmental Pollutants/toxicity ; Environmental Pollution ; *Environmental Restoration and Remediation ; Risk Assessment ; }, abstract = {Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.}, }
@article {pmid37664515, year = {2023}, author = {Hill, CEL and Abbass, SG and Caporale, G and El-Khaled, YC and Kuhn, L and Schlenzig, T and Wild, C and Tilstra, A}, title = {Physiology of the widespread pulsating soft coral Xenia umbellata is affected by food sources, but not by water flow.}, journal = {Ecology and evolution}, volume = {13}, number = {9}, pages = {e10483}, pmid = {37664515}, issn = {2045-7758}, abstract = {Coral energy and nutrient acquisition strategies are complex and sensitive to environmental conditions such as water flow. While high water flow can enhance feeding in hard corals, knowledge about the effects of water flow on the feeding of soft corals, particularly those pulsating, is still limited. In this study, we thus investigated the effects of feeding and water flow on the physiology of the pulsating soft coral Xenia umbellata. We crossed three feeding treatments: (i) no feeding, (ii) particulate organic matter (POM) in the form of phytoplankton and (iii) dissolved organic carbon (DOC) in the form of glucose, with four water volume exchange rates (200, 350, 500 and 650 L h[-1]) over 15 days. Various ecophysiological parameters were assessed including pulsation rate, growth rate, isotopic and elemental ratios of carbon (C) and nitrogen (N) as well as photo-physiological parameters of the Symbiodiniaceae (cell density, chlorophyll-a and mitotic index). Water flow had no significant effect but feeding had a substantial impact on the physiology of the X. umbellata holobiont. In the absence of food, corals exhibited significantly lower pulsation rates, lower Symbiodiniaceae cell density and lower mitotic indices compared to the fed treatments, yet significantly higher chlorophyll-a per cell and total N content. Differences were also observed between the two feeding treatments, with significantly higher pulsation rates and lower chlorophyll-a per cell in the DOC treatment, but higher C and N content in the POM treatment. Our findings suggest that the X. umbellata holobiont can be viable under different trophic strategies, though favouring mixotrophy. Additionally, the physiology of the X. umbellata may be regulated through its own pulsating behaviour without any positive or negative effects from different water flow. Therefore, this study contributes to our understanding of soft coral ecology, particularly regarding the competitive success and widespread distribution of X. umbellata.}, }
@article {pmid37653089, year = {2023}, author = {Mannochio-Russo, H and Swift, SOI and Nakayama, KK and Wall, CB and Gentry, EC and Panitchpakdi, M and Caraballo-Rodriguez, AM and Aron, AT and Petras, D and Dorrestein, K and Dorrestein, TK and Williams, TM and Nalley, EM and Altman-Kurosaki, NT and Martinelli, M and Kuwabara, JY and Darcy, JL and Bolzani, VS and Wegley Kelly, L and Mora, C and Yew, JY and Amend, AS and McFall-Ngai, M and Hynson, NA and Dorrestein, PC and Nelson, CE}, title = {Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {896}, pmid = {37653089}, issn = {2399-3642}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Coral Reefs ; Symbiosis ; Metabolome ; *Anthozoa ; *Microbiota ; *Seaweed ; }, abstract = {The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, O'ahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.}, }
@article {pmid37652999, year = {2023}, author = {Sun, X and Liu, YC and Tiunov, MP and Gimranov, DO and Zhuang, Y and Han, Y and Driscoll, CA and Pang, Y and Li, C and Pan, Y and Velasco, MS and Gopalakrishnan, S and Yang, RZ and Li, BG and Jin, K and Xu, X and Uphyrkina, O and Huang, Y and Wu, XH and Gilbert, MTP and O'Brien, SJ and Yamaguchi, N and Luo, SJ}, title = {Ancient DNA reveals genetic admixture in China during tiger evolution.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {11}, pages = {1914-1929}, pmid = {37652999}, issn = {2397-334X}, support = {NSFC32070598//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18-04-00327//Russian Foundation for Basic Research (RFBR)/ ; }, mesh = {Animals ; *Tigers/genetics ; DNA, Ancient ; Phylogeny ; Russia ; China ; }, abstract = {The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.}, }
@article {pmid37650630, year = {2023}, author = {Koziol, A and Odriozola, I and Leonard, A and Eisenhofer, R and San José, C and Aizpurua, O and Alberdi, A}, title = {Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0160623}, pmid = {37650630}, issn = {2150-7511}, support = {R250-2017-1351//Lundbeck Foundation (Lundbeckfonden)/ ; DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; Mammals ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.}, }
@article {pmid37647612, year = {2024}, author = {Zhou, K and Zhang, T and Chen, XW and Xu, Y and Zhang, R and Qian, PY}, title = {Viruses in Marine Invertebrate Holobionts: Complex Interactions Between Phages and Bacterial Symbionts.}, journal = {Annual review of marine science}, volume = {16}, number = {}, pages = {467-485}, doi = {10.1146/annurev-marine-021623-093133}, pmid = {37647612}, issn = {1941-0611}, mesh = {Animals ; *Bacteriophages ; Invertebrates ; Bacteria ; *Viruses ; *Anthozoa/microbiology ; Aquatic Organisms ; }, abstract = {Marine invertebrates are ecologically and economically important and have formed holobionts by evolving symbiotic relationships with cellular and acellular microorganisms that reside in and on their tissues. In recent decades, significant focus on symbiotic cellular microorganisms has led to the discovery of various functions and a considerable expansion of our knowledge of holobiont functions. Despite this progress, our understanding of symbiotic acellular microorganisms remains insufficient, impeding our ability to achieve a comprehensive understanding of marine holobionts. In this review, we highlight the abundant viruses, with a particular emphasis on bacteriophages; provide an overview of their diversity, especially in extensively studied sponges and corals; and examine their potential life cycles. In addition, we discuss potential phage-holobiont interactions of various invertebrates, including participating in initial bacterial colonization, maintaining symbiotic relationships, and causing or exacerbating the diseases of marine invertebrates. Despite the importance of this subject, knowledge of how viruses contribute to marine invertebrate organisms remains limited. Advancements in technology and greater attention to viruses will enhance our understanding of marine invertebrate holobionts.}, }
@article {pmid37645461, year = {2023}, author = {Zuzolo, D and Ranauda, MA and Maisto, M and Tartaglia, M and Prigioniero, A and Falzarano, A and Marotta, G and Sciarrillo, R and Guarino, C}, title = {The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1205451}, pmid = {37645461}, issn = {1664-462X}, abstract = {The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.}, }
@article {pmid37638757, year = {2023}, author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L}, title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.}, journal = {Nucleic acids research}, volume = {51}, number = {18}, pages = {9785-9803}, pmid = {37638757}, issn = {1362-4962}, support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Sk&#x142;odowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; }, abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.}, }
@article {pmid37626434, year = {2023}, author = {Kelliher, JM and Robinson, AJ and Longley, R and Johnson, LYD and Hanson, BT and Morales, DP and Cailleau, G and Junier, P and Bonito, G and Chain, PSG}, title = {The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {192}, pmid = {37626434}, issn = {2049-2618}, mesh = {*Multiomics ; Data Analysis ; Eukaryota ; *Microbiota/genetics ; Prokaryotic Cells ; }, abstract = {As microbiome research has progressed, it has become clear that most, if not all, eukaryotic organisms are hosts to microbiomes composed of prokaryotes, other eukaryotes, and viruses. Fungi have only recently been considered holobionts with their own microbiomes, as filamentous fungi have been found to harbor bacteria (including cyanobacteria), mycoviruses, other fungi, and whole algal cells within their hyphae. Constituents of this complex endohyphal microbiome have been interrogated using multi-omic approaches. However, a lack of tools, techniques, and standardization for integrative multi-omics for small-scale microbiomes (e.g., intracellular microbiomes) has limited progress towards investigating and understanding the total diversity of the endohyphal microbiome and its functional impacts on fungal hosts. Understanding microbiome impacts on fungal hosts will advance explorations of how "microbiomes within microbiomes" affect broader microbial community dynamics and ecological functions. Progress to date as well as ongoing challenges of performing integrative multi-omics on the endohyphal microbiome is discussed herein. Addressing the challenges associated with the sample extraction, sample preparation, multi-omic data generation, and multi-omic data analysis and integration will help advance current knowledge of the endohyphal microbiome and provide a road map for shrinking microbiome investigations to smaller scales. Video Abstract.}, }
@article {pmid37626254, year = {2023}, author = {Hussain, A and Kumar, SHK and Prathiviraj, R and Kumar, AA and Renjith, K and Kiran, GS and Selvin, J}, title = {The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India.}, journal = {Archives of microbiology}, volume = {205}, number = {9}, pages = {319}, pmid = {37626254}, issn = {1432-072X}, support = {BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR40420/NDB/39/741/2020.//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Coral Reefs ; Ecosystem ; Bays ; *Anthozoa ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; India ; }, abstract = {An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.}, }
@article {pmid37625782, year = {2023}, author = {Prabhakaran, P and Nazir, MYM and Thananusak, R and Hamid, AA and Vongsangnak, W and Song, Y}, title = {Uncovering global lipid accumulation routes towards docosahexaenoic acid (DHA) production in Aurantiochytrium sp. SW1 using integrative proteomic analysis.}, journal = {Biochimica et biophysica acta. Molecular and cell biology of lipids}, volume = {1868}, number = {11}, pages = {159381}, doi = {10.1016/j.bbalip.2023.159381}, pmid = {37625782}, issn = {1879-2618}, mesh = {*Docosahexaenoic Acids/metabolism ; Acetyl Coenzyme A/metabolism ; Proteomics ; *Stramenopiles/genetics/metabolism ; Gene Expression Profiling ; }, abstract = {Aurantiochytrium sp., a marine thraustochytrid possesses a remarkable ability to produce lipid rich in polyunsaturated fatty acids (PUFAs), such as docosahexaenoic acid (DHA). Although gene regulation underlying lipid biosynthesis has been previously reported, proteomic analysis is still limited. In this study, high DHA accumulating strain Aurantiochytrium sp. SW1 has been used as a study model to elucidate the alteration in proteome profile under different cultivation phases i.e. growth, nitrogen-limitation and lipid accumulation. Of the total of 5146 identified proteins, 852 proteins were differentially expressed proteins (DEPs). The largest number of DEPs (488 proteins) was found to be uniquely expressed between lipid accumulating phase and growth phase. Interestingly, there were up-regulated proteins involved in glycolysis, glycerolipid, carotenoid and glutathione metabolism which were preferable metabolic routes towards lipid accumulation and DHA production as well as cellular oxidative defence. Integrated proteomic and transcriptomic data were also conducted to comprehend the gene and protein regulation underlying the lipid and DHA biosynthesis. A significant up-regulation of acetyl-CoA synthetase was observed which suggests alternative route of acetate metabolism for acetyl-CoA producer. This study presents the holistic routes underlying lipid accumulation and DHA production in Aurantiochytrium sp. SW1 and other relevant thraustochytrid.}, }
@article {pmid37623217, year = {2023}, author = {Petrushin, IS and Vasilev, IA and Markova, YA}, title = {Drought Tolerance of Legumes: Physiology and the Role of the Microbiome.}, journal = {Current issues in molecular biology}, volume = {45}, number = {8}, pages = {6311-6324}, pmid = {37623217}, issn = {1467-3045}, support = {23-26-00204//Russian Science Foundation/ ; }, abstract = {Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering-a promising biotech strategy to improve the yield and stress-resistance of legumes.}, }
@article {pmid37609337, year = {2023}, author = {Yee, SW and Ferrández-Peral, L and Alentorn, P and Fontsere, C and Ceylan, M and Koleske, ML and Handin, N and Artegoitia, VM and Lara, G and Chien, HC and Zhou, X and Dainat, J and Zalevsky, A and Sali, A and Brand, CM and Capra, JA and Artursson, P and Newman, JW and Marques-Bonet, T and Giacomini, KM}, title = {Illuminating the Function of the Orphan Transporter, SLC22A10 in Humans and Other Primates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37609337}, issn = {2692-8205}, support = {R01 GM117163/GM/NIGMS NIH HHS/United States ; R01 GM139875/GM/NIGMS NIH HHS/United States ; R35 GM127087/GM/NIGMS NIH HHS/United States ; }, abstract = {SLC22A10 is classified as an orphan transporter with unknown substrates and function. Here we describe the discovery of the substrate specificity and functional characteristics of SLC22A10. The human SLC22A10 tagged with green fluorescent protein was found to be absent from the plasma membrane, in contrast to the SLC22A10 orthologs found in great apes. Estradiol-17β-glucuronide accumulated in cells expressing great ape SLC22A10 orthologs (over 4-fold, p<0.001). In contrast, human SLC22A10 displayed no uptake function. Sequence alignments revealed two amino acid differences including a proline at position 220 of the human SLC22A10 and a leucine at the same position of great ape orthologs. Site-directed mutagenesis yielding the human SLC22A10-P220L produced a protein with excellent plasma membrane localization and associated uptake function. Neanderthal and Denisovan genomes show human-like sequences at proline 220 position, corroborating that SLC22A10 were rendered nonfunctional during hominin evolution after the divergence from the pan lineage (chimpanzees and bonobos). These findings demonstrate that human SLC22A10 is a unitary pseudogene and was inactivated by a missense mutation that is fixed in humans, whereas orthologs in great apes transport sex steroid conjugates.}, }
@article {pmid37604380, year = {2023}, author = {Yu, X and Yu, K and Liao, Z and Chen, B and Qin, Z and Liang, J and Gao, X}, title = {Adaptation strategies of relatively high-latitude marginal reef corals in response to severe temperature fluctuations.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166439}, doi = {10.1016/j.scitotenv.2023.166439}, pmid = {37604380}, issn = {1879-1026}, abstract = {The large seasonal temperature fluctuations caused by global warming and frequent marine heatwaves pose new challenges to survival of relatively high-latitude marginal reef corals. However, the adaptation strategies of high-latitude marginal corals are not fully understood. We employed integrated approach to investigate the response mechanism of hosts, Symbiodiniaceae, and symbiotic bacteria of marginal reef corals Acropora pruinosa and Pavona decussate in response to large seasonal temperature fluctuations. The coral holobiont maintained a high level of immunity to adapt to seasonal pressure by increasing Symbiodiniaceae energy supply. The symbiotic Symbiodiniaceae of two coral was dominated by C1 subgroup, and was stable across seasons. The α-diversity of symbiotic bacteria P. decussata and A. pruinosa in summer was higher than that in winter. The symbiotic bacterial community of two coral reorganized during different seasons. Scleractinian corals improve adaptability to seasonal stress by increasing energy supply to maintain high levels of immunity, increasing symbiotic bacterial α-diversity, and changing dominant bacteria. This study demonstrates the adaptation strategies of marginal reef corals to seasonal temperature fluctuations and provides novel insights into the study of the adaptation of corals and relatively high-latitude coral refuges in the context of global warming and intensified marine heatwaves.}, }
@article {pmid37601769, year = {2023}, author = {Mochales-Riaño, G and Fontsere, C and de Manuel, M and Talavera, A and Burriel-Carranza, B and Tejero-Cicuéndez, H and AlGethami, RHM and Shobrak, M and Marques-Bonet, T and Carranza, S}, title = {Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard (Panthera pardus nimr).}, journal = {iScience}, volume = {26}, number = {9}, pages = {107481}, pmid = {37601769}, issn = {2589-0042}, abstract = {In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.}, }
@article {pmid37601376, year = {2023}, author = {Caetano-Anollés, G and Claverie, JM and Nasir, A}, title = {A critical analysis of the current state of virus taxonomy.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1240993}, pmid = {37601376}, issn = {1664-302X}, abstract = {Taxonomical classification has preceded evolutionary understanding. For that reason, taxonomy has become a battleground fueled by knowledge gaps, technical limitations, and a priorism. Here we assess the current state of the challenging field, focusing on fallacies that are common in viral classification. We emphasize that viruses are crucial contributors to the genomic and functional makeup of holobionts, organismal communities that behave as units of biological organization. Consequently, viruses cannot be considered taxonomic units because they challenge crucial concepts of organismality and individuality. Instead, they should be considered processes that integrate virions and their hosts into life cycles. Viruses harbor phylogenetic signatures of genetic transfer that compromise monophyly and the validity of deep taxonomic ranks. A focus on building phylogenetic networks using alignment-free methodologies and molecular structure can help mitigate the impasse, at least in part. Finally, structural phylogenomic analysis challenges the polyphyletic scenario of multiple viral origins adopted by virus taxonomy, defeating a polyphyletic origin and supporting instead an ancient cellular origin of viruses. We therefore, prompt abandoning deep ranks and urgently reevaluating the validity of taxonomic units and principles of virus classification.}, }
@article {pmid37587369, year = {2023}, author = {Gavriilidou, A and Avcı, B and Galani, A and Schorn, MA and Ingham, CJ and Ettema, TJG and Smidt, H and Sipkema, D}, title = {Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1808-1818}, pmid = {37587369}, issn = {1751-7370}, mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; In Situ Hybridization, Fluorescence ; Bacteria/genetics ; Metagenome ; }, abstract = {Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.}, }
@article {pmid37586539, year = {2023}, author = {He, R and Hu, S and Li, Q and Zhao, D and Wu, QL and Zeng, J}, title = {Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166229}, doi = {10.1016/j.scitotenv.2023.166229}, pmid = {37586539}, issn = {1879-1026}, abstract = {Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.}, }
@article {pmid37580830, year = {2023}, author = {Tignat-Perrier, R and van de Water, JAJM and Allemand, D and Ferrier-Pagès, C}, title = {Holobiont responses of mesophotic precious red coral Corallium rubrum to thermal anomalies.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {70}, pmid = {37580830}, issn = {2524-6372}, abstract = {Marine heat waves (MHWs) have increased in frequency and intensity worldwide, causing mass mortality of benthic organisms and loss of biodiversity in shallow waters. The Mediterranean Sea is no exception, with shallow populations of habitat-forming octocorals facing the threat of local extinction. The mesophotic zone, which is less affected by MHWs, may be of ecological importance in conservation strategies for these species. However, our understanding of the response of mesophotic octocoral holobionts to changes in seawater temperature remains limited. To address this knowledge gap, we conducted a study on an iconic Mediterranean octocoral, the red coral Corallium rubrum sampled at 60 m depth and 15 °C. We exposed the colonies to temperatures they occasionally experience (18 °C) and temperatures that could occur at the end of the century if global warming continues (21 °C). We also tested their response to extremely cold and warm temperatures (12 °C and 24 °C). Our results show a high tolerance of C. rubrum to a two-month long exposure to temperatures ranging from 12 to 21 °C as no colony showed signs of tissue loss, reduced feeding ability, stress-induced gene expression, or disruption of host-bacterial symbioses. At 24 °C, however, we measured a sharp decrease in the relative abundance of Spirochaetaceae, which are the predominant bacterial symbionts under healthy conditions, along with a relative increase in Vibrionaceae. Tissue loss and overexpression of the tumor necrosis factor receptor 1 gene were also observed after two weeks of exposure. In light of ongoing global warming, our study helps predict the consequences of MHWs on mesophotic coralligenous reefs and the biodiversity that depends on them.}, }
@article {pmid37570868, year = {2023}, author = {Ujlaki, G and Kovács, T and Vida, A and Kókai, E and Rauch, B and Schwarcz, S and Mikó, E and Janka, E and Sipos, A and Hegedűs, C and Uray, K and Nagy, P and Bai, P}, title = {Identification of Bacterial Metabolites Modulating Breast Cancer Cell Proliferation and Epithelial-Mesenchymal Transition.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {15}, pages = {}, pmid = {37570868}, issn = {1420-3049}, support = {K123975//National Research, Development and Innovation Office/ ; K124141//National Research, Development and Innovation Office/ ; FK128387//National Research, Development and Innovation Office/ ; TKP2021-EGA-19//National Research, Development and Innovation Office/ ; TKP2021-EGA-20//National Research, Development and Innovation Office/ ; POST-COVID2021-33//Hungarian Academy of Sciences/ ; }, mesh = {Humans ; Animals ; Mice ; Female ; *Breast Neoplasms/drug therapy/metabolism ; Epithelial-Mesenchymal Transition ; *Cytostatic Agents/pharmacology ; Butyric Acid/pharmacology ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology/therapeutic use ; Cell Proliferation ; }, abstract = {Breast cancer patients are characterized by the oncobiotic transformation of multiple microbiome communities, including the gut microbiome. Oncobiotic transformation of the gut microbiome impairs the production of antineoplastic bacterial metabolites. The goal of this study was to identify bacterial metabolites with antineoplastic properties. We constructed a 30-member bacterial metabolite library and screened the library compounds for effects on cell proliferation and epithelial-mesenchymal transition. The metabolites were applied to 4T1 murine breast cancer cells in concentrations corresponding to the reference serum concentrations. However, yric acid, glycolic acid, d-mannitol, 2,3-butanediol, and trans-ferulic acid exerted cytostatic effects, and 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, and vanillic acid exerted hyperproliferative effects. Furthermore, 3-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, 2,3-butanediol, and hydrocinnamic acid inhibited epithelial-to-mesenchymal (EMT) transition. We identified redox sets among the metabolites (d-mannitol-d-mannose, 1-butanol-butyric acid, ethylene glycol-glycolic acid-oxalic acid), wherein only one partner within the set (d-mannitol, butyric acid, glycolic acid) possessed bioactivity in our system, suggesting that changes to the local redox potential may affect the bacterial secretome. Of the nine bioactive metabolites, 2,3-butanediol was the only compound with both cytostatic and anti-EMT properties.}, }
@article {pmid37559898, year = {2023}, author = {Ciucani, MM and Ramos-Madrigal, J and Hernández-Alonso, G and Carmagnini, A and Aninta, SG and Sun, X and Scharff-Olsen, CH and Lanigan, LT and Fracasso, I and Clausen, CG and Aspi, J and Kojola, I and Baltrūnaitė, L and Balčiauskas, L and Moore, J and Åkesson, M and Saarma, U and Hindrikson, M and Hulva, P and Bolfíková, B&#x10c; and Nowak, C and Godinho, R and Smith, S and Paule, L and Nowak, S and Mysłajek, RW and Lo Brutto, S and Ciucci, P and Boitani, L and Vernesi, C and Stenøien, HK and Smith, O and Frantz, L and Rossi, L and Angelici, FM and Cilli, E and Sinding, MS and Gilbert, MTP and Gopalakrishnan, S}, title = {The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs.}, journal = {iScience}, volume = {26}, number = {8}, pages = {107307}, pmid = {37559898}, issn = {2589-0042}, abstract = {The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.}, }
@article {pmid37552896, year = {2024}, author = {González-Pech, RA and Li, VY and Garcia, V and Boville, E and Mammone, M and Kitano, H and Ritchie, KB and Medina, M}, title = {The Evolution, Assembly, and Dynamics of Marine Holobionts.}, journal = {Annual review of marine science}, volume = {16}, number = {}, pages = {443-466}, doi = {10.1146/annurev-marine-022123-104345}, pmid = {37552896}, issn = {1941-0611}, mesh = {*Biodiversity ; *Symbiosis ; }, abstract = {The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.}, }
@article {pmid37550887, year = {2024}, author = {Hernández, M and Hereira-Pacheco, S and Alberdi, A and Díaz DE LA Vega-Pérez, AH and Estrada-Torres, A and Ancona, S and Navarro-Noya, YE}, title = {DNA metabarcoding reveals seasonal changes in diet composition across four arthropod-eating lizard species (Phrynosomatidae: Sceloporus).}, journal = {Integrative zoology}, volume = {19}, number = {3}, pages = {480-495}, doi = {10.1111/1749-4877.12755}, pmid = {37550887}, issn = {1749-4877}, support = {//Consejo Nacional de Ciencia y Tecnolog&#xed;a (CONACyT)/ ; 205945//Infraestructura project/ ; 137748//Ciencia de Frontera project/ ; 883//C&#xe1;tedras CONACyT project/ ; //Universidad Nacional Aut&#xf3;noma de M&#xe9;xico (UNAM)/ ; }, mesh = {Animals ; *Lizards/physiology ; *Seasons ; *Diet/veterinary ; *DNA Barcoding, Taxonomic ; Arthropods/physiology/genetics ; Species Specificity ; Phylogeny ; Feeding Behavior ; }, abstract = {Diet composition and its ecological drivers are rarely investigated in coexisting closely related species. We used a molecular approach to characterize the seasonal variation in diet composition in four spiny lizard species inhabiting a mountainous ecosystem. DNA metabarcoding revealed that the lizards Sceloporus aeneus, S. bicanthalis, S. grammicus, and S. spinosus mostly consumed arthropods of the orders Hemiptera, Araneae, Hymenoptera, and Coleoptera. The terrestrial lizards S. aeneus and S. bicanthalis mostly predated ants and spiders, whereas the arboreal-saxicolous S. grammicus and saxicolous S. spinosus largely consumed grasshoppers and leafhoppers. The taxonomic and phylogenetic diversity of the prey was higher during the dry season than the rainy season, likely because reduced prey availability in the dry season forced lizards to diversify their diets to meet their nutritional demands. Dietary and phylogenetic composition varied seasonally depending on the species, but only dietary composition varied with altitude. Seasonal dietary turnover was greater in S. spinosus than in S. bicanthalis, suggesting site-specific seasonal variability in prey availability; no other differences among species were observed. S. bicanthalis, which lives at the highest altitude in our study site, displayed interseasonal variation in diet breadth. Dietary differences were correlated with the species' feeding strategies and elevational distribution, which likely contributed to the coexistence of these lizard species in the studied geographic area and beyond.}, }
@article {pmid37549265, year = {2023}, author = {Hung, TH and So, T and Thammavong, B and Chamchumroon, V and Theilade, I and Phourin, C and Bouamanivong, S and Hartvig, I and Gaisberger, H and Jalonen, R and Boshier, DH and MacKay, JJ}, title = {Range-wide differential adaptation and genomic offset in critically endangered Asian rosewoods.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {33}, pages = {e2301603120}, pmid = {37549265}, issn = {1091-6490}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Adaptation, Physiological/genetics ; *Acclimatization/genetics ; Genomics ; Climate Change ; }, abstract = {In the billion-dollar global illegal wildlife trade, rosewoods have been the world's most trafficked wild product since 2005. Dalbergia cochinchinensis and Dalbergia oliveri are the most sought-after rosewoods in the Greater Mekong Subregion. They are exposed to significant genetic risks and the lack of knowledge on their adaptability limits the effectiveness of conservation efforts. Here, we present genome assemblies and range-wide genomic scans of adaptive variation, together with predictions of genomic offset to climate change. Adaptive genomic variation was differentially associated with temperature and precipitation-related variables between the species, although their natural ranges overlap. The findings are consistent with differences in pioneering ability and in drought tolerance. We predict their genomic offsets will increase over time and with increasing carbon emission pathway but at a faster pace in D. cochinchinensis than in D. oliveri. These results and the distinct gene-environment association in the eastern coastal edge of Vietnam suggest species-specific conservation actions: germplasm representation across the range in D. cochinchinensis and focused on hotspots of genomic offset in D. oliveri. We translated our genomic models into a seed source matching application, seedeR, to rapidly inform restoration efforts. Our ecological genomic research uncovering contrasting selection forces acting in sympatric rosewoods is of relevance to conserving tropical trees globally and combating risks from climate change.}, }
@article {pmid37548791, year = {2023}, author = {Rotini, A and Conte, C and Winters, G and Vasquez, MI and Migliore, L}, title = {Undisturbed Posidonia oceanica meadows maintain the epiphytic bacterial community in different environments.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {42}, pages = {95464-95474}, pmid = {37548791}, issn = {1614-7499}, support = {COST-STSM- CA15121-39495//COST Action CA 15121 Mar Cons/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/analysis ; *Alismatales/chemistry ; Bacteria ; Plant Leaves/chemistry ; Enterobacteriaceae ; Mediterranean Sea ; }, abstract = {Seagrasses harbour different and rich epiphytic bacterial communities. These microbes may establish intimate and symbiotic relationships with the seagrass plants and change according to host species, environmental conditions, and/or ecophysiological status of their seagrass host. Although Posidonia oceanica is one of the most studied seagrasses in the world, and bacteria associated with seagrasses have been studied for over a decade, P. oceanica's microbiome remains hitherto little explored. Here, we applied 16S rRNA amplicon sequencing to explore the microbiome associated with the leaves of P. oceanica growing in two geomorphologically different meadows (e.g. depth, substrate, and turbidity) within the Limassol Bay (Cyprus). The morphometric (leaf area, meadow density) and biochemical (pigments, total phenols) descriptors highlighted the healthy conditions of both meadows. The leaf-associated bacterial communities showed similar structure and composition in the two sites; core microbiota members were dominated by bacteria belonging to the Thalassospiraceae, Microtrichaceae, Enterobacteriaceae, Saprospiraceae, and Hyphomonadaceae families. This analogy, even under different geomorphological conditions, suggest that in the absence of disturbances, P. oceanica maintains characteristic-associated bacterial communities. This study provides a baseline for the knowledge of the P. oceanica microbiome and further supports its use as a putative seagrass descriptor.}, }
@article {pmid37546572, year = {2023}, author = {Hernández-Alonso, G and Ramos-Madrigal, J and Sun, X and Scharff-Olsen, CH and Sinding, MS and Martins, NF and Ciucani, MM and Mak, SST and Lanigan, LT and Clausen, CG and Bhak, J and Jeon, S and Kim, C and Eo, KY and Cho, SH and Boldgiv, B and Gantulga, G and Unudbayasgalan, Z and Kosintsev, PA and Stenøien, HK and Gilbert, MTP and Gopalakrishnan, S}, title = {Conservation implications of elucidating the Korean wolf taxonomic ambiguity through whole-genome sequencing.}, journal = {Ecology and evolution}, volume = {13}, number = {8}, pages = {e10404}, pmid = {37546572}, issn = {2045-7758}, abstract = {The taxonomic status of the now likely extirpated Korean Peninsula wolf has been extensively debated, with some arguing it represents an independent wolf lineage, Canis coreanus. To investigate the Korean wolf's genetic affiliations and taxonomic status, we sequenced and analysed the genomes of a Korean wolf dated to the beginning of the 20th century, and a captive wolf originally from the Pyongyang Central Zoo. Our results indicated that the Korean wolf bears similar genetic ancestry to other regional East Asian populations, therefore suggesting it is not a distinct taxonomic lineage. We identified regional patterns of wolf population structure and admixture in East Asia with potential conservation consequences in the Korean Peninsula and on a regional scale. We find that the Korean wolf has similar genomic diversity and inbreeding to other East Asian wolves. Finally, we show that, in contrast to the historical sample, the captive wolf is genetically more similar to wolves from the Tibetan Plateau; hence, Korean wolf conservation programmes might not benefit from the inclusion of this specimen.}, }
@article {pmid37540022, year = {2023}, author = {Balasubramaniam, HM and Tze Yan, F and Michelle JiaMin, L and Parimannan, S and Mutusamy, P and Jaya Jothi, S and Rajandas, H}, title = {Genome characterization of Dickeya solani bacteriophage W2B.}, journal = {Microbiology resource announcements}, volume = {12}, number = {9}, pages = {e0045223}, pmid = {37540022}, issn = {2576-098X}, support = {FRGS/1/2021/STG01/AIMST/03/1//Ministry of Higher Education Malaysia/ ; }, abstract = {We have successfully characterized the complete genome sequence of the lytic Dickeya solani bacteriophage W2B, isolated from the Bunus Sewage Treatment Plant. The lytic phage from the Ningirsuvirus family has a 40,385-bp linear double-stranded DNA genome containing 51 coding sequences (CDSs).}, }
@article {pmid37530752, year = {2023}, author = {Jiménez-Guerrero, I and López-Baena, FJ and Borrero-de Acuña, JM and Pérez-Montaño, F}, title = {Membrane vesicle engineering with "à la carte" bacterial-immunogenic molecules for organism-free plant vaccination.}, journal = {Microbial biotechnology}, volume = {16}, number = {12}, pages = {2223-2235}, pmid = {37530752}, issn = {1751-7915}, support = {EMERGIA20_00048//Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n, Ciencia y Empleo, Junta de Andaluc&#xed;a/ ; ProyExcel_00450//Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n, Ciencia y Empleo, Junta de Andaluc&#xed;a/ ; //European Union NextGenerationEU/PRTR/ ; PID2019-107634RB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2020-118279R (MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; PID2021-122395OA-I00 (MCIN/AEI/ 10.13039/501100011)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; TED2021-130357B-I00 (MCIN/AEI/ 10.13039/5011000110)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; }, mesh = {Humans ; *Plant Development/physiology ; *Plants/microbiology ; Agriculture/methods ; Soil ; Crop Production ; Antigens, Bacterial ; }, abstract = {The United Nations heralds a world population exponential increase exceeding 9.7 billion by 2050. This poses the challenge of covering the nutritional needs of an overpopulated world by the hand of preserving the environment. Extensive agriculture practices harnessed the employment of fertilizers and pesticides to boost crop productivity and prevent economic and harvest yield losses attributed to plagues and diseases. Unfortunately, the concomitant hazardous effects stemmed from such agriculture techniques are cumbersome, that is, biodiversity loss, soils and waters contaminations, and human and animal poisoning. Hence, the so-called 'green agriculture' research revolves around designing novel biopesticides and plant growth-promoting bio-agents to the end of curbing the detrimental effects. In this field, microbe-plant interactions studies offer multiple possibilities for reshaping the plant holobiont physiology to its benefit. Along these lines, bacterial extracellular membrane vesicles emerge as an appealing molecular tool to capitalize on. These nanoparticles convey a manifold of molecules that mediate intricate bacteria-plant interactions including plant immunomodulation. Herein, we bring into the spotlight bacterial extracellular membrane vesicle engineering to encase immunomodulatory effectors into their cargo for their application as biocontrol agents. The overarching goal is achieving plant priming by deploying its innate immune responses thereby preventing upcoming infections.}, }
@article {pmid37525683, year = {2023}, author = {Giraud, &#xc9; and Milon, G}, title = {[Elucidating and characterizing the dynamic biological processes that account for the sustainability of Leishmania populations].}, journal = {Medecine tropicale et sante internationale}, volume = {3}, number = {2}, pages = {}, pmid = {37525683}, issn = {2778-2034}, mesh = {Cricetinae ; Humans ; Mice ; Rats ; Animals ; *Leishmania ; Ecosystem ; *Leishmaniasis ; *Phlebotomus ; *Psychodidae ; Rodentia ; }, abstract = {To attempt resolving this issue accurately, it was necessary to anchor our experimental approaches in the observations and pioneering work of our predecessors, notably Alphonse Laveran, Louis Parrot, Edmond and Étienne Sergent. The latter, among other things, had identified as natural hosts of leishmaniasis, rodent populations with which hematophagous telmophagous sand fly populations cohabited closely.When human populations emerged in these natural ecosystems, after the sedentarization of Homo sapiens, more or less important disturbances would have led to a transition of sand fly hematophagy, from zoophilia, to zoo-anthropophilia and anthropophilia.The creation of infrastructures that allow the breeding and integration into experimental groups of both holobiont sand flies and holobiont laboratory rodents (rats, mice, hamsters, etc.) remains crucial. With such infrastructures, it becomes possible to grasp and characterize the multilateral dynamic processes - mostly clinically silent - that account for the biogenesis of tissue and/or cellular niches protecting populations of Leishmania developmental morphotypes, including those ensuring host-to-host transmission, albeit in small numbers.}, }
@article {pmid37520373, year = {2023}, author = {Roy, A and Houot, B and Kushwaha, S and Anderson, P}, title = {Impact of transgenerational host switch on gut bacterial assemblage in generalist pest, Spodoptera littoralis (Lepidoptera: Noctuidae).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172601}, pmid = {37520373}, issn = {1664-302X}, abstract = {Diet composition is vital in shaping gut microbial assemblage in many insects. Minimal knowledge is available about the influence of transgenerational diet transition on gut microbial community structure and function in polyphagous pests. This study investigated transgenerational diet-induced changes in Spodoptera littoralis larval gut bacteriome using 16S ribosomal sequencing. Our data revealed that 88% of bacterial populations in the S. littoralis larval gut comprise Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The first diet transition experiment from an artificial diet (F0) to a plant diet (F1), cabbage and cotton, caused an alteration of bacterial communities in the S. littoralis larval gut. The second transgenerational diet switch, where F1 larvae feed on the same plant in the F2 generation, displayed a significant variation suggesting further restructuring of the microbial communities in the Spodoptera larval gut. F1 larvae were also challenged with the plant diet transition at the F2 generation (cabbage to cotton or cotton to cabbage). After feeding on different plant diets, the microbial assemblage of F2 larvae pointed to considerable differences from other F2 larvae that continued on the same diet. Our results showed that S. littoralis larval gut bacteriome responds rapidly and inexplicably to different diet changes. Further experiments must be conducted to determine the developmental and ecological consequences of such changes. Nevertheless, this study improves our perception of the impact of transgenerational diet switches on the resident gut bacteriome in S. littoralis larvae and could facilitate future research to understand the importance of symbiosis in lepidopteran generalists better.}, }
@article {pmid37516623, year = {2023}, author = {Venegas, L and López, P and Derome, N and Yáñez, JM}, title = {Leveraging microbiome information for animal genetic improvement.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {10}, pages = {721-723}, doi = {10.1016/j.tig.2023.07.004}, pmid = {37516623}, issn = {0168-9525}, mesh = {Animals ; *Microbiota/genetics ; Genome/genetics ; Genomics ; Phenotype ; Models, Genetic ; }, abstract = {There is growing evidence that the microbiome influences host phenotypic variation. Incorporating information about the holobiont - the host and its microbiome - into genomic prediction models may accelerate genetic improvements in farmed animal populations. Importantly, these models must account for the indirect effects of the host genome on microbiome-mediated phenotypes.}, }
@article {pmid37511931, year = {2023}, author = {Costa, DA and Dolbeth, M and Christoffersen, ML and Zúñiga-Upegui, PT and Venâncio, M and de Lucena, RFP}, title = {An Overview of Rhodoliths: Ecological Importance and Conservation Emergency.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, pmid = {37511931}, issn = {2075-1729}, support = {UIDB/04423/2020 and UIDP/04423/2020; CEECINST/00027/2021/CP2789/CT0001//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; Finance Code 001; PDSE/Edital n&#xba; 47/2017//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; Edital n&#xba; 03/2016//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado da Para&#xed;ba/ ; }, abstract = {Red calcareous algae create bio-aggregations ecosystems constituted by carbonate calcium, with two main morphotypes: geniculate and non-geniculate structures (rhodoliths may form bio-encrustations on hard substrata or unattached nodules). This study presents a bibliographic review of the order Corallinales (specifically, rhodoliths), highlighting on morphology, ecology, diversity, related organisms, major anthropogenic influences on climate change and current conservation initiatives. These habitats are often widespread geographically and bathymetrically, occurring in the photic zone from the intertidal area to depths of 270 m. Due to its diverse morphology, this group offers a special biogenic environment that is favourable to epiphyte algae and a number of marine invertebrates. They also include holobiont microbiota made up of tiny eukaryotes, bacteria and viruses. The morphology of red calcareous algae and outside environmental conditions are thought to be the key forces regulating faunistic communities in algae reefs. The impacts of climate change, particularly those related to acidification, might substantially jeopardise the survival of the Corallinales. Despite the significance of these ecosystems, there are a number of anthropogenic stresses on them. Since there have been few attempts to conserve them, programs aimed at their conservation and management need to closely monitor their habitats, research the communities they are linked with and assess the effects they have on the environment.}, }
@article {pmid37508443, year = {2023}, author = {Wuerz, M and Lawson, CA and Oakley, CA and Possell, M and Wilkinson, SP and Grossman, AR and Weis, VM and Suggett, DJ and Davy, SK}, title = {Symbiont Identity Impacts the Microbiome and Volatilome of a Model Cnidarian-Dinoflagellate Symbiosis.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508443}, issn = {2079-7737}, support = {DP200100091//Australian Research Council discovery project/ ; 19-VUW-086//Marsden Fund/ ; }, abstract = {The symbiosis between cnidarians and dinoflagellates underpins the success of reef-building corals in otherwise nutrient-poor habitats. Alterations to symbiotic state can perturb metabolic homeostasis and thus alter the release of biogenic volatile organic compounds (BVOCs). While BVOCs can play important roles in metabolic regulation and signalling, how the symbiotic state affects BVOC output remains unexplored. We therefore characterised the suite of BVOCs that comprise the volatilome of the sea anemone Exaiptasia diaphana ('Aiptasia') when aposymbiotic and in symbiosis with either its native dinoflagellate symbiont Breviolum minutum or the non-native symbiont Durusdinium trenchii. In parallel, the bacterial community structure in these different symbiotic states was fully characterised to resolve the holobiont microbiome. Based on rRNA analyses, 147 unique amplicon sequence variants (ASVs) were observed across symbiotic states. Furthermore, the microbiomes were distinct across the different symbiotic states: bacteria in the family Vibrionaceae were the most abundant in aposymbiotic anemones; those in the family Crocinitomicaceae were the most abundant in anemones symbiotic with D. trenchii; and anemones symbiotic with B. minutum had the highest proportion of low-abundance ASVs. Across these different holobionts, 142 BVOCs were detected and classified into 17 groups based on their chemical structure, with BVOCs containing multiple functional groups being the most abundant. Isoprene was detected in higher abundance when anemones hosted their native symbiont, and dimethyl sulphide was detected in higher abundance in the volatilome of both Aiptasia-Symbiodiniaceae combinations relative to aposymbiotic anemones. The volatilomes of aposymbiotic anemones and anemones symbiotic with B. minutum were distinct, while the volatilome of anemones symbiotic with D. trenchii overlapped both of the others. Collectively, our results are consistent with previous reports that D. trenchii produces a metabolically sub-optimal symbiosis with Aiptasia, and add to our understanding of how symbiotic cnidarians, including corals, may respond to climate change should they acquire novel dinoflagellate partners.}, }
@article {pmid37491455, year = {2023}, author = {von der Dunk, SHA and Hogeweg, P and Snel, B}, title = {Obligate endosymbiosis enables genome expansion during eukaryogenesis.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {777}, pmid = {37491455}, issn = {2399-3642}, mesh = {Phylogeny ; *Eukaryotic Cells/metabolism ; *Symbiosis/genetics ; Biological Evolution ; Mitochondria/genetics ; }, abstract = {The endosymbiosis of an alpha-proteobacterium that gave rise to mitochondria was one of the key events in eukaryogenesis. One striking outcome of eukaryogenesis was a much more complex cell with a large genome. Despite the existence of many alternative hypotheses for this and other patterns potentially related to endosymbiosis, a constructive evolutionary model in which these hypotheses can be studied is still lacking. Here, we present a theoretical approach in which we focus on the consequences rather than the causes of mitochondrial endosymbiosis. Using a constructive evolutionary model of cell-cycle regulation, we find that genome expansion and genome size asymmetry arise from emergent host-symbiont cell-cycle coordination. We also find that holobionts with large host and small symbiont genomes perform best on long timescales and mimic the outcome of eukaryogenesis. By designing and studying a constructive evolutionary model of obligate endosymbiosis, we uncovered some of the forces that may drive the patterns observed in nature. Our results provide a theoretical foundation for patterns related to mitochondrial endosymbiosis, such as genome size asymmetry, and reveal evolutionary outcomes that have not been considered so far, such as cell-cycle coordination without direct communication.}, }
@article {pmid37486074, year = {2023}, author = {Li, Y and He, X and Lin, Y and Li, YX and Kamenev, GM and Li, J and Qiu, JW and Sun, J}, title = {Reduced chemosymbiont genome in the methane seep thyasirid and the cooperated metabolisms in the holobiont under anaerobic sediment.}, journal = {Molecular ecology resources}, volume = {23}, number = {8}, pages = {1853-1867}, doi = {10.1111/1755-0998.13846}, pmid = {37486074}, issn = {1755-0998}, support = {LSKJ202203104//Science and Technology Innovation Project of Laoshan Laboratory/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 202241002//Fundamental Research Funds for the Central Universities/ ; 12101021//General Research Fund of Hong Kong Special Administrative Region/ ; KF2022NO03//Open Fund of CAS and Shandong Province Key Laboratory of Experimental Marine Biology/ ; tsqn202103036//Young Taishan Scholars Program of Shandong Province/ ; }, mesh = {Animals ; Phylogeny ; *Methane ; Anaerobiosis ; Genome ; *Bivalvia/genetics ; Symbiosis/genetics ; }, abstract = {Previous studies have deciphered the genomic basis of host-symbiont metabolic complementarity in vestimentiferans, bathymodioline mussels, vesicomyid clams and Alviniconcha snails, yet little is known about the chemosynthetic symbiosis in Thyasiridae-a family of Bivalvia regarded as an excellent model in chemosymbiosis research due to their wide distribution in both deep-sea and shallow-water habitats. We report the first circular thyasirid symbiont genome, named Candidatus Ruthturnera sp. Tsphm01, with a size of 1.53 Mb, 1521 coding genes and 100% completeness. Compared to its free-living relatives, Ca. Ruthturnera sp. Tsphm01 genome is reduced, lacking components for chemotaxis, citric acid cycle and de novo biosynthesis of small molecules (e.g. amino acids and cofactors), indicating it is likely an obligate intracellular symbiont. Nevertheless, the symbiont retains complete genomic components of sulphur oxidation and assimilation of inorganic carbon, and these systems were highly and actively expressed. Moreover, the symbiont appears well-adapted to anoxic environment, including capable of anaerobic respiration (i.e. reductions of DMSO and nitrate) and possession of a low oxygen-adapted type of cytochrome c oxidase. Analysis of the host transcriptome revealed its metabolic complementarity to the incomplete metabolic pathways of the symbiont and the acquisition of nutrients from the symbiont via phagocytosis and exosome. By providing the first complete genome of reduced size in a thyasirid symbiont, this study enhances our understanding of the diversity of symbiosis that has enabled bivalves to thrive in chemosynthetic habitats. The resources will be widely used in phylogenetic, geographic and evolutionary studies of chemosynthetic bacteria and bivalves.}, }
@article {pmid37485344, year = {2023}, author = {Sakai, R and Goto-Inoue, N and Yamashita, H and Aimoto, N and Kitai, Y and Maruyama, T}, title = {Smart utilization of betaine lipids in the giant clam Tridacna crocea.}, journal = {iScience}, volume = {26}, number = {7}, pages = {107250}, pmid = {37485344}, issn = {2589-0042}, abstract = {The giant clam Tridacna crocea thrives in poorly nourished coral reef water by forming a holobiont with zooxanthellae and utilizing photosynthetic products of the symbiont. However, detailed metabolic crosstalk between clams and symbionts is elusive. Here, we discovered that the nonphosphorous microalgal betaine lipid DGCC (diacylglycerylcarboxy-hydroxymethylcholine) and its deacylated derivative GCC are present in all tissues and organs, including algae-free sperm and eggs, and are metabolized. Colocalization of DGCC and PC (phosphatidylcholine) evidenced by MS imaging suggested that DGCC functions as a PC substitute. The high content of GCC in digestive diverticula (DD) suggests that the algal DGCC was digested in DD for further utilization. Lipidomics analysis showing the organ-specific distribution pattern of DGCC species suggests active utilization of DGCC as membrane lipids in the clam. Thus, the utilization of zooxanthellal DGCC in animal cells is a unique evolutionary outcome in phosphorous-deficient coral reef waters.}, }
@article {pmid37481685, year = {2023}, author = {Leiva, C and Pérez-Portela, R and Lemer, S}, title = {Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic CO2 seeps.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {769}, pmid = {37481685}, issn = {2399-3642}, mesh = {Animals ; *Carbon Dioxide ; *Anthozoa/genetics ; Ocean Acidification ; Hydrogen-Ion Concentration ; Seawater ; Genomics ; }, abstract = {Ocean acidification, caused by anthropogenic CO2 emissions, is predicted to have major consequences for reef-building corals, jeopardizing the scaffolding of the most biodiverse marine habitats. However, whether corals can adapt to ocean acidification and how remains unclear. We addressed these questions by re-examining transcriptome and genome data of Acropora millepora coral holobionts from volcanic CO2 seeps with end-of-century pH levels. We show that adaptation to ocean acidification is a wholistic process involving the three main compartments of the coral holobiont. We identified 441 coral host candidate adaptive genes involved in calcification, response to acidification, and symbiosis; population genetic differentiation in dinoflagellate photosymbionts; and consistent transcriptional microbiome activity despite microbial community shifts. Coral holobionts from natural analogues to future ocean conditions harbor beneficial genetic variants with far-reaching rapid adaptation potential. In the face of climate change, these populations require immediate conservation strategies as they could become key to coral reef survival.}, }
@article {pmid37475177, year = {2023}, author = {Carvalho, J and Morales, HE and Faria, R and Butlin, RK and Sousa, VC}, title = {Integrating Pool-seq uncertainties into demographic inference.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1737-1755}, doi = {10.1111/1755-0998.13834}, pmid = {37475177}, issn = {1755-0998}, support = {2020.00275.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CEECINST/00032/2018/CP1523/CT0008//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PD/BD/128350/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; PTDC/BIA-EVL/1614/2021//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2021.09795.CPCA//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; ERC-2015-AdG-693030-BARRIERS//H2020 European Research Council/ ; RGY0081/2020//Human Frontier Science Program/ ; }, mesh = {*Genetics, Population ; Bayes Theorem ; *Ecotype ; Genome ; Demography ; }, abstract = {Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.}, }
@article {pmid37471099, year = {2023}, author = {Mesny, F and Hacquard, S and Thomma, BP}, title = {Co-evolution within the plant holobiont drives host performance.}, journal = {EMBO reports}, volume = {24}, number = {9}, pages = {e57455}, pmid = {37471099}, issn = {1469-3178}, mesh = {*Plants ; *Microbiota/physiology ; Symbiosis ; }, abstract = {Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.}, }
@article {pmid37457347, year = {2023}, author = {Ferrarezi, JA and Defant, H and de Souza, LF and Azevedo, JL and Hungria, M and Quecine, MC}, title = {Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1172839}, pmid = {37457347}, issn = {1664-462X}, abstract = {Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10[-3], 10[-6], 10[-9] and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10[-3] +Ab-V5 and NS 10[-6] Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10[-3] + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.}, }
@article {pmid37437771, year = {2023}, author = {Prosdocimi, F and Cortines, JR and José, MV and Farias, ST}, title = {Decoding viruses: An alternative perspective on their history, origins and role in nature.}, journal = {Bio Systems}, volume = {231}, number = {}, pages = {104960}, doi = {10.1016/j.biosystems.2023.104960}, pmid = {37437771}, issn = {1872-8324}, mesh = {Animals ; *Ecosystem ; *Viruses/genetics ; Evolution, Molecular ; Bacteria ; Eukaryota/genetics ; Phylogeny ; Mammals ; }, abstract = {This article provides an alternative perspective on viruses, exploring their origins, ecology, and evolution. Viruses are recognized as the most prevalent biological entities on Earth, permeating nearly all environments and forming the virosphere-a significant biological layer. They play a crucial role in regulating bacterial populations within ecosystems and holobionts, influencing microbial communities and nutrient recycling. Viruses are also key drivers of molecular evolution, actively participating in the maintenance and regulation of ecosystems and cellular organisms. Many eukaryotic genomes contain genomic elements with viral origins, which contribute to organismal equilibrium and fitness. Viruses are involved in the generation of species-specific orphan genes, facilitating adaptation and the development of unique traits in biological lineages. They have been implicated in the formation of vital structures like the eukaryotic nucleus and the mammalian placenta. The presence of virus-specific genes absent in cellular organisms suggests that viruses may pre-date cellular life. Like progenotes, viruses are ribonucleoprotein entities with simpler capsid architectures compared to proteolipidic membranes. This article presents a comprehensive scenario describing major transitions in prebiotic evolution and proposes that viruses emerged prior to the Last Universal Common Ancestor (LUCA) during the progenote era. However, it is important to note that viruses do not form a monophyletic clade, and many viral taxonomic groups originated more recently as reductions of cellular structures. Thus, viral architecture should be seen as an ancient and evolutionarily stable strategy adopted by biological systems. The goal of this article is to reshape perceptions of viruses, highlighting their multifaceted significance in the complex tapestry of life and fostering a deeper understanding of their origins, ecological impact, and evolutionary dynamics.}, }
@article {pmid37423403, year = {2023}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Quintanilla-Carvajal, MX and Díaz, LE and Alzate, JF and Junca, H and Rodríguez Orjuela, JA and Villamil Diaz, LM}, title = {Evaluation of dietary single probiotic isolates and probiotic multistrain consortia in growth performance, gut histology, gut microbiota, immune regulation, and infection resistance of Nile tilapia, Oreochromis niloticus, shows superior monostrain performance.}, journal = {Fish &amp; shellfish immunology}, volume = {140}, number = {}, pages = {108928}, doi = {10.1016/j.fsi.2023.108928}, pmid = {37423403}, issn = {1095-9947}, mesh = {Animals ; *Cichlids ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Diet/veterinary ; *Tilapia ; Animal Feed/analysis ; *Fish Diseases ; Dietary Supplements ; }, abstract = {The probiotic potential of a designed bacterial consortia isolated from a competitive exclusion culture originally obtained from the intestinal contents of tilapia juveniles were evaluated on Nile tilapia alevins. The growth performance, intestinal histology, microbiota effects, resistance to Streptococcus agalactiae challenge, and immune response were assessed. In addition, the following treatments were included in a commercial feed: A12+M4+M10 (Lactococcus lactis A12, Priestia megaterium M4, and Priestia sp. M10), M4+M10 (P. megaterium M4, and Priestia sp. M10) and the single bacteria as controls; A12 (L. lactis A12), M4 (P. megaterium M4), M10 (Priestia sp. M10), also a commercial feed without any probiotic addition was included as a control. The results showed that all probiotic treatments improved the growth performance, intestinal histology, and resistance during experimental infection with S. agalactiae in comparison to the control fish. Also, the administration of probiotics resulted in the modulation of genes associated with the innate and adaptive immune systems that were non-dependent on microbial colonization. Surprisingly, L. lactis A12 alone induced benefits in fish compared to the microbial consortia, showing the highest increase in growth rate, survival during experimental infection with S. agalactiae, increased intestinal fold length, and the number of differentially expressed genes. Lastly, we conclude that a competitive exclusion culture is a reliable source of probiotics, and monostrain L. lactis A12 has comparable or even greater probiotic potential than the bacterial consortia.}, }
@article {pmid37415044, year = {2023}, author = {King, NG and Uribe, R and Moore, PJ and Earp, HS and Gouraguine, A and Hinostroza, D and Perez-Matus, A and Smith, K and Smale, DA}, title = {Multiscale Spatial Variability and Stability in the Structure and Diversity of Bacterial Communities Associated with the Kelp Eisenia cokeri in Peru.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2574-2582}, pmid = {37415044}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Kelp/microbiology ; Ecosystem ; Peru ; Bacteria/genetics ; Biodiversity ; *Microbiota ; }, abstract = {Ecological communities are structured by a range of processes that operate over a range of spatial scales. While our understanding of such biodiversity patterns in macro-communities is well studied, our understanding at the microbial level is still lacking. Bacteria can be free living or associated with host eukaryotes, forming part of a wider "microbiome," which is fundamental for host performance and health. For habitat forming foundation-species, host-bacteria relationships likely play disproportionate roles in mediating processes for the wider ecosystem. Here, we describe host-bacteria communities across multiple spatial scales (i.e., from 10s of m to 100s of km) in the understudied kelp, Eisenia cokeri, in Peru. We found that E. cokeri supports a distinct bacterial community compared to the surrounding seawater, but the structure of these communities varied markedly at the regional (~480 km), site (1-10 km), and individual (10s of m) scale. The marked regional-scale differences we observed may be driven by a range of processes, including temperature, upwelling intensity, or regional connectivity patterns. However, despite this variability, we observed consistency in the form of a persistent core community at the genus level. Here, the genera Arenicella, Blastopirellula, Granulosicoccus, and Litorimonas were found in >80% of samples and comprised ~53% of total sample abundance. These genera have been documented within bacterial communities associated with kelps and other seaweed species from around the world and may be important for host function and wider ecosystem health in general.}, }
@article {pmid37404156, year = {2023}, author = {Hu, S and He, R and He, X and Zeng, J and Zhao, D}, title = {Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0071723}, pmid = {37404156}, issn = {1098-5336}, mesh = {*Ammonium Compounds ; Bacteria ; *Microbiota ; Biomass ; Rhizosphere ; *Hydrocharitaceae ; }, abstract = {Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.}, }
@article {pmid37401172, year = {2023}, author = {Hardoim, CCP and Hardoim, PR and Lôbo-Hajdu, G and Custódio, MR and Thomas, T}, title = {The microbiome of the sponge Aplysina caissara in two sites with different levels of anthropogenic impact.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad064}, pmid = {37401172}, issn = {1574-6968}, mesh = {Animals ; *Anthropogenic Effects ; Brazil ; *Microbiota/genetics ; Phylogeny ; *Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Geologic Sediments/microbiology ; Host Microbial Interactions ; *Biodiversity ; Archaea/classification/genetics ; Bacteria/classification/genetics ; }, abstract = {Despite the important roles that marine sponges play in ecosystem functioning and structuring, little is known about how the sponge holobiont responds to local anthropogenic impacts. Here we assess the influence of an impacted environment (Praia Preta) on the microbial community associated with the endemic sponge Aplysina caissara in comparison to a less-impacted area (Praia do Guaecá) from the coast of São Paulo state (Brazil, southwestern Atlantic coast). We hypothesized that the local anthropogenic impacts will change the microbiome of A. caissara and that the community assembly will be driven by a different process (i.e. deterministic versus stochastic) under distinct levels of impact. The microbiome at the amplicon sequence variants level was found to be statistically distinct between sponges from the different sites, and this was also seen for the microbial communities of the surrounding seawater and sediments. Microbial communities of A. caissara from both sites were found to be assembled by deterministic processes, even though the sites presented distinct anthropogenic impacts, showing a pivotal role of the sponge host in selecting its own microbiome. Overall, this study revealed that local anthropogenic impacts altered the microbiome of A. caissara; however, assembly processes are largely determined by the sponge host.}, }
@article {pmid37382454, year = {2023}, author = {Liu, W and Cui, X and Wang, X and Shen, C and Ji, L and Zhang, M and Wong, MH and Zhang, J and Shan, S}, title = {Sugarcane mosaic virus reduced bacterial diversity and network complexity in the maize root endosphere.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0019823}, pmid = {37382454}, issn = {2379-5077}, mesh = {*Microbiota/genetics ; RNA, Ribosomal, 16S ; Potyvirus ; Soil Microbiology ; *Zea mays/genetics ; Plant Roots/microbiology ; Endophytes/genetics ; Bacteria/genetics ; }, abstract = {Sugarcane mosaic virus (SCMV) causes mosaic disease in crops such as maize and sugarcane by its vector-an aphid-and is transmitted top-down into the root system. However, understanding of the effects of the aphid-borne virus on root-associated microbes after plant invasion remains limited. The current project investigated maize root-associated (rhizosphere and endosphere) bacterial communities, potential interspecies interaction, and assembly processes in response to SCMV invasion based on 16S rRNA gene amplicon sequencing. SCMV was detected in the roots 9 days after inoculation, and leaf mosaic and chlorosis appeared. The SCMV invasion markedly reduced the α-diversity of endosphere bacteria compared with uninoculated controls (Mock). The connectivity and complexity of the bacterial co-occurrence network in the root endosphere decreased after SCMV invasion, implying that the plant virus may alter root endophyte-microbial interactions. Moreover, a signature that deviates more from stochastic processes was observed in virus-infected plants. Unexpectedly, the rhizosphere bacterial communities were rarely affected by the viral invasion. This study lays the foundation for elucidating the fate of the microbial component of the plant holobiont following aphid-borne virus exposure. IMPORTANCE Biotic (e.g., soil-borne viruses) stress can alter root-associated bacterial communities, essential in maintaining host plant growth and health. However, the regulation of root-associated microorganisms by plant viruses from shoots is still largely unknown. Our results show that plant virus invasion leads to reduced and simpler inter-microbial communication in the maize endosphere. In addition, stochastic processes act on bacterial community assembly in both rhizosphere and endosphere, and bacterial communities in virus-invaded plant endosphere tend to shift toward deterministic processes. Our study highlights the negative effects of plant viruses on root endophytes from the microbial ecology perspective, which may be microbially mediated mechanisms of plant diseases.}, }
@article {pmid37367660, year = {2023}, author = {Sikorskaya, TV}, title = {Coral Lipidome: Molecular Species of Phospholipids, Glycolipids, Betaine Lipids, and Sphingophosphonolipids.}, journal = {Marine drugs}, volume = {21}, number = {6}, pages = {}, pmid = {37367660}, issn = {1660-3397}, mesh = {Animals ; *Anthozoa/microbiology ; Phospholipids ; Ecosystem ; Lipidomics ; Betaine ; Glycolipids ; Coral Reefs ; Phosphatidylcholines ; *Dinoflagellida ; Phosphatidylglycerols ; Symbiosis ; }, abstract = {Coral reefs are the most biodiversity-rich ecosystems in the world's oceans. Coral establishes complex interactions with various microorganisms that constitute an important part of the coral holobiont. The best-known coral endosymbionts are Symbiodiniaceae dinoflagellates. Each member of the coral microbiome contributes to its total lipidome, which integrates many molecular species. The present study summarizes available information on the molecular species of the plasma membrane lipids of the coral host and its dinoflagellates (phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), ceramideaminoethylphosphonate, and diacylglyceryl-3-O-carboxyhydroxymethylcholine), and the thylakoid membrane lipids of dinoflagellates (phosphatidylglycerol (PG) and glycolipids). Alkyl chains of PC and PE molecular species differ between tropical and cold-water coral species, and features of their acyl chains depend on the coral's taxonomic position. PS and PI structural features are associated with the presence of an exoskeleton in the corals. The dinoflagellate thermosensitivity affects the profiles of PG and glycolipid molecular species, which can be modified by the coral host. Coral microbiome members, such as bacteria and fungi, can also be the source of the alkyl and acyl chains of coral membrane lipids. The lipidomics approach, providing broader and more detailed information about coral lipid composition, opens up new opportunities in the study of biochemistry and ecology of corals.}, }
@article {pmid37360551, year = {2023}, author = {Monti, M and Giorgi, A and Kemp, DW and Olson, JB}, title = {Spatial, temporal and network analyses provide insights into the dynamics of the bacterial communities associated with two species of Caribbean octocorals and indicate possible key taxa.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {1-14}, pmid = {37360551}, issn = {0334-5114}, abstract = {UNLABELLED: Despite the current decline of scleractinian coral populations, octocorals are thriving on reefs in the Caribbean Sea and western North Atlantic Ocean. These cnidarians are holobiont entities, interacting with a diverse array of microorganisms. Few studies have investigated the spatial and temporal stability of the bacterial communities associated with octocoral species and information regarding the co-occurrence and potential interactions between specific members of these bacterial communities remain sparse. To address this knowledge gap, this study investigated the stability of the bacterial assemblages associated with two common Caribbean octocoral species, Eunicea flexuosa and Antillogorgia americana, across time and geographical locations and performed network analyses to investigate potential bacterial interactions. Results demonstrated that general inferences regarding the spatial and temporal stability of octocoral-associated bacterial communities should not be made, as host-specific characteristics may influence these factors. In addition, network analyses revealed differences in the complexity of the interactions between bacteria among the octocoral species analyzed, while highlighting the presence of genera known to produce bioactive secondary metabolites in both octocorals that may play fundamental roles in structuring the octocoral-associated bacteriome.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13199-023-00923-x.}, }
@article {pmid37344276, year = {2023}, author = {Dussex, N and Morales, HE and Grossen, C and Dalén, L and van Oosterhout, C}, title = {Purging and accumulation of genetic load in conservation.}, journal = {Trends in ecology &amp; evolution}, volume = {38}, number = {10}, pages = {961-969}, doi = {10.1016/j.tree.2023.05.008}, pmid = {37344276}, issn = {1872-8383}, mesh = {*Genetics, Population ; *Genetic Load ; Population Density ; Inbreeding ; Genetic Variation ; }, abstract = {Our ability to assess the threat posed by the genetic load to small and declining populations has been greatly improved by advances in genome sequencing and computational approaches. Yet, considerable confusion remains around the definitions of the genetic load and its dynamics, and how they impact individual fitness and population viability. We illustrate how both selective purging and drift affect the distribution of deleterious mutations during population size decline and recovery. We show how this impacts the composition of the genetic load, and how this affects the extinction risk and recovery potential of populations. We propose a framework to examine load dynamics and advocate for the introduction of load estimates in the management of endangered populations.}, }
@article {pmid37336945, year = {2023}, author = {Vinha, B and Rossi, S and Gori, A and Hanz, U and Pennetta, A and De Benedetto, GE and Mienis, F and Huvenne, VAI and Hebbeln, D and Wienberg, C and Titschack, J and Freiwald, A and Piraino, S and Orejas, C}, title = {Trophic ecology of Angolan cold-water coral reefs (SE Atlantic) based on stable isotope analyses.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9933}, pmid = {37336945}, issn = {2045-2322}, mesh = {Animals ; *Coral Reefs ; *Anthozoa ; Ecology ; Water ; Nitrogen Isotopes ; Carbon Isotopes/analysis ; }, abstract = {Cold-water coral (CWC) reefs of the Angolan margin (SE Atlantic) are dominated by Desmophyllum pertusum and support a diverse community of associated fauna, despite hypoxic conditions. In this study, we use carbon and nitrogen stable isotope analyses (δ[13]C and δ[15]N) to decipher the trophic network of this relatively unknown CWC province. Although fresh phytodetritus is available to the reef, δ[15]N signatures indicate that CWCs (12.90 ± 1.00 ‰) sit two trophic levels above Suspended Particulate Organic Matter (SPOM) (4.23 ± 1.64 ‰) suggesting that CWCs are highly reliant on an intermediate food source, which may be zooplankton. Echinoderms and the polychaete Eunice norvegica occupy the same trophic guild, with high δ[13]C signatures (-14.00 ± 1.08 ‰) pointing to a predatory feeding behavior on CWCs and sponges, although detrital feeding on [13]C enriched particles might also be important for this group. Sponges presented the highest δ[15]N values (20.20 ± 1.87 ‰), which could be due to the role of the sponge holobiont and bacterial food in driving intense nitrogen cycling processes in sponges' tissue, helping to cope with the hypoxic conditions of the reef. Our study provides first insights to understand trophic interactions of CWC reefs under low-oxygen conditions.}, }
@article {pmid37332135, year = {2023}, author = {Vadillo Gonzalez, S and Vranken, S and Coleman, MA and Wernberg, T and Steinberg, PD and Marzinelli, EM}, title = {Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata.}, journal = {Molecular ecology}, volume = {32}, number = {16}, pages = {4584-4598}, doi = {10.1111/mec.17056}, pmid = {37332135}, issn = {1365-294X}, mesh = {Humans ; *Kelp/genetics ; *Microbiota/genetics ; Genotype ; }, abstract = {A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.}, }
@article {pmid37326290, year = {2023}, author = {Perez-Lamarque, B and Sommeria-Klein, G and Duret, L and Morlon, H}, title = {Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota.}, journal = {Molecular biology and evolution}, volume = {40}, number = {7}, pages = {}, pmid = {37326290}, issn = {1537-1719}, mesh = {Animals ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Vertebrates/genetics ; *Microbiota/genetics ; Mammals/genetics/microbiology ; Birds/genetics ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {How host-associated microbial communities evolve as their hosts diversify remains equivocal: how conserved is their composition? What was the composition of ancestral microbiota? Do microbial taxa covary in abundance over millions of years? Multivariate phylogenetic models of trait evolution are key to answering similar questions for complex host phenotypes, yet they are not directly applicable to relative abundances, which usually characterize microbiota. Here, we extend these models in this context, thereby providing a powerful approach for estimating phylosymbiosis (the extent to which closely related host species harbor similar microbiota), ancestral microbiota composition, and integration (evolutionary covariations in bacterial abundances). We apply our model to the gut microbiota of mammals and birds. We find significant phylosymbiosis that is not entirely explained by diet and geographic location, indicating that other evolutionary-conserved traits shape microbiota composition. We identify main shifts in microbiota composition during the evolution of the two groups and infer an ancestral mammalian microbiota consistent with an insectivorous diet. We also find remarkably consistent evolutionary covariations among bacterial orders in mammals and birds. Surprisingly, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of host evolutionary history.}, }
@article {pmid37325891, year = {2023}, author = {Urban, L and Perlas, A and Francino, O and Martí-Carreras, J and Muga, BA and Mwangi, JW and Boykin Okalebo, L and Stanton, JL and Black, A and Waipara, N and Fontsere, C and Eccles, D and Urel, H and Reska, T and Morales, HE and Palmada-Flores, M and Marques-Bonet, T and Watsa, M and Libke, Z and Erkenswick, G and van Oosterhout, C}, title = {Real-time genomics for One Health.}, journal = {Molecular systems biology}, volume = {19}, number = {8}, pages = {e11686}, pmid = {37325891}, issn = {1744-4292}, mesh = {Humans ; *Ecosystem ; *One Health ; Genomics ; Biodiversity ; Genome ; }, abstract = {The ongoing degradation of natural systems and other environmental changes has put our society at a crossroad with respect to our future relationship with our planet. While the concept of One Health describes how human health is inextricably linked with environmental health, many of these complex interdependencies are still not well-understood. Here, we describe how the advent of real-time genomic analyses can benefit One Health and how it can enable timely, in-depth ecosystem health assessments. We introduce nanopore sequencing as the only disruptive technology that currently allows for real-time genomic analyses and that is already being used worldwide to improve the accessibility and versatility of genomic sequencing. We showcase real-time genomic studies on zoonotic disease, food security, environmental microbiome, emerging pathogens, and their antimicrobial resistances, and on environmental health itself - from genomic resource creation for wildlife conservation to the monitoring of biodiversity, invasive species, and wildlife trafficking. We stress why equitable access to real-time genomics in the context of One Health will be paramount and discuss related practical, legal, and ethical limitations.}, }
@article {pmid37317893, year = {2023}, author = {Connelly, MT and Snyder, G and Palacio-Castro, AM and Gillette, PR and Baker, AC and Traylor-Knowles, N}, title = {Antibiotics reduce Pocillopora coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression.}, journal = {Molecular ecology}, volume = {32}, number = {16}, pages = {4677-4694}, doi = {10.1111/mec.17049}, pmid = {37317893}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics/microbiology ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Symbiosis/genetics ; Bacteria/genetics ; Oxygen Consumption ; *Dinoflagellida/genetics ; Gene Expression ; Coral Reefs ; }, abstract = {Corals are important models for understanding invertebrate host-microbe interactions; however, to fully discern mechanisms involved in these relationships, experimental approaches for manipulating coral-bacteria associations are needed. Coral-associated bacteria affect holobiont health via nutrient cycling, metabolic exchanges and pathogen exclusion, yet it is not fully understood how bacterial community shifts affect holobiont health and physiology. In this study, a combination of antibiotics (ampicillin, streptomycin and ciprofloxacin) was used to disrupt the bacterial communities of 14 colonies of the reef framework-building corals Pocillopora meandrina and P. verrucosa, originally collected from Panama and hosting diverse algal symbionts (family Symbiodiniaceae). Symbiodiniaceae photochemical efficiencies and holobiont oxygen consumption (as proxies for coral health) were measured throughout a 5-day exposure. Antibiotics altered bacterial community composition and reduced alpha and beta diversity, however, several bacteria persisted, leading to the hypothesis that these bacteria are either antibiotics resistant or occupy internal niches that are shielded from antibiotics. While antibiotics did not affect Symbiodiniaceae photochemical efficiency, antibiotics-treated corals had lower oxygen consumption rates. RNAseq revealed that antibiotics increased expression of Pocillopora immunity and stress response genes at the expense of cellular maintenance and metabolism functions. Together, these results reveal that antibiotic disruption of corals' native bacteria negatively impacts holobiont health by decreasing oxygen consumption and activating host immunity without directly impairing Symbiodiniaceae photosynthesis, underscoring the critical role of coral-associated bacteria in holobiont health. They also provide a baseline for future experiments that manipulate Pocillopora corals' symbioses by first reducing the diversity and complexity of coral-associated bacteria.}, }
@article {pmid37317290, year = {2023}, author = {Massé, A and Detang, J and Duval, C and Duperron, S and Woo, AC and Domart-Coulon, I}, title = {Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317290}, issn = {2076-2607}, support = {ATM 2022 'MIcrobiote Bact&#xe9;rien de l'Ulvophyceae Ostreobium et tol&#xe9;rance &#xe0; la Salinit&#xe9;'//National Museum of Natural History/ ; MNHN 2022 Masters fellowship to Juliette Detang//National Museum of Natural History/ ; MNHN ATER fellowship 2020/2022 to Ana&#xef;s Mass&#xe9;//National Museum of Natural History/ ; MCAM laboratory (CNRS7245-MNHN)//National Museum of Natural History/ ; }, abstract = {Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.}, }
@article {pmid37311801, year = {2023}, author = {Botté, ES and Bennett, H and Engelberts, JP and Thomas, T and Bell, JJ and Webster, NS and Luter, HM}, title = {Future ocean conditions induce necrosis, microbial dysbiosis and nutrient cycling imbalance in the reef sponge Stylissa flabelliformis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {53}, pmid = {37311801}, issn = {2730-6151}, support = {Appropriation fund//Australian Institute of Marine Science (AIMS)/ ; Appropriation funding//Australian Institute of Marine Science (AIMS)/ ; VUW1505//Faculty of Science, Victoria University of Wellington (Faculty of Science, VUW)/ ; }, abstract = {Oceans are rapidly warming and acidifying in the context of climate change, threatening sensitive marine biota including coral reef sponges. Ocean warming (OW) and ocean acidification (OA) can impact host health and associated microbiome, but few studies have investigated these effects, which are generally studied in isolation, on a specific component of the holobiont. Here we present a comprehensive view of the consequences of simultaneous OW and OA for the tropical sponge Stylissa flabelliformis. We found no interactive effect on the host health or microbiome. Furthermore, OA (pH 7.6 versus pH 8.0) had no impact, while OW (31.5 °C versus 28.5 °C) caused tissue necrosis, as well as dysbiosis and shifts in microbial functions in healthy tissue of necrotic sponges. Major taxonomic shifts included a complete loss of archaea, reduced proportions of Gammaproteobacteria and elevated relative abundances of Alphaproteobacteria. OW weakened sponge-microbe interactions, with a reduced capacity for nutrient exchange and phagocytosis evasion, indicating lower representations of stable symbionts. The potential for microbially-driven nitrogen and sulphur cycling was reduced, as was amino acid metabolism. Crucially, the dysbiosis annihilated the potential for ammonia detoxification, possibly leading to accumulation of toxic ammonia, nutrient imbalance, and host tissue necrosis. Putative defence against reactive oxygen species was greater at 31.5 °C, perhaps as microorganisms capable of resisting temperature-driven oxidative stress were favoured. We conclude that healthy symbiosis in S. flabelliformis is unlikely to be disrupted by future OA but will be deeply impacted by temperatures predicted for 2100 under a "business-as-usual" carbon emission scenario.}, }
@article {pmid37310733, year = {2023}, author = {Ma, M and Zhuang, Y and Chang, L and Xiao, L and Lin, Q and Qiu, Q and Chen, D and Egan, S and Wang, G}, title = {Naturally occurring beneficial bacteria Vibrio alginolyticus X-2 protects seaweed from bleaching disease.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0006523}, pmid = {37310733}, issn = {2150-7511}, mesh = {Vibrio alginolyticus/genetics ; *Seaweed ; Bacteria ; *Microbiota ; Aquaculture ; }, abstract = {Microbiome manipulation is gaining fresh attention as a way to mitigate diseases in aquaculture. The commercially farmed seaweed Saccharina japonica suffers from a bacterial-induced bleaching disease, which has major implications for the reliable supply of healthy sporelings. Here, we identify a beneficial bacterium, Vibrio alginolyticus X-2 that significantly reduces the risk of bleaching disease. By combining infection assays and multi-omic analyses, we provide evidence to suggest that the underlying protective mechanisms of V. alginolyticus X-2 involve maintaining epibacterial communities, increasing the gene expression of S. japonica related to immune and stress protection pathways, and stimulating betaine concentrations in S. japonica holobionts. Thus, V. alginolyticus X-2 can elicit a suite of microbial and host responses to mitigate the bleaching disease. Our study provides insights into disease control in farmed S. japonica through the application of beneficial bacteria. IMPORTANCE Beneficial bacteria can elicit a suite of microbial and host responses to enhance the resistance to bleaching disease.}, }
@article {pmid37308970, year = {2023}, author = {Mariadassou, M and Nouvel, LX and Constant, F and Morgavi, DP and Rault, L and Barbey, S and Helloin, E and Rué, O and Schbath, S and Launay, F and Sandra, O and Lefebvre, R and Le Loir, Y and Germon, P and Citti, C and Even, S}, title = {Microbiota members from body sites of dairy cows are largely shared within individual hosts throughout lactation but sharing is limited in the herd.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {32}, pmid = {37308970}, issn = {2524-4671}, support = {MICROCOSM project funded by the INRAE Metaprogramme MEM//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; }, abstract = {BACKGROUND: Host-associated microbes are major determinants of the host phenotypes. In the present study, we used dairy cows with different scores of susceptibility to mastitis with the aim to explore the relationships between microbiota composition and different factors in various body sites throughout lactation as well as the intra- and inter-animal microbial sharing.<br><br>RESULTS: Microbiotas from the mouth, nose, vagina and milk of 45 lactating dairy cows were characterized by metataxonomics at four time points during the first lactation, from 1-week pre-partum to 7&#xa0;months post-partum. Each site harbored a specific community that changed with time, likely reflecting physiological changes in the transition period and changes in diet and housing. Importantly, we found a significant number of microbes shared among different anatomical sites within each animal. This was between nearby anatomic sites, with up to 32% of the total number of Amplicon Sequence Variants (ASVs) of the oral microbiota shared with the nasal microbiota but also between distant ones (e.g. milk with nasal and vaginal microbiotas). In contrast, the share of microbes between animals was limited (<&#x2009;7% of ASVs shared by more than 50% of the herd for a given site and time point). The latter widely shared ASVs were mainly found in the oral and nasal microbiotas. These results thus indicate that despite a common environment and diet, each animal hosted a specific set of bacteria, supporting a tight interplay between each animal and its microbiota. The score of susceptibility to mastitis was slightly but significantly related to the microbiota associated to milk suggesting a link between host genetics and microbiota.<br><br>CONCLUSIONS: This work highlights an important sharing of microbes between relevant microbiotas involved in health and production at the animal level, whereas the presence of common microbes was limited between animals of the herd. This suggests a host regulation of body-associated microbiotas that seems to be differently expressed depending on the body site, as suggested by changes in the milk microbiota that were associated to genotypes of susceptibility to mastitis.}, }
@article {pmid37299176, year = {2023}, author = {Giannelli, G and Potestio, S and Visioli, G}, title = {The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37299176}, issn = {2223-7747}, abstract = {Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.}, }
@article {pmid37288516, year = {2023}, author = {Vargas, S and Leiva, L and Eitel, M and Curdt, F and Rohde, S and Arnold, C and Nickel, M and Schupp, P and Orsi, WD and Adamska, M and Wörheide, G}, title = {Body-Plan Reorganization in a Sponge Correlates with Microbiome Change.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37288516}, issn = {1537-1719}, mesh = {Animals ; *Microbiota ; Bacteria/genetics ; Biological Evolution ; *Porifera ; Symbiosis ; }, abstract = {Mounting evidence suggests that animals and their associated bacteria interact via intricate molecular mechanisms, and it is hypothesized that disturbances to the microbiome influence animal development. Here, we show that the loss of a key photosymbiont (i.e., bleaching) upon shading correlates with a stark body-plan reorganization in the common aquarium cyanosponge Lendenfeldia chondrodes. The morphological changes observed in shaded sponges include the development of a thread-like morphology that contrasts with the flattened, foliose morphology of control specimens. The microanatomy of shaded sponges markedly differed from that of control sponges, with shaded specimens lacking a well-developed cortex and choanosome. Also, the palisade of polyvacuolar gland-like cells typical in control specimens was absent in shaded sponges. The morphological changes observed in shaded specimens are coupled with broad transcriptomic changes and include the modulation of signaling pathways involved in animal morphogenesis and immune response, such as the Wnt, transforming growth factor β (TGF-β), and TLR-ILR pathways. This study provides a genetic, physiological, and morphological assessment of the effect of microbiome changes on sponge postembryonic development and homeostasis. The correlated response of the sponge host to the collapse of the population of symbiotic cyanobacteria provides evidence for a coupling between the sponge transcriptomic state and the state of its microbiome. This coupling suggests that the ability of animals to interact with their microbiomes and respond to microbiome perturbations has deep evolutionary origins in this group.}, }
@article {pmid37287087, year = {2023}, author = {Li, J and Chai, G and Xiao, Y and Li, Z}, title = {The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {49}, pmid = {37287087}, issn = {2524-6372}, support = {42176146//National Natural Science Foundation of China/ ; 31861143020//National Natural Science Foundation of China/ ; 41776138//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Reef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont's homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification-warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control.<br><br>RESULTS: A, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects.<br><br>CONCLUSIONS: The metatranscriptome-based study indicates that acidification and/or warming might change coral's in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont's ability for acclimatization under future climate change.}, }
@article {pmid37285390, year = {2023}, author = {Rubin, JD and Vogel, NA and Gopalakrishnan, S and Sackett, PW and Renaud, G}, title = {HaploCart: Human mtDNA haplogroup classification using a pangenomic reference graph.}, journal = {PLoS computational biology}, volume = {19}, number = {6}, pages = {e1011148}, pmid = {37285390}, issn = {1553-7358}, mesh = {Humans ; *DNA, Mitochondrial/genetics ; Bayes Theorem ; Haplotypes/genetics ; *Mitochondria/genetics ; Mutation ; }, abstract = {Current mitochondrial DNA (mtDNA) haplogroup classification tools map reads to a single reference genome and perform inference based on the detected mutations to this reference. This approach biases haplogroup assignments towards the reference and prohibits accurate calculations of the uncertainty in assignment. We present HaploCart, a probabilistic mtDNA haplogroup classifier which uses a pangenomic reference graph framework together with principles of Bayesian inference. We demonstrate that our approach significantly outperforms available tools by being more robust to lower coverage or incomplete consensus sequences and producing phylogenetically-aware confidence scores that are unbiased towards any haplogroup. HaploCart is available both as a command-line tool and through a user-friendly web interface. The C++ program accepts as input consensus FASTA, FASTQ, or GAM files, and outputs a text file with the haplogroup assignments of the samples along with the level of confidence in the assignments. Our work considerably reduces the amount of data required to obtain a confident mitochondrial haplogroup assignment.}, }
@article {pmid37283898, year = {2023}, author = {McRae, CJ and Keshavmurthy, S and Chen, HK and Ye, ZM and Meng, PJ and Rosset, SL and Huang, WB and Chen, CA and Fan, TY and Côté, IM}, title = {Baseline dynamics of Symbiodiniaceae genera and photochemical efficiency in corals from reefs with different thermal histories.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15421}, pmid = {37283898}, issn = {2167-8359}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida ; Coral Bleaching ; Climate Change ; }, abstract = {Ocean warming and marine heatwaves induced by climate change are impacting coral reefs globally, leading to coral bleaching and mortality. Yet, coral resistance and resilience to warming are not uniform across reef sites and corals can show inter- and intraspecific variability. To understand changes in coral health and to elucidate mechanisms of coral thermal tolerance, baseline data on the dynamics of coral holobiont performance under non-stressed conditions are needed. We monitored the seasonal dynamics of algal symbionts (family Symbiodiniaceae) hosted by corals from a chronically warmed and thermally variable reef compared to a thermally stable reef in southern Taiwan over 15 months. We assessed the genera and photochemical efficiency of Symbiodiniaceae in three coral species: Acropora nana, Pocillopora acuta, and Porites lutea. Both Durusdinium and Cladocopium were present in all coral species at both reef sites across all seasons, but general trends in their detection (based on qPCR cycle) varied between sites and among species. Photochemical efficiency (i.e., maximum quantum yield; Fv/Fm) was relatively similar between reef sites but differed consistently among species; no clear evidence of seasonal trends in Fv/Fm was found. Quantifying natural Symbiodiniaceae dynamics can help facilitate a more comprehensive interpretation of thermal tolerance response as well as plasticity potential of the coral holobiont.}, }
@article {pmid37277669, year = {2023}, author = {Duval, P and Antonelli, P and Aschan-Leygonie, C and Valiente Moro, C}, title = {Impact of Human Activities on Disease-Spreading Mosquitoes in Urban Areas.}, journal = {Journal of urban health : bulletin of the New York Academy of Medicine}, volume = {100}, number = {3}, pages = {591-611}, pmid = {37277669}, issn = {1468-2869}, mesh = {Animals ; Humans ; *Culicidae ; Ecosystem ; Urbanization ; Public Health ; Human Activities ; }, abstract = {Urbanization is one of the leading global trends of the twenty-first century that has a significant impact on health. Among health challenges caused by urbanization, the relationship of urbanization between emergence and the spread of mosquito-borne infectious diseases (MBIDs) is a great public health concern. Urbanization processes encompass social, economic, and environmental changes that directly impact the biology of mosquito species. In particular, urbanized areas experience higher temperatures and pollution levels than outlying areas but also favor the development of infrastructures and objects that are favorable to mosquito development. All these modifications may influence mosquito life history traits and their ability to transmit diseases. This review aimed to summarize the impact of urbanization on mosquito spreading in urban areas and the risk associated with the emergence of MBIDs. Moreover, mosquitoes are considered as holobionts, as evidenced by numerous studies highlighting the role of mosquito-microbiota interactions in mosquito biology. Taking into account this new paradigm, this review also represents an initial synthesis on how human-driven transformations impact microbial communities in larval habitats and further interfere with mosquito behavior and life cycle in urban areas.}, }
@article {pmid37275175, year = {2023}, author = {Timmusk, S and Pall, T and Raz, S and Fetsiukh, A and Nevo, E}, title = {The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141862}, pmid = {37275175}, issn = {1664-302X}, abstract = {Global climate change poses challenges to land use worldwide, and we need to reconsider agricultural practices. While it is generally accepted that biodiversity can be used as a biomarker for healthy agroecosystems, we must specify what specifically composes a healthy microbiome. Therefore, understanding how holobionts function in native, harsh, and wild habitats and how rhizobacteria mediate plant and ecosystem biodiversity in the systems enables us to identify key factors for plant fitness. A systems approach to engineering microbial communities by connecting host phenotype adaptive traits would help us understand the increased fitness of holobionts supported by genetic diversity. Identification of genetic loci controlling the interaction of beneficial microbiomes will allow the integration of genomic design into crop breeding programs. Bacteria beneficial to plants have traditionally been conceived as "promoting and regulating plant growth". The future perspective for agroecosystems should be that microbiomes, via multiple cascades, define plant phenotypes and provide genetic variability for agroecosystems.}, }
@article {pmid37270649, year = {2023}, author = {Khakisahneh, S and Zhang, XY and Han, SY and Song, EJ and Nam, YD and Kim, H}, title = {Yijung-tang improves thermogenesis and reduces inflammation associated with gut microbiota in hypothyroid rats.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {32}, pmid = {37270649}, issn = {2055-5008}, mesh = {Rats ; Humans ; Animals ; *Gastrointestinal Microbiome ; Inflammation/drug therapy ; Thermogenesis ; *Hypothyroidism/drug therapy ; }, abstract = {Currently, considerable attention is focused on exploring the potential relationship between herbal medicine (HM) and the gut microbiome in terms of thermoregulation, which is an important aspect of human health, in modern system biology. However, our knowledge of the mechanisms of HM in thermoregulation is inadequate. Here, we demonstrate that the canonical herbal formula, Yijung-tang (YJT), protects against hypothermia, hyperinflammation, and intestinal microbiota dysbiosis in PTU-induced hypothyroid rats. Notably, these properties were associated with alterations in the gut microbiota and signaling crosstalk between the thermoregulatory and inflammatory mediators in the small intestine and brown adipose tissue (BAT). In contrast to the conventional drug L-thyroxine for curing hypothyroidism, YJT has an efficacy for attenuating systematic inflammatory responses, related with depression in intestinal TLR4 and Nod2/Pglyrp1 signaling pathways. Our findings suggest that YJT could promote BAT thermogenesis and prevent systemic inflammation in PTU-induced hypothyroid rats, which was associated with its prebiotic effect on modulating of the gut microbiota and gene expression with relevance in the enteroendocrine function and innate immune systems. These findings may strengthen the rationale of the microbiota-gut-BAT axis for a paradigm shift to enable holobiont-centric medicine.}, }
@article {pmid37269833, year = {2023}, author = {Kim, SM and Park, S and Hwang, SH and Lee, EY and Kim, JH and Lee, GS and Lee, G and Chang, DH and Lee, JG and Hwang, J and Lee, Y and Kyung, M and Kim, EK and Kim, JH and Kim, TH and Moon, JH and Kim, BC and Ko, G and Kim, SY and Ryu, JH and Lee, JS and Lee, CH and Kim, JY and Kim, S and Lee, WJ and Kim, MH}, title = {Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis.}, journal = {Cell host &amp; microbe}, volume = {31}, number = {6}, pages = {1021-1037.e10}, doi = {10.1016/j.chom.2023.05.007}, pmid = {37269833}, issn = {1934-6069}, mesh = {Homeostasis ; Akkermansia ; Phosphatidylinositol 3-Kinases/metabolism ; Interleukin-10/metabolism ; Mice ; *Threonine-tRNA Ligase/metabolism ; Verrucomicrobia/metabolism ; Animals ; RNA, Transfer/metabolism ; }, abstract = {Commensal bacteria are critically involved in the establishment of tolerance against inflammatory challenges, the molecular mechanisms of which are just being uncovered. All kingdoms of life produce aminoacyl-tRNA synthetases (ARSs). Thus far, the non-translational roles of ARSs have largely been reported in eukaryotes. Here, we report that the threonyl-tRNA synthetase (AmTARS) of the gut-associated bacterium Akkermansia muciniphila is secreted and functions to monitor and modulate immune homeostasis. Secreted AmTARS triggers M2 macrophage polarization and orchestrates the production of anti-inflammatory IL-10 via its unique, evolutionary-acquired regions, which mediates specific interactions with TLR2. This interaction activates the MAPK and PI3K/AKT signaling pathways, which converge on CREB, leading to an efficient production of IL-10 and suppression of the central inflammatory mediator NF-κB. AmTARS restores IL-10-positive macrophages, increases IL-10 levels in the serum, and attenuates the pathological effects in colitis mice. Thus, commensal tRNA synthetases can act as intrinsic mediators that maintain homeostasis.}, }
@article {pmid37268692, year = {2023}, author = {de Souza, MR and Caruso, C and Ruiz-Jones, L and Drury, C and Gates, RD and Toonen, RJ}, title = {Importance of depth and temperature variability as drivers of coral symbiont composition despite a mass bleaching event.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8957}, pmid = {37268692}, issn = {2045-2322}, mesh = {Animals ; *Anthozoa/physiology ; Temperature ; Coral Reefs ; Heat-Shock Response ; *Dinoflagellida/physiology ; Symbiosis ; Hot Temperature ; }, abstract = {Coral reefs are iconic examples of climate change impacts because climate-induced heat stress causes the breakdown of the coral-algal symbiosis leading to a spectacular loss of color, termed 'coral bleaching'. To examine the fine-scale dynamics of this process, we re-sampled 600 individually marked Montipora capitata colonies from across Kāne'ohe Bay, Hawai'i and compared the algal symbiont composition before and after the 2019 bleaching event. The relative proportion of the heat-tolerant symbiont Durusdinium in corals increased in most parts of the bay following the bleaching event. Despite this widespread increase in abundance of Durusdinium, the overall algal symbiont community composition was largely unchanged, and hydrodynamically defined regions of the bay retained their distinct pre-bleaching compositions. We explain ~ 21% of the total variation, of which depth and temperature variability were the most significant environmental drivers of Symbiodiniaceae community composition by site regardless of bleaching intensity or change in relative proportion of Durusdinium. We hypothesize that the plasticity of symbiont composition in corals may be constrained to adaptively match the long-term environmental conditions surrounding the holobiont, despite an individual coral's stress and bleaching response.}, }
@article {pmid37264047, year = {2023}, author = {Belser, C and Poulain, J and Labadie, K and Gavory, F and Alberti, A and Guy, J and Carradec, Q and Cruaud, C and Da Silva, C and Engelen, S and Mielle, P and Perdereau, A and Samson, G and Gas, S and ,  and Voolstra, CR and Galand, PE and Flores, JM and Hume, BCC and Perna, G and Ziegler, M and Ruscheweyh, HJ and Boissin, E and Romac, S and Bourdin, G and Iwankow, G and Moulin, C and Paz García, DA and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Sunagawa, S and Thomas, OP and Troublé, R and Thurber, RV and Zoccola, D and Scarpelli, C and Jacoby, EK and Oliveira, PH and Aury, JM and Allemand, D and Planes, S and Wincker, P}, title = {Integrative omics framework for characterization of coral reef ecosystems from the Tara Pacific expedition.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {326}, pmid = {37264047}, issn = {2052-4463}, mesh = {Animals ; *Anthozoa ; Biodiversity ; *Coral Reefs ; Ecosystem ; }, abstract = {Coral reef science is a fast-growing field propelled by the need to better understand coral health and resilience to devise strategies to slow reef loss resulting from environmental stresses. Key to coral resilience are the symbiotic interactions established within a complex holobiont, i.e. the multipartite assemblages comprising the coral host organism, endosymbiotic dinoflagellates, bacteria, archaea, fungi, and viruses. Tara Pacific is an ambitious project built upon the experience of previous Tara Oceans expeditions, and leveraging state-of-the-art sequencing technologies and analyses to dissect the biodiversity and biocomplexity of the coral holobiont screened across most archipelagos spread throughout the entire Pacific Ocean. Here we detail the Tara Pacific workflow for multi-omics data generation, from sample handling to nucleotide sequence data generation and deposition. This unique multidimensional framework also includes a large amount of concomitant metadata collected side-by-side that provide new assessments of coral reef biodiversity including micro-biodiversity and shape future investigations of coral reef dynamics and their fate in the Anthropocene.}, }
@article {pmid37264015, year = {2023}, author = {Hochart, C and Paoli, L and Ruscheweyh, HJ and Salazar, G and Boissin, E and Romac, S and Poulain, J and Bourdin, G and Iwankow, G and Moulin, C and Ziegler, M and Porro, B and Armstrong, EJ and Hume, BCC and Aury, JM and Pogoreutz, C and Paz-García, DA and Nugues, MM and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Thomas, OP and Troublé, R and Wincker, P and Zoccola, D and Allemand, D and Planes, S and Thurber, RV and Voolstra, CR and Sunagawa, S and Galand, PE}, title = {Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3037}, pmid = {37264015}, issn = {2041-1723}, mesh = {Animals ; *Anthozoa/microbiology ; Pacific Ocean ; Ecology ; *Gammaproteobacteria ; Bacteria ; Coral Reefs ; }, abstract = {Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.}, }
@article {pmid37258653, year = {2023}, author = {Garritano, AN and Majzoub, ME and Ribeiro, B and Damasceno, T and Modolon, F and Messias, C and Vilela, C and Duarte, G and Hill, L and Peixoto, R and Thomas, T}, title = {Species-specific relationships between deep sea sponges and their symbiotic Nitrosopumilaceae.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1517-1519}, pmid = {37258653}, issn = {1751-7370}, mesh = {Animals ; Phylogeny ; Archaea/genetics ; *Microbiota ; Ecology ; *Porifera ; }, abstract = {Sponges thrive in the deep, dark and nutrient-depleted ocean and may rely on microbial symbionts for carbon acquisition and energy generation. However, these symbiotic relationships remain largely unexplored. In this study, we analyze the microbiome of deep-sea sponges and show that ammonia-oxidizing archaea (AOA) of the family Nitrosopumilaceae make up at least 75% of the microbial communities of the sponges Aphrocallistes sp., Farrea sp. and Paratimea sp.. Given the known autotrophic metabolism of AOAs, this implies that these sponge holobionts can have the capacity for primary production in the deep-sea. We also show that specific AOA lineages are highly specific towards their hosts, hinting towards an unprecedent vertical transmission of these symbionts in deep-sea sponges. Our results show that the ecology and evolution of symbiotic relationships in deep-sea sponge is distinct from that of their shallow-water counterparts.}, }
@article {pmid37255458, year = {2023}, author = {Ramayo-Caldas, Y and Crespo-Piazuelo, D and Morata, J and González-Rodríguez, O and Sebastià, C and Castello, A and Dalmau, A and Ramos-Onsins, S and Alexiou, KG and Folch, JM and Quintanilla, R and Ballester, M}, title = {Copy Number Variation on ABCC2-DNMBP Loci Affects the Diversity and Composition of the Fecal Microbiota in Pigs.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0527122}, pmid = {37255458}, issn = {2165-0497}, mesh = {Swine ; Animals ; *Genome-Wide Association Study ; DNA Copy Number Variations ; Genome ; Phenotype ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut microbiota, but little is known about the relationship between structural variants and fecal microbial traits. The main goal of this study was to explore the association between porcine genome copy number variants (CNVs) and the diversity and composition of pig fecal microbiota. For this purpose, we used whole-genome sequencing data to undertake a comprehensive identification of CNVs followed by a genome-wide association analysis between the estimated CNV status and the fecal bacterial diversity in a commercial Duroc pig population. A CNV predicted as gain (DUP) partially harboring ABCC2-DNMBP loci was associated with richness (P = 5.41 × 10[-5], false discovery rate [FDR] = 0.022) and Shannon α-diversity (P = 1.42 × 10[-4], FDR = 0.057). The in silico predicted gain of copies was validated by real-time quantitative PCR (qPCR), and its segregation, and positive association with the richness and Shannon α-diversity of the porcine fecal bacterial ecosystem was confirmed in an unrelated F1 (Duroc × Iberian) cross. Our results advise the relevance of considering the role of host-genome structural variants as potential modulators of microbial ecosystems and suggest the ABCC2-DNMBP CNV as a host-genetic factor for the modulation of the diversity and composition of the fecal microbiota in pigs. IMPORTANCE A better understanding of the environmental and host factors modulating gut microbiomes is a topic of greatest interest. Recent evidence suggests that genetic variation in the pig genome partially controls the composition of porcine gut microbiota. However, since previous studies have been focused on the association between single nucleotide polymorphisms and the fecal microbiota, little is known about the relationship between other sources of genetic variation, like the structural variants and microbial traits. Here, we identified, experimentally validated, and replicated in an independent population a positive link between the gain of copies of ABCC2-DNMBP loci and the diversity and composition of pig fecal microbiota. Our results advise the relevance of considering the role of host-genome structural variants as putative modulators of microbial ecosystems and open the possibility of implementing novel holobiont-based management strategies in breeding programs for the simultaneous improvement of microbial traits and host performance.}, }
@article {pmid37254353, year = {2023}, author = {Azad, AM and Bernhard, A and Shen, A and Myrmel, LS and Lundebye, AK and Lecaudey, LA and Fjære, E and Tri Ho, Q and Sveier, H and Kristiansen, K and Limborg, MT and Madsen, L}, title = {Metabolic effects of diet containing blue mussel (Mytilus edulis) and blue mussel-fed salmon in a mouse model of obesity.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112927}, doi = {10.1016/j.foodres.2023.112927}, pmid = {37254353}, issn = {1873-7145}, mesh = {Animals ; Mice ; Diet, Western ; Fatty Acids/metabolism ; *Fatty Acids, Omega-3 ; *Mytilus edulis/metabolism ; Obesity ; *Salmo salar/metabolism ; Seafood ; }, abstract = {Alternative feed ingredients for farmed salmon are warranted due to increasing pressure on wild fish stocks. As locally farmed blue mussels may represent an environmentally sustainable substitute with a lower carbon footprint, we aimed to test the potential and safety of substituting fish meal with blue mussel meal in feed for Atlantic salmon. Salmon were fed diets in which fish meal was partially replaced with blue mussel meal in increments, accounting for up to 13.1 % of the ingredients. Fillets from the salmon were subsequently used to prepare obesity-promoting western diets for a 13-weeks mouse feeding trial. In a second mouse trial, we tested the effects of inclusion of up to 8% blue mussel meal directly in a meat-based western diet. Partial replacement of fish meal with blue mussel meal in fish feed preserved the n-3 polyunsaturated fatty acid (PUFA) content in salmon fillets. The observed blue mussel-induced changes in the fatty acid profiles in salmon fillets did not translate into similar changes in the livers of mice that consumed the salmon, and no clear dose-dependent responses were found. The relative levels of the marine n-3 fatty acids, EPA, and DHA were not reduced, and the n-3/n-6 PUFA ratios in livers from all salmon-fed mice were unchanged. The inclusion of blue mussel meal in a meat-based western diet led to a small, but dose-dependent increase in the n-3/n-6 PUFA ratios in mice livers. Diet-induced obesity, glucose intolerance, and hepatic steatosis were unaffected in both mice trials and no blue mussel-induced adverse effects were observed. In conclusion, our results suggest that replacing fish meal with blue mussel meal in salmon feed will not cause adverse effects in those who consume the salmon fillets.}, }
@article {pmid37249392, year = {2023}, author = {Kliver, S and Houck, ML and Perelman, PL and Totikov, A and Tomarovsky, A and Dudchenko, O and Omer, AD and Colaric, Z and Weisz, D and Aiden, EL and Chan, S and Hastie, A and Komissarov, A and Ryder, OA and Graphodatsky, A and Johnson, WE and Maldonado, JE and Pukazhenthi, BS and Marinari, PE and Wildt, DE and Koepfli, KP}, title = {Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).}, journal = {The Journal of heredity}, volume = {114}, number = {5}, pages = {539-548}, pmid = {37249392}, issn = {1465-7333}, support = {RM1 HG011016/HG/NHGRI NIH HHS/United States ; UM1 HG009375/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Male ; *Ferrets/genetics ; *Endangered Species ; Karyotype ; Karyotyping ; Fertility ; }, abstract = {The black-footed ferret (Mustela nigripes) narrowly avoided extinction to become an oft-cited example of the benefits of intensive management, research, and collaboration to save a species through ex situ conservation breeding and reintroduction into its former range. However, the species remains at risk due to possible inbreeding, disease susceptibility, and multiple fertility challenges. Here, we report the de novo genome assembly of a male black-footed ferret generated through a combination of linked-read sequencing, optical mapping, and Hi-C proximity ligation. In addition, we report the karyotype for this species, which was used to anchor and assign chromosome numbers to the chromosome-length scaffolds. The draft assembly was ~2.5 Gb in length, with 95.6% of it anchored to 19 chromosome-length scaffolds, corresponding to the 2n = 38 chromosomes revealed by the karyotype. The assembly has contig and scaffold N50 values of 148.8 kbp and 145.4 Mbp, respectively, and is up to 96% complete based on BUSCO analyses. Annotation of the assembly, including evidence from RNA-seq data, identified 21,406 protein-coding genes and a repeat content of 37.35%. Phylogenomic analyses indicated that the black-footed ferret diverged from the European polecat/domestic ferret lineage 1.6 million yr ago. This assembly will enable research on the conservation genomics of black-footed ferrets and thereby aid in the further restoration of this endangered species.}, }
@article {pmid37237923, year = {2023}, author = {Doering, T and Maire, J and Chan, WY and Perez-Gonzalez, A and Meyers, L and Sakamoto, R and Buthgamuwa, I and Blackall, LL and van Oppen, MJH}, title = {Comparing the Role of ROS and RNS in the Thermal Stress Response of Two Cnidarian Models, Exaiptasia diaphana and Galaxea fascicularis.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37237923}, issn = {2076-3921}, support = {FL180100036//Australian Research Council/ ; Melbourne Research Scholarship//Environmental Microbiology Research Initiative/ ; Research Award//Northern Australian Animals Trust/ ; }, abstract = {Coral reefs are threatened by climate change, because it causes increasingly frequent and severe summer heatwaves, resulting in mass coral bleaching and mortality. Coral bleaching is believed to be driven by an excess production of reactive oxygen (ROS) and nitrogen species (RNS), yet their relative roles during thermal stress remain understudied. Here, we measured ROS and RNS net production, as well as activities of key enzymes involved in ROS scavenging (superoxide dismutase and catalase) and RNS synthesis (nitric oxide synthase) and linked these metrics to physiological measurements of cnidarian holobiont health during thermal stress. We did this for both an established cnidarian model, the sea anemone Exaiptasia diaphana, and an emerging scleractinian model, the coral Galaxea fascicularis, both from the Great Barrier Reef (GBR). Increased ROS production was observed during thermal stress in both species, but it was more apparent in G. fascicularis, which also showed higher levels of physiological stress. RNS did not change in thermally stressed G. fascicularis and decreased in E. diaphana. Our findings in combination with variable ROS levels in previous studies on GBR-sourced E. diaphana suggest G. fascicularis is a more suitable model to study the cellular mechanisms of coral bleaching.}, }
@article {pmid37233466, year = {2023}, author = {De Domenico, S and De Rinaldis, G and Mammone, M and Bosch-Belmar, M and Piraino, S and Leone, A}, title = {The Zooxanthellate Jellyfish Holobiont Cassiopea andromeda, a Source of Soluble Bioactive Compounds.}, journal = {Marine drugs}, volume = {21}, number = {5}, pages = {}, pmid = {37233466}, issn = {1660-3397}, support = {"National Biodiversity Future Center - NBFC", Project code CN_00000033, Concession Decree No. 1034 of 17 June 2022//National Recovery and Resilience Plan (NRRP)/ ; Program "REFIN-Research for Innovation" Code: AFD9B120.//Apulian Region, Italy/ ; "GoJelly - A gelatinous solution to plastic pollution" No. 774499//European Commission/ ; ACTNOW - "Advancing understanding of Cumulative Impacts on European marine biodiversity, ecosystem functions and services for human wellbeing" 101060072//European Commission/ ; }, mesh = {Animals ; *Cnidaria ; *Scyphozoa/chemistry ; Antioxidants/pharmacology/chemistry ; Proteins ; Fatty Acids ; }, abstract = {Cassiopea andromeda (Forsskål, 1775), commonly found across the Indo-Pacific Ocean, the Red Sea, and now also in the warmest areas of the Mediterranean Sea, is a scyphozoan jellyfish that hosts autotrophic dinoflagellate symbionts (family Symbiodiniaceae). Besides supplying photosynthates to their host, these microalgae are known to produce bioactive compounds as long-chain unsaturated fatty acids, polyphenols, and pigments, including carotenoids, with antioxidant properties and other beneficial biological activities. By the present study, a fractionation method was applied on the hydroalcoholic extract from two main body parts (oral arms and umbrella) of the jellyfish holobiont to obtain an improved biochemical characterization of the obtained fractions from the two body parts. The composition of each fraction (i.e., proteins, phenols, fatty acids, and pigments) as well as the associated antioxidant activity were analyzed. The oral arms proved richer in zooxanthellae and pigments than the umbrella. The applied fractionation method was effective in separating pigments and fatty acids into a lipophilic fraction from proteins and pigment-protein complexes. Therefore, the C. andromeda-dinoflagellate holobiont might be considered as a promising natural source of multiple bioactive compounds produced through mixotrophic metabolism, which are of interest for a wide range of biotechnological applications.}, }
@article {pmid37233257, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {37233257}, issn = {2309-608X}, support = {031B0824A//Federal Ministry of Education and Research/ ; }, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, }
@article {pmid37231184, year = {2023}, author = {Zheng, R and Wang, Q and Wu, R and Paradkar, PN and Hoffmann, AA and Wang, GH}, title = {Holobiont perspectives on tripartite interactions among microbiota, mosquitoes, and pathogens.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1143-1152}, pmid = {37231184}, issn = {1751-7370}, mesh = {Animals ; Humans ; *Culicidae ; Mosquito Vectors ; *Microbiota/physiology ; *Malaria ; *Wolbachia/physiology ; }, abstract = {Mosquito-borne diseases like dengue and malaria cause a significant global health burden. Unfortunately, current insecticides and environmental control strategies aimed at the vectors of these diseases are only moderately effective in decreasing disease burden. Understanding and manipulating the interaction between the mosquito holobiont (i.e., mosquitoes and their resident microbiota) and the pathogens transmitted by these mosquitoes to humans and animals could help in developing new disease control strategies. Different microorganisms found in the mosquito's microbiota affect traits related to mosquito survival, development, and reproduction. Here, we review the physiological effects of essential microbes on their mosquito hosts; the interactions between the mosquito holobiont and mosquito-borne pathogen (MBP) infections, including microbiota-induced host immune activation and Wolbachia-mediated pathogen blocking (PB); and the effects of environmental factors and host regulation on the composition of the microbiota. Finally, we briefly overview future directions in holobiont studies, and how these may lead to new effective control strategies against mosquitoes and their transmitted diseases.}, }
@article {pmid37229712, year = {2023}, author = {Roughgarden, J}, title = {Holobiont Evolution: Population Theory for the Hologenome.}, journal = {The American naturalist}, volume = {201}, number = {6}, pages = {763-778}, doi = {10.1086/723782}, pmid = {37229712}, issn = {1537-5323}, mesh = {*Biological Evolution ; Symbiosis/physiology ; *Microbiota/genetics ; Population Dynamics ; Cell Nucleus ; }, abstract = {AbstractThis article develops mathematical theory for the population dynamics of microbiomes with their hosts and for holobiont evolution caused by holobiont selection. The objective is to account for the formation of microbiome-host integration. Microbial population dynamic parameters must mesh with the host's for coexistence. A horizontally transmitted microbiome is a genetic system with "collective inheritance." The microbial source pool in the environment corresponds to the gamete pool for nuclear genes. Poisson sampling of the microbial source pool corresponds to binomial sampling of the gamete pool. However, holobiont selection on the microbiome does not lead to a counterpart of the Hardy-Weinberg law or to directional selection that always fixes microbial genes conferring the highest holobiont fitness. A microbe might strike an optimal fitness balance between lowering its within-host fitness while increasing holobiont fitness. Such microbes are replaced by otherwise identical microbes that contribute nothing to holobiont fitness. This replacement can be reversed by hosts that initiate immune responses to nonhelpful microbes. This discrimination leads to microbial species sorting. Host-orchestrated species sorting followed by microbial competition, rather than coevolution or multilevel selection, is predicted to be the cause of microbiome-host integration.}, }
@article {pmid37228141, year = {2023}, author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N}, title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286293}, pmid = {37228141}, issn = {1932-6203}, mesh = {Animals ; Viverridae/genetics ; *Anthozoa/genetics/microbiology ; *Microbiota/genetics ; Gene Expression Profiling ; Serratia marcescens/genetics ; Coral Reefs ; }, abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.}, }
@article {pmid37217641, year = {2023}, author = {Lintner, M and Lintner, B and Schagerl, M and Wanek, W and Heinz, P}, title = {The change in metabolic activity of a large benthic foraminifera as a function of light supply.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8240}, pmid = {37217641}, issn = {2045-2322}, mesh = {*Foraminifera/metabolism ; Photosynthesis ; Isotopes/metabolism ; }, abstract = {We studied metabolic activity of the symbiont-bearing large benthic foraminifer Heterostegina depressa under different light conditions. Besides the overall photosynthetic performance of the photosymbionts estimated by means of variable fluorescence, the isotope uptake ([13]C and [15]N) of the specimens (= holobionts) was measured. Heterostegina depressa was either incubated in darkness over a period of 15 days or exposed to an 16:8 h light:dark cycle mimicking natural light conditions. We found photosynthetic performance to be highly related to light supply. The photosymbionts, however, survived prolonged darkness and could be reactivated after 15 days of darkness. The same pattern was found in the isotope uptake of the holobionts. Based on these results, we propose that [13]C-carbonate and [15]N-nitrate assimilation is mainly controlled by the photosymbionts, whereas [15]N-ammonium and [13]C-glucose utilization is regulated by both, the symbiont and the host cells.}, }
@article {pmid37217368, year = {2023}, author = {Aizpurua, O and Blijleven, K and Trivedi, U and Gilbert, MTP and Alberdi, A}, title = {Unravelling animal-microbiota evolution on a chip.}, journal = {Trends in microbiology}, volume = {31}, number = {10}, pages = {995-1002}, doi = {10.1016/j.tim.2023.04.010}, pmid = {37217368}, issn = {1878-4380}, mesh = {Animals ; *Microbiota/genetics ; Models, Animal ; Host Microbial Interactions ; Lab-On-A-Chip Devices ; }, abstract = {Whether and how microorganisms have shaped the evolution of their animal hosts is a major question in biology. Although many animal evolutionary processes appear to correlate with changes in their associated microbial communities, the mechanistic processes leading to these patterns and their causal relationships are still far from being resolved. Gut-on-a-chip models provide an innovative approach that expands beyond the potential of conventional microbiome profiling to study how different animals sense and react to microbes by comparing responses of animal intestinal tissue models to different microbial stimuli. This complementary knowledge can contribute to our understanding of how host genetic features facilitate or prevent different microbiomes from being assembled, and in doing so elucidate the role of host-microbiota interactions in animal evolution.}, }
@article {pmid37214652, year = {2023}, author = {Clokie, M and Sicheritz-Pontén, T}, title = {Lungs, Liposomes, Libraries, and Likely Interactions Between Phages and Eukaryotic Cells.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {4}, number = {1}, pages = {1-2}, doi = {10.1089/phage.2023.29041.editorial}, pmid = {37214652}, issn = {2641-6549}, }
@article {pmid37210404, year = {2023}, author = {Zvi-Kedem, T and Vintila, S and Kleiner, M and Tchernov, D and Rubin-Blum, M}, title = {Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {48}, pmid = {37210404}, issn = {2730-6151}, support = {913/19//Israel Science Foundation (ISF)/ ; 2019055//United States - Israel Binational Science Foundation (BSF)/ ; 2019055//United States - Israel Binational Science Foundation (BSF)/ ; 2003107//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; }, abstract = {Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.}, }
@article {pmid37209745, year = {2023}, author = {Núñez-Pons, L and Cunning, R and Nelson, CE and Amend, AS and Sogin, EM and Gates, R and Ritson-Williams, R}, title = {Hawaiian coral holobionts reveal algal and prokaryotic host specificity, intraspecific variability in bleaching resistance, and common interspecific microbial consortia modulating thermal stress responses.}, journal = {The Science of the total environment}, volume = {889}, number = {}, pages = {164040}, doi = {10.1016/j.scitotenv.2023.164040}, pmid = {37209745}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Hawaii ; Microbial Consortia ; Host Specificity ; RNA, Ribosomal, 16S/genetics ; *Dinoflagellida ; Bacteria/genetics ; }, abstract = {Historically, Hawai'i had few massive coral bleaching events, until two consecutive heatwaves in 2014-2015. Consequent mortality and thermal stress were observed in Kāne'ohe Bay (O'ahu). The two most dominant local species exhibited a phenotypic dichotomy of either bleaching resistance or susceptibility (Montipora capitata and Porites compressa), while the third predominant species (Pocillopora acuta) was broadly susceptible to bleaching. In order to survey shifts in coral microbiomes during bleaching and recovery, 50 colonies were tagged and periodically monitored. Metabarcoding of three genetic markers (16S rRNA gene ITS1 and ITS2) followed by compositional approaches for community structure analysis, differential abundance and correlations for longitudinal data were used to temporally compare Bacteria/Archaea, Fungi and Symbiodiniaceae dynamics. P. compressa corals recovered faster than P. acuta and Montipora capitata. Prokaryotic and algal communities were majorly shaped by host species, and had no apparent pattern of temporal acclimatization. Symbiodiniaceae signatures were identified at the colony scale, and were often related to bleaching susceptibility. Bacterial compositions were practically constant between bleaching phenotypes, and more diverse in P. acuta and M. capitata. P. compressa's prokaryotic community was dominated by a single bacterium. Compositional approaches (via microbial balances) allowed the identification of fine-scale differences in the abundance of a consortium of microbes, driving changes by bleaching susceptibility and time across all hosts. The three major coral reef founder-species in Kāne'ohe Bay revealed different phenotypic and microbiome responses after 2014-2015 heatwaves. It is difficult to forecast, a more successful strategy towards future scenarios of global warming. Differentially abundant microbial taxa across time and/or bleaching susceptibility were broadly shared among all hosts, suggesting that locally, the same microbes may modulate stress responses in sympatric coral species. Our study highlights the potential of investigating microbial balances to identify fine-scale microbiome changes, serving as local diagnostic tools of coral reef fitness.}, }
@article {pmid37209734, year = {2023}, author = {Sun, H and Xie, Z and Yang, X and Yang, B and Liao, B and Yin, J and Xiao, B}, title = {New insights into microbial and metabolite signatures of coral bleaching.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164258}, doi = {10.1016/j.scitotenv.2023.164258}, pmid = {37209734}, issn = {1879-1026}, mesh = {Animals ; Coral Bleaching ; Coral Reefs ; *Anthozoa/physiology ; Heat-Shock Response ; *Microbiota ; Bacteria ; Symbiosis ; }, abstract = {Coral bleaching and coral reef degradation have been severely increased due to anthropogenic impacts, especially global warming. Studies have indicated the key role of host-microbiome symbiotic relationships for the coral holobiont health and development, although not all of the mechanisms of interaction have been fully explored. Here, we explore bacterial and metabolic shifts within coral holobionts under thermal stress, and its correlation with bleaching. Our results showed obvious signs of coral bleaching after 13 days of heating treatment, and a more-complex co-occurrence network was observed in the coral-associated bacterial community of the heating group. The bacterial community and metabolites changed significantly under thermal stress, and genera Flavobacterium, Shewanella and Psychrobacter increased from <0.1 % to 43.58 %, 6.95 % and 6.35 %, respectively. Bacteria potentially associated with stress tolerance, biofilm formation and mobile elements decreased from 80.93 %, 62.15 % and 49.27 % to 56.28 %, 28.41 % and 18.76 %, respectively. The differentially expressed metabolites of corals after heating treatment, such as Cer(d18:0/17:0), 1-Methyladenosine, Trp-P-1 and Marasmal, were associated with cell cycle regulation and antioxidant properties. Our results can contribute to our current understanding on the correlations between coral-symbiotic bacteria, metabolites and the coral physiological response to thermal stress. These new insights into the metabolomics of heat-stressed coral holobionts may expand our knowledge on the mechanisms underlying bleaching.}, }
@article {pmid37194081, year = {2023}, author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B}, title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {108}, pmid = {37194081}, issn = {2049-2618}, mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; }, abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.<br><br>RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.<br><br>CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.}, }
@article {pmid37191552, year = {2023}, author = {Xu, M and Cheng, K and Xiao, B and Tong, M and Cai, Z and Jong, MC and Chen, G and Zhou, J}, title = {Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0491022}, pmid = {37191552}, issn = {2165-0497}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria ; Coral Reefs ; *Microbiota ; *Gammaproteobacteria ; }, abstract = {Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.}, }
@article {pmid37191521, year = {2023}, author = {Norfolk, WA and Melendez-Declet, C and Lipp, EK}, title = {Coral Disease and Ingestion: Investigating the Role of Heterotrophy in the Transmission of Pathogenic Vibrio spp. using a Sea Anemone (Exaiptasia pallida) Model System.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0018723}, pmid = {37191521}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; *Sea Anemones/microbiology ; Heterotrophic Processes ; *Vibrio ; Eating ; }, abstract = {Understanding disease transmission in corals can be complicated given the intricacy of the holobiont and difficulties associated with ex situ coral cultivation. As a result, most of the established transmission pathways for coral disease are associated with perturbance (i.e., damage) rather than evasion of immune defenses. Here, we investigate ingestion as a potential pathway for the transmission of coral pathogens that evades the mucus membrane. Using sea anemones (Exaiptasia pallida) and brine shrimp (Artemia sp.) to model coral feeding, we tracked the acquisition of the putative pathogens, Vibrio alginolyticus, V. harveyi, and V. mediterranei using GFP-tagged strains. Vibrio sp. were provided to anemones using 3 experimental exposures (i) direct water exposure alone, (ii) water exposure in the presence of a food source (non-spiked Artemia), and (iii) through a "spiked" food source (Vibrio-colonized Artemia) created by exposing Artemia cultures to GFP-Vibrio via the ambient water overnight. Following a 3 h feeding/exposure duration, the level of acquired GFP-Vibrio was quantified from anemone tissue homogenate. Ingestion of spiked Artemia resulted in a significantly greater burden of GFP-Vibrio equating to an 830-fold, 3,108-fold, and 435-fold increase in CFU mL[-1] when compared to water exposed trials and a 207-fold, 62-fold, and 27-fold increase in CFU mL[-1] compared to water exposed with food trials for V. alginolyticus, V. harveyi, and V. mediterranei, respectively. These data suggest that ingestion can facilitate delivery of an elevated dose of pathogenic bacteria in cnidarians and may describe an important portal of entry for pathogens in the absence of perturbing conditions. IMPORTANCE The front line of pathogen defense in corals is the mucus membrane. This membrane coats the surface body wall creating a semi-impermeable layer that inhibits pathogen entry from the ambient water both physically and biologically through mutualistic antagonism from resident mucus microbes. To date, much of the coral disease transmission research has been focused on mechanisms associated with perturbance of this membrane such as direct contact, vector lesions (predation/biting), and waterborne exposure through preexisting lesions. The present research describes a potential transmission pathway that evades the defenses provided by this membrane allowing unencumbered entry of bacteria as in association with food. This pathway may explain an important portal of entry for emergence of idiopathic infections in otherwise healthy corals and can be used to improve management practices for coral conservation.}, }
@article {pmid37184242, year = {2023}, author = {Quigley, K and Carey, N and Alvarez Roa, C}, title = {Physiological Characterization of the Coral Holobiont Using a New Micro-Respirometry Tool.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {194}, pages = {}, doi = {10.3791/64812}, pmid = {37184242}, issn = {1940-087X}, mesh = {Animals ; *Anthozoa/physiology ; Ecosystem ; Coral Reefs ; Symbiosis ; }, abstract = {Metabolic activity, defined as the sum of organismal processes that involve energy, is of critical importance in understanding the function and evolution of life on earth. Measuring organismal metabolic rates is, therefore, at the center of explaining the physiological states of organisms, their ecological roles, and the impact of environmental change on species within terrestrial and aquatic ecosystems. On coral reefs, measures of metabolism have been used to quantify symbiosis functioning between corals and their obligate algal symbionts (Symbiodiniaceae), as well as assess how environmental stressors, including climate change, will impact coral health. Despite this significance, there is a lack of methods, and therefore data, relating to metabolic rate measurements in coral offspring, likely due to their small size. To address this gap, this study aimed to develop a custom setup for measuring the respiration of small (millimeter size range) marine animal ecologies. This low cost and easy setup should allow for the improved measurement of metabolic rate. This will be essential for applied ecological research utilizing the sexual production of corals for reef restoration.}, }
@article {pmid37175775, year = {2023}, author = {Kazakova, P and Abasolo, N and de Cripan, SM and Marquès, E and Cereto-Massagué, A and Garcia, L and Canela, N and Tormo, R and Torrell, H}, title = {Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175775}, issn = {1422-0067}, mesh = {Infant, Newborn ; Humans ; Infant ; *Meconium ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Milk, Human ; Bacteria/genetics ; DNA, Viral ; }, abstract = {The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.}, }
@article {pmid37174660, year = {2023}, author = {Cuffaro, B and Boutillier, D and Desramaut, J and Jablaoui, A and Werkmeister, E and Trottein, F and Waligora-Dupriet, AJ and Rhimi, M and Maguin, E and Grangette, C}, title = {Characterization of Two Parabacteroides distasonis Candidate Strains as New Live Biotherapeutics against Obesity.}, journal = {Cells}, volume = {12}, number = {9}, pages = {}, pmid = {37174660}, issn = {2073-4409}, mesh = {Animals ; Mice ; *Obesity/therapy/metabolism ; Bacteroidetes ; *Gastrointestinal Microbiome ; Adipose Tissue/metabolism ; }, abstract = {The gut microbiota is now considered as a key player in the development of metabolic dysfunction. Therefore, targeting gut microbiota dysbiosis has emerged as a new therapeutic strategy, notably through the use of live gut microbiota-derived biotherapeutics. We previously highlighted the anti-inflammatory abilities of two Parabacteroides distasonis strains. We herein evaluate their potential anti-obesity abilities and show that the two strains induced the secretion of the incretin glucagon-like peptide 1 in vitro and limited weight gain and adiposity in obese mice. These beneficial effects are associated with reduced inflammation in adipose tissue and the improvement of lipid and bile acid metabolism markers. P. distasonis supplementation also modified the Actinomycetota, Bacillota and Bacteroidota taxa of the mice gut microbiota. These results provide better insight into the capacity of P. distasonis to positively influence host metabolism and to be used as novel source of live biotherapeutics in the treatment and prevention of metabolic-related diseases.}, }
@article {pmid37153718, year = {2023}, author = {W B, M and A S, R and P, M and F, B}, title = {Cellular and Natural Viral Engineering in Cognition-Based Evolution.}, journal = {Communicative &amp; integrative biology}, volume = {16}, number = {1}, pages = {2196145}, pmid = {37153718}, issn = {1942-0889}, abstract = {Neo-Darwinism conceptualizes evolution as the continuous succession of predominately random genetic variations disciplined by natural selection. In that frame, the primary interaction between cells and the virome is relegated to host-parasite dynamics governed by selective influences. Cognition-Based Evolution regards biological and evolutionary development as a reciprocating cognition-based informational interactome for the protection of self-referential cells. To sustain cellular homeorhesis, cognitive cells collaborate to assess the validity of ambiguous biological information. That collective interaction involves coordinate measurement, communication, and active deployment of resources as Natural Cellular Engineering. These coordinated activities drive multicellularity, biological development, and evolutionary change. The virome participates as the vital intercessory among the cellular domains to ensure their shared permanent perpetuation. The interactions between the virome and the cellular domains represent active virocellular cross-communications for the continual exchange of resources. Modular genetic transfers between viruses and cells carry bioactive potentials. Those exchanges are deployed as nonrandom flexible tools among the domains in their continuous confrontation with environmental stresses. This alternative framework fundamentally shifts our perspective on viral-cellular interactions, strengthening established principles of viral symbiogenesis. Pathogenesis can now be properly appraised as one expression of a range of outcomes between cells and viruses within a larger conceptual framework of Natural Viral Engineering as a co-engineering participant with cells. It is proposed that Natural Viral Engineering should be viewed as a co-existent facet of Natural Cellular Engineering within Cognition-Based Evolution.}, }
@article {pmid37149185, year = {2023}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Nanetti, E and Iuffrida, L and Wathsala, RHGR and Interino, N and Marini, M and Porru, E and Turroni, S and Fiori, J and Franzellitti, S and Candela, M}, title = {Seasonal dynamics of the microbiome-host response to pharmaceuticals and pesticides in Mytilus galloprovincialis farmed in the Northwestern Adriatic Sea.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {163948}, doi = {10.1016/j.scitotenv.2023.163948}, pmid = {37149185}, issn = {1879-1026}, mesh = {Animals ; *Mytilus/metabolism ; Seasons ; *Pesticides/analysis ; Xenobiotics/metabolism ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. Even if the response to multiple xenobiotic exposure is well known at the host level, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. Here, we characterized the microbiome-host integrative response of M. galloprovincialis in a real-world setting, involving exposure to a complex pattern of emerging pollutants, as occurs in the Northwestern Adriatic Sea. A total of 387 mussel individuals from 3 commercial farms, spanning about 200 km along the Northwestern Adriatic coast, and in 3 different seasons, were collected. Multiresidue analysis (for quantitative xenobiotic determination), transcriptomics (for host physiological response), and metagenomics (for host-associated microbial taxonomical and functional features) analyses were performed on the digestive glands. According to our findings, M. galloprovincialis responds to the presence of the complex pattern of multiple emerging pollutants - including the antibiotics sulfamethoxazole, erythromycin, and tetracycline, the herbicides atrazine and metolachlor, and the insecticide N,N-diethyl-m-toluamide - integrating host defense mechanisms, e.g., through upregulation of transcripts involved in animal metabolic activity, and microbiome-mediated detoxification functions, including microbial functionalities involved in multidrug or tetracycline resistance. Overall, our data highlight the importance of the mussel-associated microbiome as a strategic player for the orchestration of resistance to the multixenobiotic exposure at the holobiont level, providing strategic functionalities for the detoxification of multiple xenobiotic substances, as occurring in real world exposure settings. Complementing the host with microbiome-dependent xenobiotic degradative and resistance genes, the M. galloprovincialis digestive gland associated microbiome can have an important role in the detoxification of emerging pollutants in a context of high anthropogenic pressure, supporting the relevance of mussel systems as potential animal-based bioremediation tool.}, }
@article {pmid37145211, year = {2023}, author = {Schwarcz, S and Kovács, P and Kovács, T and Ujlaki, G and Nyerges, P and Uray, K and Bai, P and Mikó, E}, title = {The pro- and antineoplastic effects of deoxycholic acid in pancreatic adenocarcinoma cell models.}, journal = {Molecular biology reports}, volume = {50}, number = {6}, pages = {5273-5282}, pmid = {37145211}, issn = {1573-4978}, support = {K124141//NKFIH/ ; TKP2021-EGA-19//NKFIH/ ; TKP2021-EGA-20//NKFIH/ ; FK128387//NKFIH/ ; POST-COVID2021-33//Hungarian Academy of Sciences/ ; &#xda;NKP-20-3-I-DE-301//New National Excellence Program of the Ministry of Human Capacities/ ; &#xda;NKP-21-3-I-DE-105//New National Excellence Program of the Ministry of Human Capacities/ ; &#xda;NKP-22-3-II-DE-230//New National Excellence Program of the Ministry of Human Capacities/ ; }, mesh = {Humans ; *Pancreatic Neoplasms/drug therapy/genetics/metabolism ; *Adenocarcinoma/drug therapy/genetics ; Epithelial-Mesenchymal Transition ; *Antineoplastic Agents/pharmacology ; Deoxycholic Acid/pharmacology ; Cell Line, Tumor ; }, abstract = {BACKGROUND: Commensal bacteria secrete metabolites that reach distant cancer cells through the circulation and influence cancer behavior. Deoxycholic acid (DCA), a hormone-like metabolite, is a secondary bile acid specifically synthesized by intestinal microbes. DCA may have both pro- and antineoplastic effects in cancers.<br><br>METHODS AND RESULTS: The pancreatic adenocarcinoma cell lines, Capan-2 and BxPC-3, were treated with 0.7&#xa0;&#xb5;M DCA, which corresponds to the reference concentration of DCA in human serum. DCA influenced the expression of epithelial to mesenchymal transition (EMT)-related genes, significantly decreased the expression level of the mesenchymal markers, transcription factor 7- like 2 (TCF7L2), snail family transcriptional repressor 2 (SLUG), CLAUDIN-1, and increased the expression of the epithelial genes, zona occludens 1 (ZO-1) and E-CADHERIN, as shown by real-time PCR and Western blotting. Consequently, DCA reduced the invasion capacity of pancreatic adenocarcinoma cells in Boyden chamber experiments. DCA induced the protein expression of oxidative/nitrosative stress markers. Moreover, DCA reduced aldehyde dehydrogenase 1 (ALDH1) activity in an Aldefluor assay and ALDH1 protein level, suggesting that DCA reduced stemness in pancreatic adenocarcinoma. In Seahorse experiments, DCA induced all fractions of mitochondrial respiration and glycolytic flux. The ratio of mitochondrial oxidation and glycolysis did not change after DCA treatment, suggesting that cells became hypermetabolic.<br><br>CONCLUSION: DCA induced antineoplastic effects in pancreatic adenocarcinoma cells by inhibiting EMT, reducing cancer stemness, and inducing oxidative/nitrosative stress and procarcinogenic effects such as hypermetabolic bioenergetics.}, }
@article {pmid37141369, year = {2023}, author = {Brown, CC and Rudensky, AY}, title = {Spatiotemporal regulation of peripheral T cell tolerance.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6644}, pages = {472-478}, doi = {10.1126/science.adg6425}, pmid = {37141369}, issn = {1095-9203}, mesh = {Autoantigens ; *Peripheral Tolerance ; *T-Lymphocytes/immunology ; Thymus Gland/cytology ; Humans ; Animals ; Mice ; }, abstract = {The incomplete removal of T cells that are reactive against self-proteins during their differentiation in the thymus requires mechanisms of tolerance that prevent their effector function within the periphery. A further challenge is imposed by the need to establish tolerance to the holobiont self, which comprises a highly complex community of commensal microorganisms. Here, we review recent advances in the investigation of peripheral T cell tolerance, focusing on new insights into mechanisms of tolerance to the gut microbiota, including tolerogenic antigen-presenting cell types and immunomodulatory lymphocytes, and their layered ontogeny that underlies developmental windows for establishing intestinal tolerance. While emphasizing the intestine as a model tissue for studying peripheral T cell tolerance, we highlight overlapping and distinct pathways that underlie tolerance to self-antigens versus commensal antigens within a broader framework for immune tolerance.}, }
@article {pmid37138624, year = {2023}, author = {Wolfgang, A and Temme, N and Tilcher, R and Berg, G}, title = {Understanding the sugar beet holobiont for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1151052}, pmid = {37138624}, issn = {1664-302X}, abstract = {The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.}, }
@article {pmid37137926, year = {2023}, author = {Froidevaux, JSP and Toshkova, N and Barbaro, L and Benítez-López, A and Kerbiriou, C and Le Viol, I and Pacifici, M and Santini, L and Stawski, C and Russo, D and Dekker, J and Alberdi, A and Amorim, F and Ancillotto, L and Barré, K and Bas, Y and Cantú-Salazar, L and Dechmann, DKN and Devaux, T and Eldegard, K and Fereidouni, S and Furmankiewicz, J and Hamidovic, D and Hill, DL and Ibáñez, C and Julien, JF and Juste, J and Kaňuch, P and Korine, C and Laforge, A and Legras, G and Leroux, C and Lesiński, G and Mariton, L and Marmet, J and Mata, VA and Mifsud, CM and Nistreanu, V and Novella-Fernandez, R and Rebelo, H and Roche, N and Roemer, C and Ruczyński, I and Sørås, R and Uhrin, M and Vella, A and Voigt, CC and Razgour, O}, title = {A species-level trait dataset of bats in Europe and beyond.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {253}, pmid = {37137926}, issn = {2052-4463}, support = {NE/M018660/1//RCUK | Natural Environment Research Council (NERC)/ ; ECF-2020-571//Leverhulme Trust/ ; CP-06-COST/15//Bulgarian National Science Fund (Bulgarian Scientific Fund)/ ; }, mesh = {Animals ; Biodiversity ; *Chiroptera/physiology ; Ecosystem ; Europe ; Mammals ; }, abstract = {Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.}, }
@article {pmid37137368, year = {2023}, author = {Zhu, W and Liu, X and Zhang, J and Zhao, H and Li, Z and Wang, H and Chen, R and Wang, A and Li, X}, title = {Response of coral bacterial composition and function to water quality variations under anthropogenic influence.}, journal = {The Science of the total environment}, volume = {884}, number = {}, pages = {163837}, doi = {10.1016/j.scitotenv.2023.163837}, pmid = {37137368}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Water Quality ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Microbiota ; }, abstract = {Microbial communities play key roles in the adaptation of corals living in adverse environments, as the microbiome flexibility can enhance environmental plasticity of coral holobiont. However, the ecological association of coral microbiome and related function to locally deteriorating water quality remains underexplored. In this work, we used 16S rRNA gene sequencing and quantitative microbial element cycling (QMEC) to investigate the seasonal changes of bacterial communities, particularly their functional genes related to carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) cycle, of the scleractinian coral Galaxea fascicularis from nearshore reefs exposed anthropogenic influence. We used nutrient concentrations as the indicator of anthropogenic activities in coastal reefs, and found a higher nutrient pressure in spring than summer. The bacterial diversity, community structure and dominant bacteria of coral shifted significantly due to seasonal variations dominated by nutrient concentrations. Additionally, the network structure and nutrient cycling gene profiles in summer under low nutrient stress was distinct from that under poor environmental conditions in spring, with lower network complexity and abundance of CNPS cycling genes in summer compared with spring. We further identified significant correlations between microbial community (taxonomic composition and co-occurrence network) and geochemical functions (abundance of multiple functional genes and functional community). Nutrient enrichment was proved to be the most important environmental fluctuation in controlling the diversity, community structure, interactional network and functional genes of the coral microbiome. These results highlight that seasonal shifts in coral-associated bacteria due to anthropogenic activities alter the functional potentials, and provide novel insight about the mechanisms of coral adaptation to locally deteriorating environments.}, }
@article {pmid37133380, year = {2023}, author = {Michelle JiaMin, L and Mutusamy, P and Karthikeyan, P and Kumaresan, R and Millard, A and Parimannan, S and Rajandas, H}, title = {Genome Characterization of Enterococcus faecalis Bacteriophage EFKL.}, journal = {Microbiology resource announcements}, volume = {12}, number = {6}, pages = {e0016023}, pmid = {37133380}, issn = {2576-098X}, support = {FRGS/1/2018/SKK14/AIMST/03/1//Ministry of Higher Education, Malaysia (MOHE)/ ; }, abstract = {We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.}, }
@article {pmid37127575, year = {2023}, author = {Calle-García, J and Ramayo-Caldas, Y and Zingaretti, LM and Quintanilla, R and Ballester, M and Pérez-Enciso, M}, title = {On the holobiont 'predictome' of immunocompetence in pigs.}, journal = {Genetics, selection, evolution : GSE}, volume = {55}, number = {1}, pages = {29}, pmid = {37127575}, issn = {1297-9686}, support = {PID2019-108829RB-I00//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; PID2020-112677RB-C2//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, mesh = {Animals ; Swine ; Bayes Theorem ; Genotype ; Phenotype ; *Genome ; *Genomics/methods ; }, abstract = {BACKGROUND: Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available.<br><br>METHODS: We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70&#xa0;k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only.<br><br>RESULTS: Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy.<br><br>CONCLUSIONS: Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.}, }
@article {pmid37124465, year = {2023}, author = {Cheng, SC and Liu, CB and Yao, XQ and Hu, JY and Yin, TT and Lim, BK and Chen, W and Wang, GD and Zhang, CL and Irwin, DM and Zhang, ZG and Zhang, YP and Yu, L}, title = {Hologenomic insights into mammalian adaptations to myrmecophagy.}, journal = {National science review}, volume = {10}, number = {4}, pages = {nwac174}, pmid = {37124465}, issn = {2053-714X}, abstract = {Highly specialized myrmecophagy (ant- and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes' activities, in the species of three mammalian orders (anteaters, echidnas and pangolins of the orders Xenarthra, Monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants' and termites' chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.}, }
@article {pmid37122591, year = {2023}, author = {Bergman, JL and Ricci, F and Leggat, W and Ainsworth, TD}, title = {Characteristics of The Bleached Microbiome of The Generalist Coral Pocillopora damicornis from Two Distinct Reef Habitats.}, journal = {Integrative organismal biology (Oxford, England)}, volume = {5}, number = {1}, pages = {obad012}, pmid = {37122591}, issn = {2517-4843}, abstract = {Generalist coral species may play an important role in predicting, managing, and responding to the growing coral reef crisis as sea surface temperatures are rising and reef wide bleaching events are becoming more common. Pocilloporids are amongst the most widely distributed and studied of generalist corals, characterized by a broad geographic distribution, phenotypic plasticity, and tolerance of sub-optimal conditions for coral recruitment and survival. Emerging research indicates that microbial communities associated with Pocilloporid corals may be contributing to their persistence on coral reefs impacted by thermal stress; however, we lack detailed information on shifts in the coral-bacterial symbiosis during bleaching events across many of the reef habitats these corals are found. Here, we characterized the bacterial communities of healthy and bleached Pocillopora damicornis corals during the bleaching events that occurred during the austral summer of 2020 on Heron Island, on the southern Great Barrier Reef, and the austral summer of 2019 on Lord Howe Island, the most southerly coral reef in Australia. Regardless of reef location, significant differences in α and β diversities, core bacterial community, and inferred functional profile of the bleached microbiome of P. damicornis were not detected. Consistent with previous reports, patterns in the Pocilloporid coral microbiome, including no increase in pathogenic taxa or evidence of dysbiosis, are conserved during bleaching responses. We hypothesize that the resilience of holobiont interactions may aid the Pocilloporids to survive Symbiodiniaceae loss and contribute to the success of Pocilloporids.}, }
@article {pmid37120592, year = {2023}, author = {Botero, J and Sombolestani, AS and Cnockaert, M and Peeters, C and Borremans, W and De Vuyst, L and Vereecken, NJ and Michez, D and Smagghe, G and Bonilla-Rosso, G and Engel, P and Vandamme, P}, title = {A phylogenomic and comparative genomic analysis of Commensalibacter, a versatile insect symbiont.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {25}, pmid = {37120592}, issn = {2524-4671}, support = {/WT_/Wellcome Trust/United Kingdom ; CLiPS, no.3094785//FNRS/FWO joint program "EOS - Excellence Of Science/ ; }, abstract = {BACKGROUND: To understand mechanisms of adaptation and plasticity of pollinators and other insects a better understanding of diversity and function of their key symbionts is required. Commensalibacter is a genus of acetic acid bacterial symbionts in the gut of honey bees and other insect species, yet little information is available on the diversity and function of Commensalibacter bacteria. In the present study, whole-genome sequences of 12 Commensalibacter isolates from bumble bees, butterflies, Asian hornets and rowan berries were determined, and publicly available genome assemblies of 14 Commensalibacter strains were used in a phylogenomic and comparative genomic analysis.<br><br>RESULTS: The phylogenomic analysis revealed that the 26 Commensalibacter isolates represented four species, i.e. Commensalibacter intestini and three novel species for which we propose the names Commensalibacter melissae sp. nov., Commensalibacter communis sp. nov. and Commensalibacter papalotli sp. nov. Comparative genomic analysis revealed that the four Commensalibacter species had similar genetic pathways for central metabolism characterized by a complete tricarboxylic acid cycle and pentose phosphate pathway, but their genomes differed in size, G&#x2009;+&#x2009;C content, amino acid metabolism and carbohydrate-utilizing enzymes. The reduced genome size, the large number of species-specific gene clusters, and the small number of gene clusters shared between C. melissae and other Commensalibacter species suggested a unique evolutionary process in C. melissae, the Western honey bee symbiont.<br><br>CONCLUSION: The genus Commensalibacter is a widely distributed insect symbiont that consists of multiple species, each contributing in a species specific manner to the physiology of the holobiont host.}, }
@article {pmid37110191, year = {2023}, author = {Clergeaud, F and Giraudo, M and Rodrigues, AMS and Thorel, E and Lebaron, P and Stien, D}, title = {On the Fate of Butyl Methoxydibenzoylmethane (Avobenzone) in Coral Tissue and Its Effect on Coral Metabolome.}, journal = {Metabolites}, volume = {13}, number = {4}, pages = {}, pmid = {37110191}, issn = {2218-1989}, support = {ANR-21-CE34-0027//Agence Nationale de la Recherche/ ; }, abstract = {The intensive use of sunscreen products has raised concerns regarding their environmental toxicity and the adverse impacts of ultraviolet (UV) filters on ecologically important coral communities. Prior metabolomic analyses on symbiotic coral Pocillopora damicornis exposed to the UV filter butyl methoxydibenzoylmethane (BM, avobenzone) revealed unidentified ions in the holobiont metabolome. In the present study, follow-up differential metabolomic analyses in BM-exposed P. damicornis detected 57 ions with significantly different relative concentrations in exposed corals. The results showed an accumulation of 17 BM derivatives produced through BM reduction and esterification. The major derivative identified C16:0-dihydroBM, which was synthesized and used as a standard to quantify BM derivatives in coral extracts. The results indicated that relative amounts of BM derivatives made up to 95% of the total BM (w/w) absorbed in coral tissue after 7 days of exposure. Among the remaining metabolites annotated, seven compounds significantly affected by BM exposure could be attributed to the coral dinoflagellate symbiont, indicating that BM exposure might impair the photosynthetic capacity of the holobiont. The present results suggest that the potential role of BM in coral bleaching in anthropogenic areas should be investigated and that BM derivatives should be considered in future assessments on the fate and effects of BM in the environment.}, }
@article {pmid37106156, year = {2023}, author = {Germain, RR and Feng, S and Chen, G and Graves, GR and Tobias, JA and Rahbek, C and Lei, F and Fjeldså, J and Hosner, PA and Gilbert, MTP and Zhang, G and Nogués-Bravo, D}, title = {Species-specific traits mediate avian demographic responses under past climate change.}, journal = {Nature ecology &amp; evolution}, volume = {7}, number = {6}, pages = {862-872}, pmid = {37106156}, issn = {2397-334X}, support = {32170626//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31901214//National Natural Science Foundation of China (National Science Foundation of China)/ ; CF16-0663//Carlsbergfondet (Carlsberg Foundation)/ ; 25900//Villum Fonden (Villum Foundation)/ ; 8021-00282B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; }, mesh = {Animals ; *Climate Change ; *Biodiversity ; Cold Temperature ; Birds/physiology ; Demography ; }, abstract = {Anticipating species' responses to environmental change is a pressing mission in biodiversity conservation. Despite decades of research investigating how climate change may affect population sizes, historical context is lacking, and the traits that mediate demographic sensitivity to changing climate remain elusive. We use whole-genome sequence data to reconstruct the demographic histories of 263 bird species over the past million years and identify networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. Our results identify direct and indirect effects of key traits representing dispersal, reproduction and survival on long-term demographic responses to climate change, thereby highlighting traits most likely to influence population responses to ongoing climate warming.}, }
@article {pmid37100093, year = {2023}, author = {Hansen, SB and Bozzi, D and Mak, SST and Clausen, CG and Nielsen, TK and Kodama, M and Hansen, LH and Gilbert, MTP and Limborg, MT}, title = {Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition.}, journal = {Genomics}, volume = {115}, number = {3}, pages = {110629}, doi = {10.1016/j.ygeno.2023.110629}, pmid = {37100093}, issn = {1089-8646}, mesh = {Epigenomics ; Genotype ; *Gastrointestinal Microbiome ; *Salmo salar/genetics ; Animals ; Intestines/microbiology ; DNA Methylation ; Genome ; }, abstract = {It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish phenotype. To manipulate the microbiota towards the desired host traits, it is critical to understand the factors that shape it. The bacterial gut microbiota composition can vary greatly among fish, even when reared in the same closed system. While such microbiota differences can be linked to diseases, the molecular effect of disease on host-microbiota interactions and the potential involvement of epigenetic factors remain largely unknown. The aim of this study was to investigate the DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in the gut of Atlantic salmon. Using Whole Genome Bisulfite Sequencing (WGBS) of distal gut tissue from 20 salmon, we compared the genome-wide DNA methylation levels between uninfected individuals and sick fish suffering from tenacibaculosis and microbiota displacement. We discovered >19,000 differentially methylated cytosine sites, often located in differentially methylated regions, and aggregated around genes. The 68 genes connected to the most significant regions had functions related to the ulcerous disease such as epor and slc48a1a but also included prkcda and LOC106590732 whose orthologs are linked to microbiota changes in other species. Although the expression level was not analysed, our epigenetic analysis suggests specific genes potentially involved in host-microbiota interactions and more broadly it highlights the value of considering epigenetic factors in efforts to manipulate the microbiota of farmed fish.}, }
@article {pmid37071808, year = {2023}, author = {Roux, F and Frachon, L and Bartoli, C}, title = {The Genetic Architecture of Adaptation to Leaf and Root Bacterial Microbiota in Arabidopsis thaliana.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37071808}, issn = {1537-1719}, mesh = {*Arabidopsis/genetics ; Bacteria/genetics ; Plant Leaves/genetics ; Acclimatization ; *Microbiota/genetics ; Plant Roots/genetics ; }, abstract = {Understanding the role of the host genome in modulating microbiota variation is a need to shed light on the holobiont theory and overcome the current limits on the description of host-microbiota interactions at the genomic and molecular levels. However, the host genetic architecture structuring microbiota is only partly described in plants. In addition, most association genetic studies on microbiota are often carried out outside the native habitats where the host evolves and the identification of signatures of local adaptation on the candidate genes has been overlooked. To fill these gaps and dissect the genetic architecture driving adaptive plant-microbiota interactions, we adopted a genome-environment association (GEA) analysis on 141 whole-genome sequenced natural populations of Arabidopsis thaliana characterized in situ for their leaf and root bacterial communities in fall and spring, and a large range of nonmicrobial ecological factors (i.e., climate, soil, and plant communities). A much higher fraction of among-population microbiota variance was explained by the host genetics than by nonmicrobial ecological factors. Importantly, the relative importance of host genetics and nonmicrobial ecological factors in explaining the presence of particular operational taxonomic units (OTUs) differs between bacterial families and genera. In addition, the polygenic architecture of adaptation to bacterial communities was highly flexible between plant compartments and seasons. Relatedly, signatures of local adaptation were stronger on quantitative trait loci (QTLs) of the root microbiota in spring. Finally, plant immunity appears as a major source of adaptive genetic variation structuring bacterial assemblages in A. thaliana.}, }
@article {pmid37068234, year = {2023}, author = {Cohen, P and Bacilieri, R and Ramos-Madrigal, J and Privman, E and Boaretto, E and Weber, A and Fuks, D and Weiss, E and Erickson-Gini, T and Bucking, S and Tepper, Y and Cvikel, D and Schmidt, J and Gilbert, MTP and Wales, N and Bar-Oz, G and Meiri, M}, title = {Ancient DNA from a lost Negev Highlands desert grape reveals a Late Antiquity wine lineage.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {17}, pages = {e2213563120}, pmid = {37068234}, issn = {1091-6490}, mesh = {History, Ancient ; *Vitis/genetics ; *Wine ; DNA, Ancient ; Archaeology ; Israel ; }, abstract = {Recent excavations of Late Antiquity settlements in the Negev Highlands of southern Israel uncovered a society that established commercial-scale viticulture in an arid environment [D. Fuks et al., Proc. Natl. Acad. Sci. U.S.A. 117, 19780-19791 (2020)]. We applied target-enriched genome-wide sequencing and radiocarbon dating to examine grapevine pips that were excavated at three of these sites. Our analyses revealed centuries long and continuous grape cultivation in the Southern Levant. The genetically diverse pips also provided clues to ancient cultivation strategies aimed at improving agricultural productivity and ensuring food security. Applying genomic prediction analysis, a pip dated to the eighth century CE was determined to likely be from a white grape, to date the oldest to be identified. In a kinship analysis, another pip was found to be descendant from a modern Greek cultivar and was thus linked with several popular historic wines that were once traded across the Byzantine Empire. These findings shed light on historical Byzantine trading networks and on the genetic contribution of Levantine varieties to the classic Aegean landscape.}, }
@article {pmid37067424, year = {2023}, author = {Chakraborty, A and Šobotník, J and Votýpková, K and Hradecký, J and Stiblik, P and Synek, J and Bourguignon, T and Baldrian, P and Engel, MS and Novotný, V and Odriozola, I and Větrovský, T}, title = {Impact of Wood Age on Termite Microbial Assemblages.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0036123}, pmid = {37067424}, issn = {1098-5336}, mesh = {Animals ; *Wood/metabolism ; Ecosystem ; *Isoptera/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria/genetics ; }, abstract = {The decomposition of wood and detritus is challenging to most macroscopic organisms due to the recalcitrant nature of lignocellulose. Moreover, woody plants often protect themselves by synthesizing toxic or nocent compounds which infuse their tissues. Termites are essential wood decomposers in warmer terrestrial ecosystems and, as such, they have to cope with high concentrations of plant toxins in wood. In this paper, we evaluated the influence of wood age on the gut microbial (bacterial and fungal) communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) (Kollar, 1837) and Microcerotermes biroi (Termitidae) (Desneux, 1905). We confirmed that the secondary metabolite concentration decreased with wood age. We identified a core microbial consortium maintained in the gut of R. flavipes and M. biroi and found that its diversity and composition were not altered by the wood age. Therefore, the concentration of secondary metabolites had no effect on the termite gut microbiome. We also found that both termite feeding activities and wood age affect the wood microbiome. Whether the increasing relative abundance of microbes with termite activities is beneficial to the termites is unknown and remains to be investigated. IMPORTANCE Termites can feed on wood thanks to their association with their gut microbes. However, the current understanding of termites as holobiont is limited. To our knowledge, no studies comprehensively reveal the influence of wood age on the termite-associated microbial assemblage. The wood of many tree species contains high concentrations of plant toxins that can vary with their age and may influence microbes. Here, we studied the impact of Norway spruce wood of varying ages and terpene concentrations on the microbial communities associated with the termites Reticulitermes flavipes (Rhinotermitidae) and Microcerotermes biroi (Termitidae). We performed a bacterial 16S rRNA and fungal ITS2 metabarcoding study to reveal the microbial communities associated with R. flavipes and M. biroi and their impact on shaping the wood microbiome. We noted that a stable core microbiome in the termites was unaltered by the feeding substrate, while termite activities influenced the wood microbiome, suggesting that plant secondary metabolites have negligible effects on the termite gut microbiome. Hence, our study shed new insights into the termite-associated microbial assemblage under the influence of varying amounts of terpene content in wood and provides a groundwork for future investigations for developing symbiont-mediated termite control measures.}, }
@article {pmid37065434, year = {2023}, author = {Reeve, AH and Gower, G and Pujolar, JM and Smith, BT and Petersen, B and Olsson, U and Haryoko, T and Koane, B and Maiah, G and Blom, MPK and Ericson, PGP and Irestedt, M and Racimo, F and Jønsson, KA}, title = {Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.}, journal = {Evolution letters}, volume = {7}, number = {1}, pages = {24-36}, pmid = {37065434}, issn = {2056-3744}, abstract = {Tropical islands are renowned as natural laboratories for evolutionary study. Lineage radiations across tropical archipelagos are ideal systems for investigating how colonization, speciation, and extinction processes shape biodiversity patterns. The expansion of the island thrush across the Indo-Pacific represents one of the largest yet most perplexing island radiations of any songbird species. The island thrush exhibits a complex mosaic of pronounced plumage variation across its range and is arguably the world's most polytypic bird. It is a sedentary species largely restricted to mountain forests, yet it has colonized a vast island region spanning a quarter of the globe. We conducted a comprehensive sampling of island thrush populations and obtained genome-wide SNP data, which we used to reconstruct its phylogeny, population structure, gene flow, and demographic history. The island thrush evolved from migratory Palearctic ancestors and radiated explosively across the Indo-Pacific during the Pleistocene, with numerous instances of gene flow between populations. Its bewildering plumage variation masks a biogeographically intuitive stepping stone colonization path from the Philippines through the Greater Sundas, Wallacea, and New Guinea to Polynesia. The island thrush's success in colonizing Indo-Pacific mountains can be understood in light of its ancestral mobility and adaptation to cool climates; however, shifts in elevational range, degree of plumage variation and apparent dispersal rates in the eastern part of its range raise further intriguing questions about its biology.}, }
@article {pmid37065131, year = {2023}, author = {Birt, HWG and Pattison, AB and Skarshewski, A and Daniells, J and Raghavendra, A and Dennis, PG}, title = {The core fungal microbiome of banana (Musa spp.).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1127779}, pmid = {37065131}, issn = {1664-302X}, abstract = {Here, we report a metabarcoding (ITS2) study to define the common core fungal microbiome (mycobiome) of healthy Musa spp. (bananas and plantains). To identify a list of 21 core fungal taxa, we first characterised the effects of edaphic conditions and host genotype - two factors that are likely to differ between farms - on the diversity of fungal communities in bulk soil and seven plant compartments. This experiment facilitated shortlisting of core 'candidates', which were then elevated to full core status if also found to frequent a wide-range of field-grown Musa spp. and exhibit hub-like characteristics in network analyses. Subsequently, we conducted a meta-analysis of eleven publicly available datasets of Musa spp. associated fungi demonstrating that the core fungi identified in our study have close relatives in other countries. The diversity and composition of mycobiomes differed between plant compartments and soils, but not genotypes. The core mycobiome included Fusarium oxysporum and its relatives, which dominated all plant compartments, as well as members of the Sordariomycetes, Dothideomycetes, and Mortierellomycota. Our study provides a robust list of common core fungal taxa for Musa spp. Further studies may consider how changes in the frequencies and activities of these taxa influence host fitness and whether they can be managed to improve banana production.}, }
@article {pmid37061589, year = {2023}, author = {Pande, PM and Azarbad, H and Tremblay, J and St-Arnaud, M and Yergeau, E}, title = {Metatranscriptomic response of the wheat holobiont to decreasing soil water content.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {30}, pmid = {37061589}, issn = {2730-6151}, abstract = {Crops associate with microorganisms that help their resistance to biotic stress. However, it is not clear how the different partners of this association react during exposure to stress. This knowledge is needed to target the right partners when trying to adapt crops to climate change. Here, we grew wheat in the field under rainout shelters that let through 100%, 75%, 50% and 25% of the precipitation. At the peak of the growing season, we sampled plant roots and rhizosphere, and extracted and sequenced their RNA. We compared the 100% and the 25% treatments using differential abundance analysis. In the roots, most of the differentially abundant (DA) transcripts belonged to the fungi, and most were more abundant in the 25% precipitation treatment. About 10% of the DA transcripts belonged to the plant and most were less abundant in the 25% precipitation treatment. In the rhizosphere, most of the DA transcripts belonged to the bacteria and were generally more abundant in the 25% precipitation treatment. Taken together, our results show that the transcriptomic response of the wheat holobiont to decreasing precipitation levels is stronger for the fungal and bacterial partners than for the plant.}, }
@article {pmid37049406, year = {2023}, author = {Cardilli, A and Hamad, I and Dyczko, A and Thijs, S and Vangronsveld, J and Müller, DN and Rosshart, SP and Kleinewietfeld, M}, title = {Impact of High Salt-Intake on a Natural Gut Ecosystem in Wildling Mice.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049406}, issn = {2072-6643}, support = {640116/ERC_/European Research Council/International ; }, mesh = {Mice ; Humans ; Animals ; Bacteria/genetics ; Diet ; *Gastrointestinal Microbiome ; *Microbiota ; Feeding Behavior ; Firmicutes ; Clostridiales/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals ; }, abstract = {The mammalian holobiont harbors a complex and interdependent mutualistic gut bacterial community. Shifts in the composition of this bacterial consortium are known to be a key element in host health, immunity and disease. Among many others, dietary habits are impactful drivers for a potential disruption of the bacteria-host mutualistic interaction. In this context, we previously demonstrated that a high-salt diet (HSD) leads to a dysbiotic condition of murine gut microbiota, characterized by a decrease or depletion of well-known health-promoting gut bacteria. However, due to a controlled and sanitized environment, conventional laboratory mice (CLM) possess a less diverse gut microbiota compared to wild mice, leading to poor translational outcome for gut microbiome studies, since a reduced gut microbiota diversity could fail to depict the complex interdependent networks of the microbiome. Here, we evaluated the HSD effect on gut microbiota in CLM in comparison to wildling mice, which harbor a natural gut ecosystem more closely mimicking the situation in humans. Mice were treated with either control food or HSD and gut microbiota were profiled using amplicon-based methods targeting the 16S ribosomal gene. In line with previous findings, our results revealed that HSD induced significant loss of alpha diversity and extensive modulation of gut microbiota composition in CLM, characterized by the decrease in potentially beneficial bacteria from Firmicutes phylum such as the genera Lactobacillus, Roseburia, Tuzzerella, Anaerovorax and increase in Akkermansia and Parasutterella. However, HSD-treated wildling mice did not show the same changes in terms of alpha diversity and loss of Firmicutes bacteria as CLM, and more generally, wildlings exhibited only minor shifts in the gut microbiota composition upon HSD. In line with this, 16S-based functional analysis suggested only major shifts of gut microbiota ecological functions in CLM compared to wildling mice upon HSD. Our findings indicate that richer and wild-derived gut microbiota is more resistant to dietary interventions such as HSD, compared to gut microbiota of CLM, which may have important implications for future translational microbiome research.}, }
@article {pmid37043058, year = {2023}, author = {Houck, ML and Koepfli, KP and Hains, T and Khan, R and Charter, SJ and Fronczek, JA and Misuraca, AC and Kliver, S and Perelman, PL and Beklemisheva, V and Graphodatsky, A and Luo, SJ and O'Brien, SJ and Lim, NT and Chin, JSC and Guerra, V and Tamazian, G and Omer, A and Weisz, D and Kaemmerer, K and Sturgeon, G and Gaspard, J and Hahn, A and McDonough, M and Garcia-Treviño, I and Gentry, J and Coke, RL and Janecka, JE and Harrigan, RJ and Tinsman, J and Smith, TB and Aiden, EL and Dudchenko, O}, title = {Chromosome-length genome assemblies and cytogenomic analyses of pangolins reveal remarkable chromosome counts and plasticity.}, journal = {Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology}, volume = {31}, number = {2}, pages = {13}, pmid = {37043058}, issn = {1573-6849}, support = {UM1 HG009375/HG/NHGRI NIH HHS/United States ; RM1 HG011016/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Male ; Female ; *Pangolins/genetics ; *Mammals/genetics ; Genome ; Chromosomes/genetics ; }, abstract = {We report the first chromosome-length genome assemblies for three species in the mammalian order Pholidota: the white-bellied, Chinese, and Sunda pangolins. Surprisingly, we observe extraordinary karyotypic plasticity within this order and, in female white-bellied pangolins, the largest number of chromosomes reported in a Laurasiatherian mammal: 2n = 114. We perform the first karyotype analysis of an African pangolin and report a Y-autosome fusion in white-bellied pangolins, resulting in 2n = 113 for males. We employ a novel strategy to confirm the fusion and identify the autosome involved by finding the pseudoautosomal region (PAR) in the female genome assembly and analyzing the 3D contact frequency between PAR sequences and the rest of the genome in male and female white-bellied pangolins. Analyses of genetic variability show that white-bellied pangolins have intermediate levels of genome-wide heterozygosity relative to Chinese and Sunda pangolins, consistent with two moderate declines of historical effective population size. Our results reveal a remarkable feature of pangolin genome biology and highlight the need for further studies of these unique and endangered mammals.}, }
@article {pmid37032282, year = {2023}, author = {Gonzalez-Recio, O and Scrobota, N and López-Paredes, J and Saborío-Montero, A and Fernández, A and López de Maturana, E and Villanueva, B and Goiri, I and Atxaerandio, R and García-Rodríguez, A}, title = {Review: Diving into the cow hologenome to reduce methane emissions and increase sustainability.}, journal = {Animal : an international journal of animal bioscience}, volume = {17 Suppl 2}, number = {}, pages = {100780}, doi = {10.1016/j.animal.2023.100780}, pmid = {37032282}, issn = {1751-732X}, mesh = {Female ; Cattle ; Animals ; *Methane/metabolism ; Genome-Wide Association Study/veterinary ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Rumen/metabolism ; }, abstract = {Interest on methane emissions from livestock has increased in later years as it is an anthropogenic greenhouse gas with an important warming potential. The rumen microbiota has a large influence on the production of enteric methane. Animals harbour a second genome consisting of microbes, collectively referred to as the "microbiome". The rumen microbial community plays an important role in feed digestion, feed efficiency, methane emission and health status. This review recaps the current knowledge on the genetic control that the cow exerts on the rumen microbiota composition. Heritability estimates for the rumen microbiota composition range between 0.05 and 0.40 in the literature, depending on the taxonomical group or microbial gene function. Variables depicting microbial diversity or aggregating microbial information are also heritable within the same range. This study includes a genome-wide association analysis on the microbiota composition, considering the relative abundance of some microbial taxa previously associated to enteric methane in dairy cattle (Archaea, Dialister, Entodinium, Eukaryota, Lentisphaerae, Methanobrevibacter, Neocallimastix, Prevotella and Stentor). Host genomic regions associated with the relative abundance of these microbial taxa were identified after Benjamini-Hoschberg correction (Padj < 0.05). An in-silico functional analysis using FUMA and DAVID online tools revealed that these gene sets were enriched in tissues like brain cortex, brain amigdala, pituitary, salivary glands and other parts of the digestive system, and are related to appetite, satiety and digestion. These results allow us to have greater knowledge about the composition and function of the rumen microbiome in cattle. The state-of-the art strategies to include methane traits in the selection indices in dairy cattle populations is reviewed. Several strategies to include methane traits in the selection indices have been studied worldwide, using bioeconomical models or economic functions under theoretical frameworks. However, their incorporation in the breeding programmes is still scarce. Some potential strategies to include methane traits in the selection indices of dairy cattle population are presented. Future selection indices will need to increase the weight of traits related to methane emissions and sustainability. This review will serve as a compendium of the current state of the art in genetic strategies to reduce methane emissions in dairy cattle.}, }
@article {pmid37030294, year = {2023}, author = {Díez-Del-Molino, D and Dehasque, M and Chacón-Duque, JC and Pečnerová, P and Tikhonov, A and Protopopov, A and Plotnikov, V and Kanellidou, F and Nikolskiy, P and Mortensen, P and Danilov, GK and Vartanyan, S and Gilbert, MTP and Lister, AM and Heintzman, PD and van der Valk, T and Dalén, L}, title = {Genomics of adaptive evolution in the woolly mammoth.}, journal = {Current biology : CB}, volume = {33}, number = {9}, pages = {1753-1764.e4}, doi = {10.1016/j.cub.2023.03.084}, pmid = {37030294}, issn = {1879-0445}, mesh = {Animals ; *Mammoths/genetics ; Sequence Analysis, DNA ; Genomics/methods ; Genome/genetics ; Mutation ; Fossils ; Evolution, Molecular ; }, abstract = {Ancient genomes provide a tool to investigate the genetic basis of adaptations in extinct organisms. However, the identification of species-specific fixed genetic variants requires the analysis of genomes from multiple individuals. Moreover, the long-term scale of adaptive evolution coupled with the short-term nature of traditional time series data has made it difficult to assess when different adaptations evolved. Here, we analyze 23 woolly mammoth genomes, including one of the oldest known specimens at 700,000 years old, to identify fixed derived non-synonymous mutations unique to the species and to obtain estimates of when these mutations evolved. We find that at the time of its origin, the woolly mammoth had already acquired a broad spectrum of positively selected genes, including ones associated with hair and skin development, fat storage and metabolism, and immune system function. Our results also suggest that these phenotypes continued to evolve during the last 700,000 years, but through positive selection on different sets of genes. Finally, we also identify additional genes that underwent comparatively recent positive selection, including multiple genes related to skeletal morphology and body size, as well as one gene that may have contributed to the small ear size in Late Quaternary woolly mammoths.}, }
@article {pmid37018898, year = {2023}, author = {Rasmussen, JA and Chua, PYS}, title = {Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127372}, doi = {10.1016/j.micres.2023.127372}, pmid = {37018898}, issn = {1618-0623}, mesh = {Animals ; Humans ; *Virome ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Birds/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; }, abstract = {The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.}, }
@article {pmid37002423, year = {2023}, author = {Pushpakumara, BLDU and Tandon, K and Willis, A and Verbruggen, H}, title = {The Bacterial Microbiome of the Coral Skeleton Algal Symbiont Ostreobium Shows Preferential Associations and Signatures of Phylosymbiosis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2032-2046}, pmid = {37002423}, issn = {1432-184X}, support = {DP200101613//Australian Research Council grant/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Chlorophyta ; *Microbiota ; Coral Reefs ; }, abstract = {Ostreobium, the major algal symbiont of the coral skeleton, remains understudied despite extensive research on the coral holobiont. The enclosed nature of the coral skeleton might reduce the dispersal and exposure of residing bacteria to the outside environment, allowing stronger associations with the algae. Here, we describe the bacterial communities associated with cultured strains of 5 Ostreobium clades using 16S rRNA sequencing. We shed light on their likely physical associations by comparative analysis of three datasets generated to capture (1) all algae associated bacteria, (2) enriched tightly attached and potential intracellular bacteria, and (3) bacteria in spent media. Our data showed that while some bacteria may be loosely attached, some tend to be tightly attached or potentially intracellular. Although colonised with diverse bacteria, Ostreobium preferentially associated with 34 bacterial taxa revealing a core microbiome. These bacteria include known nitrogen cyclers, polysaccharide degraders, sulphate reducers, antimicrobial compound producers, methylotrophs, and vitamin B12 producers. By analysing co-occurrence networks of 16S rRNA datasets from Porites lutea and Paragoniastrea australensis skeleton samples, we show that the Ostreobium-bacterial associations present in the cultures are likely to also occur in their natural environment. Finally, our data show significant congruence between the Ostreobium phylogeny and the community composition of its tightly associated microbiome, largely due to the phylosymbiotic signal originating from the core bacterial taxa. This study offers insight into the Ostreobium microbiome and reveals preferential associations that warrant further testing from functional and evolutionary perspectives.}, }
@article {pmid36991491, year = {2023}, author = {Hénaff, E and Najjar, D and Perez, M and Flores, R and Woebken, C and Mason, CE and Slavin, K}, title = {Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {23}, pmid = {36991491}, issn = {2524-6372}, support = {OPP1151054//Bill and Melinda Gates Foundation/ ; 1840275//National Science Foundation/ ; G-2015-13964//Alfred P. Sloan Foundation/ ; 1R01MH117406/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Over half of the world's population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city's microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms-bacteria or fungi-with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city.<br><br>RESULTS: Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for "cat scratch fever".<br><br>CONCLUSIONS: We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.}, }
@article {pmid36988668, year = {2023}, author = {Müller, M and Kües, U and Budde, KB and Gailing, O}, title = {Applying molecular and genetic methods to trees and their fungal communities.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {9}, pages = {2783-2830}, pmid = {36988668}, issn = {1432-0614}, mesh = {*Trees/microbiology ; Ecosystem ; *Mycobiome ; Forests ; Fungi/genetics ; }, abstract = {Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.}, }
@article {pmid36981014, year = {2023}, author = {Alvarez-Estape, M and Pawar, H and Fontsere, C and Trujillo, AE and Gunson, JL and Bergl, RA and Bermejo, M and Linder, JM and McFarland, K and Oates, JF and Sunderland-Groves, JL and Orkin, J and Higham, JP and Viaud-Martinez, KA and Lizano, E and Marques-Bonet, T}, title = {Past Connectivity but Recent Inbreeding in Cross River Gorillas Determined Using Whole Genomes from Single Hairs.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36981014}, issn = {2073-4425}, support = {R01 HG010898/HG/NHGRI NIH HHS/United States ; NIH 1R01HG010898-01A1/NH/NIH HHS/United States ; 864203/ERC_/European Research Council/International ; LCF/BQ/PI20/11760004/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Animals ; Humans ; *Gorilla gorilla/genetics ; Inbreeding ; *Hominidae/genetics ; Genome/genetics ; Gene Flow ; }, abstract = {The critically endangered western gorillas (Gorilla gorilla) are divided into two subspecies: the western lowland (G. g. gorilla) and the Cross River (G. g. diehli) gorilla. Given the difficulty in sampling wild great ape populations and the small estimated size of the Cross River gorilla population, only one whole genome of a Cross River gorilla has been sequenced to date, hindering the study of this subspecies at the population level. In this study, we expand the number of whole genomes available for wild western gorillas, generating 41 new genomes (25 belonging to Cross River gorillas) using single shed hairs collected from gorilla nests. By combining these genomes with publicly available wild gorilla genomes, we confirm that Cross River gorillas form three population clusters. We also found little variation in genome-wide heterozygosity among them. Our analyses reveal long runs of homozygosity (>10 Mb), indicating recent inbreeding in Cross River gorillas. This is similar to that seen in mountain gorillas but with a much more recent bottleneck. We also detect past gene flow between two Cross River sites, Afi Mountain Wildlife Sanctuary and the Mbe Mountains. Furthermore, we observe past allele sharing between Cross River gorillas and the northern western lowland gorilla sites, as well as with the eastern gorilla species. This is the first study using single shed hairs from a wild species for whole genome sequencing to date. Taken together, our results highlight the importance of implementing conservation measures to increase connectivity among Cross River gorilla sites.}, }
@article {pmid36980891, year = {2023}, author = {Yakupova, A and Tomarovsky, A and Totikov, A and Beklemisheva, V and Logacheva, M and Perelman, PL and Komissarov, A and Dobrynin, P and Krasheninnikova, K and Tamazian, G and Serdyukova, NA and Rayko, M and Bulyonkova, T and Cherkasov, N and Pylev, V and Peterfeld, V and Penin, A and Balanovska, E and Lapidus, A and Dna Zoo Consortium,  and OBrien, SJ and Graphodatsky, A and Koepfli, KP and Kliver, S}, title = {Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980891}, issn = {2073-4425}, mesh = {Animals ; *Lakes ; *Seals, Earless/genetics ; Karyotype ; }, abstract = {Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat-the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial-interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3-0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.}, }
@article {pmid36976223, year = {2023}, author = {Tan, LT}, title = {Impact of Marine Chemical Ecology Research on the Discovery and Development of New Pharmaceuticals.}, journal = {Marine drugs}, volume = {21}, number = {3}, pages = {}, pmid = {36976223}, issn = {1660-3397}, support = {RI2/20/TLT//National Institute of Education/ ; }, mesh = {*Ecosystem ; *Volatile Organic Compounds ; Ecology ; Aquatic Organisms/chemistry ; Pheromones/chemistry ; Pharmaceutical Preparations ; }, abstract = {Diverse ecologically important metabolites, such as allelochemicals, infochemicals and volatile organic chemicals, are involved in marine organismal interactions. Chemically mediated interactions between intra- and interspecific organisms can have a significant impact on community organization, population structure and ecosystem functioning. Advances in analytical techniques, microscopy and genomics are providing insights on the chemistry and functional roles of the metabolites involved in such interactions. This review highlights the targeted translational value of several marine chemical ecology-driven research studies and their impact on the sustainable discovery of novel therapeutic agents. These chemical ecology-based approaches include activated defense, allelochemicals arising from organismal interactions, spatio-temporal variations of allelochemicals and phylogeny-based approaches. In addition, innovative analytical techniques used in the mapping of surface metabolites as well as in metabolite translocation within marine holobionts are summarized. Chemical information related to the maintenance of the marine symbioses and biosyntheses of specialized compounds can be harnessed for biomedical applications, particularly in microbial fermentation and compound production. Furthermore, the impact of climate change on the chemical ecology of marine organisms-especially on the production, functionality and perception of allelochemicals-and its implications on drug discovery efforts will be presented.}, }
@article {pmid36973251, year = {2023}, author = {Battlay, P and Wilson, J and Bieker, VC and Lee, C and Prapas, D and Petersen, B and Craig, S and van Boheemen, L and Scalone, R and de Silva, NP and Sharma, A and Konstantinović, B and Nurkowski, KA and Rieseberg, LH and Connallon, T and Martin, MD and Hodgins, KA}, title = {Large haploblocks underlie rapid adaptation in the invasive weed Ambrosia artemisiifolia.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1717}, pmid = {36973251}, issn = {2041-1723}, mesh = {*Ambrosia/genetics ; *Plant Weeds/genetics ; Acclimatization ; Adaptation, Physiological/genetics ; Biological Evolution ; }, abstract = {Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. Here, we leverage extensive contemporary and historical collections of Ambrosia artemisiifolia-an aggressively invasive weed and primary cause of pollen-induced hayfever-to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-indicative of chromosomal inversions-contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolia's global spread across vast climatic gradients.}, }
@article {pmid36958561, year = {2023}, author = {Mancuso, FP and Morrissey, KL and De Clerck, O and Airoldi, L}, title = {Warming and nutrient enrichment can trigger seaweed loss by dysregulation of the microbiome structure and predicted function.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {162919}, doi = {10.1016/j.scitotenv.2023.162919}, pmid = {36958561}, issn = {1879-1026}, mesh = {Humans ; *Seaweed/physiology ; Ecosystem ; *Microbiota ; Bacteria ; *Phaeophyceae ; Nutrients ; }, abstract = {Warming and nutrient enrichment are key pervasive drivers of ecological shifts in both aquatic and terrestrial ecosystems, impairing the physiology and survival of a wide range of foundation species. But the underlying mechanisms often remain unclear, and experiments have overlooked the potential effects mediated by changes in the microbial communities. We experimentally tested in the field orthogonal stress combinations from simulated air warming and nutrient enrichment on the intertidal foundation seaweed Cystoseira compressa, and its associated bacterial communities. A total of 523 Amplicon Sequence Variance (ASVs) formed the bacterial community on C. compressa, with 222 ASVs assigned to 69 taxa at the genus level. Most bacteria taxa experienced changes in abundance as a result of additive (65 %) and antagonistic (30 %) interactions between the two stressors, with synergies (5 %) occurring less frequently. The analysis of the predicted bacterial functional profile identified 160 metabolic pathways, and showed that these were mostly affected by additive interactions (74 %) between air warming and nutrient enrichment, while antagonisms (20 %) and synergisms (6 %) were less frequent. Overall, the two stressors combined increased functions associated with seaweed disease or degradation of major cell-wall polymers and other algicidal processes, and decreased functions associated with Quorum Quenching and photosynthetic response. We conclude that warming and nutrient enrichment can dysregulate the microbiome of seaweeds, providing a plausible mechanism for their ongoing loss, and encourage more research into the effects of human impacts on crucial but yet largely unstudied host-microbiome relationships in different aquatic and terrestrial species.}, }
@article {pmid36951365, year = {2023}, author = {Ricci, F and Tandon, K and Moßhammer, M and Cho, EH and Blackall, LL and Kühl, M and Verbruggen, H}, title = {Fine-scale mapping of physicochemical and microbial landscapes of the coral skeleton.}, journal = {Environmental microbiology}, volume = {25}, number = {8}, pages = {1505-1521}, doi = {10.1111/1462-2920.16369}, pmid = {36951365}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; Coral Reefs ; }, abstract = {The coral skeleton harbours a diverse community of bacteria and microeukaryotes exposed to light, O2 and pH gradients, but how such physicochemical gradients affect the coral skeleton microbiome remains unclear. In this study, we employed chemical imaging of O2 and pH, hyperspectral reflectance imaging and spatially resolved taxonomic and inferred functional microbiome characterization to explore links between the skeleton microenvironment and microbiome in the reef-building corals Porites lutea and Paragoniastrea benhami. The physicochemical environment was more stable in the deep skeleton, and the diversity and evenness of the bacterial community increased with skeletal depth, suggesting that the microbiome was stratified along the physicochemical gradients. The bulk of the coral skeleton was in a low O2 habitat, whereas pH varied from pH 6-9 with depth. Physicochemical gradients of O2 and pH of the coral skeleton explained the β-diversity of the bacterial communities, and skeletal layers that showed O2 peaks had a higher relative abundance of endolithic algae, reflecting a link between the abiotic environment and the microbiome composition. Our study links the physicochemical, microbial and functional landscapes of the coral skeleton and provides new insights into the involvement of skeletal microbes in the coral holobiont metabolism.}, }
@article {pmid36944891, year = {2023}, author = {Penno, C and Tremblay, J and O'Connell Motherway, M and Daburon, V and El Amrani, A}, title = {Analysis of Small Non-coding RNAs as Signaling Intermediates of Environmentally Integrated Responses to Abiotic Stress.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2642}, number = {}, pages = {403-427}, pmid = {36944891}, issn = {1940-6029}, mesh = {*MicroRNAs/genetics ; Gene Library ; Plants/genetics ; Software ; Stress, Physiological/genetics ; Gene Expression Regulation, Plant ; RNA, Plant/genetics ; }, abstract = {Research to date on abiotic stress responses in plants has been largely focused on the plant itself, but current knowledge indicates that microorganisms can interact with and help plants during periods of abiotic stress. In our research, we aim to investigate the interkingdom communication between the plant root and the rhizo-microbiota. Our investigation showed that miRNA plays a pivotal role in this interkingdom communication. Here, we describe a protocol for the analysis of miRNA secreted by the plant root, which includes all of the steps from the isolation of the miRNA to the bioinformatics analysis. Because of their short nucleotide length, Next Generation Sequencing (NGS) library preparation from miRNAs can be challenging due to the presence of dimer adapter contaminants. Therefore, we highlight some strategies we adopt to inhibit the generation of dimer adapters during library preparation. Current screens of miRNA targets mostly focus on the identification of targets present in the same organism expressing the miRNA. Our bioinformatics analysis challenges the barrier of evolutionary divergent organisms to identify candidate sequences of the microbiota targeted by the miRNA of plant roots. This protocol should be of interest to researchers investigating interkingdom RNA-based communication between plants and their associated microorganisms, particularly in the context of holobiont responses to abiotic stresses.}, }
@article {pmid36938541, year = {2023}, author = {Xiang, N and Meyer, A and Pogoreutz, C and Rädecker, N and Voolstra, CR and Wild, C and Gärdes, A}, title = {Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals.}, journal = {Royal Society open science}, volume = {10}, number = {3}, pages = {221268}, pmid = {36938541}, issn = {2054-5703}, abstract = {Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N2 into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of nifH gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral Xenia umbellata and the more autotrophic gorgonian Pinnigorgia flava, under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in X. umbellata and P. flava were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l[-1]) increased the relative abundances of diazotrophs by sixfold in X. umbellata and fourfold in P. flava, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.}, }
@article {pmid36924962, year = {2023}, author = {Zhang, J and Huang, Z and Li, Y and Fu, D and Li, Q and Pei, L and Song, Y and Chen, L and Zhao, H and Kao, SJ}, title = {Synergistic/antagonistic effects of nitrate/ammonium enrichment on fatty acid biosynthesis and translocation in coral under heat stress.}, journal = {The Science of the total environment}, volume = {876}, number = {}, pages = {162834}, doi = {10.1016/j.scitotenv.2023.162834}, pmid = {36924962}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Anthozoa/physiology ; Nitrates ; *Ammonium Compounds ; Heat-Shock Response ; Nitrogen ; Coral Reefs ; Symbiosis ; *Dinoflagellida ; }, abstract = {Superimposed on ocean warming, nitrogen enrichment caused by human activity puts corals under even greater pressure. Biosynthesis of fatty acids (FA) is crucial for coral holobiont survival. However, the responses of FA biosynthesis pathways to nitrogen enrichment under heat stress in coral hosts and Symbiodiniaceae remain unknown, as do FA translocation mechanisms in corals. Herein, we used the thermosensitive coral species Acropora hyacinthus to investigate changes in FA biosynthesis pathways and polyunsaturated FA translocation of coral hosts and Symbiodiniaceae with respect to nitrate and ammonium enrichment under heat stress. Heat stress promoted pro-inflammatory FA biosynthesis in coral hosts and inhibited FA biosynthesis in Symbiodiniaceae. Nitrate enrichment inhibited anti-inflammatory FA biosynthesis in Symbiodiniaceae, and promoted pro-inflammatory FA biosynthesis in coral hosts and translocation to Symbiodiniaceae, leading to bleaching after 14 days of culture. Intriguingly, ammonium enrichment promoted anti-inflammatory FA biosynthesis in Symbiodiniaceae and translocation to hosts, allowing corals to better endure heat stress. We constructed schematic diagrams of the shift in FA biosynthesis and translocation in and between A. hyacinthus and its Symbiodiniaceae under heat stress, heat and nitrate co-stress, and heat and ammonium co-stress. The findings provide insight into the mechanisms of coral bleaching under environmental stress from a fatty acid perspective.}, }
@article {pmid36922761, year = {2023}, author = {Marynowska, M and Sillam-Dussès, D and Untereiner, B and Klimek, D and Goux, X and Gawron, P and Roisin, Y and Delfosse, P and Calusinska, M}, title = {A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {115}, pmid = {36922761}, issn = {1471-2164}, support = {C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; PDR T.0065.15//F.R.S.-FNRS Belgium/ ; }, mesh = {Animals ; *Isoptera/genetics ; Soil ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cellulose/metabolism ; }, abstract = {BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.<br><br>RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.<br><br>CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.}, }
@article {pmid36914757, year = {2023}, author = {Limborg, MT and Chua, PYS and Rasmussen, JA}, title = {Unexpected fishy microbiomes.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {6}, pages = {346}, pmid = {36914757}, issn = {1740-1534}, }
@article {pmid36906503, year = {2023}, author = {Wu, J and Wang, Q and Wang, D and Wong, ACN and Wang, GH}, title = {Axenic and gnotobiotic insect technologies in research on host-microbiota interactions.}, journal = {Trends in microbiology}, volume = {31}, number = {8}, pages = {858-871}, doi = {10.1016/j.tim.2023.02.007}, pmid = {36906503}, issn = {1878-4380}, mesh = {Animals ; *Microbiota ; Host Microbial Interactions ; Insecta ; Symbiosis ; Germ-Free Life ; }, abstract = {Insects are one of the most important animal life forms on earth. Symbiotic microbes are closely related to the growth and development of the host insects and can affect pathogen transmission. For decades, various axenic insect-rearing systems have been developed, allowing further manipulation of symbiotic microbiota composition. Here we review the historical development of axenic rearing systems and the latest progress in using axenic and gnotobiotic approaches to study insect-microbe interactions. We also discuss the challenges of these emerging technologies, possible solutions to address these challenges, and future research directions that can contribute to a more comprehensive understanding of insect-microbe interactions.}, }
@article {pmid36902126, year = {2023}, author = {Minerdi, D and Savoi, S and Sabbatini, P}, title = {Role of Cytochrome P450 Enzyme in Plant Microorganisms' Communication: A Focus on Grapevine.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36902126}, issn = {1422-0067}, mesh = {*Plant Proteins/genetics ; Cytochrome P-450 Enzyme System/metabolism ; Cytochromes/genetics ; *Vitis/genetics ; Gene Expression Regulation, Plant ; }, abstract = {Cytochromes P450 are ancient enzymes diffused in organisms belonging to all kingdoms of life, including viruses, with the largest number of P450 genes found in plants. The functional characterization of cytochromes P450 has been extensively investigated in mammals, where these enzymes are involved in the metabolism of drugs and in the detoxification of pollutants and toxic chemicals. The aim of this work is to present an overview of the often disregarded role of the cytochrome P450 enzymes in mediating the interaction between plants and microorganisms. Quite recently, several research groups have started to investigate the role of P450 enzymes in the interactions between plants and (micro)organisms, focusing on the holobiont Vitis vinifera. Grapevines live in close association with large numbers of microorganisms and interact with each other, regulating several vine physiological functions, from biotic and abiotic stress tolerance to fruit quality at harvest.}, }
@article {pmid36897260, year = {2023}, author = {Reich, HG and Camp, EF and Roger, LM and Putnam, HM}, title = {The trace metal economy of the coral holobiont: supplies, demands and exchanges.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {98}, number = {2}, pages = {623-642}, doi = {10.1111/brv.12922}, pmid = {36897260}, issn = {1469-185X}, mesh = {Animals ; *Anthozoa/physiology ; Ecosystem ; Coral Reefs ; Bacteria/metabolism ; Temperature ; Symbiosis ; }, abstract = {The juxtaposition of highly productive coral reef ecosystems in oligotrophic waters has spurred substantial interest and progress in our understanding of macronutrient uptake, exchange, and recycling among coral holobiont partners (host coral, dinoflagellate endosymbiont, endolithic algae, fungi, viruses, bacterial communities). By contrast, the contribution of trace metals to the physiological performance of the coral holobiont and, in turn, the functional ecology of reef-building corals remains unclear. The coral holobiont's trace metal economy is a network of supply, demand, and exchanges upheld by cross-kingdom symbiotic partnerships. Each partner has unique trace metal requirements that are central to their biochemical functions and the metabolic stability of the holobiont. Organismal homeostasis and the exchanges among partners determine the ability of the coral holobiont to adjust to fluctuating trace metal supplies in heterogeneous reef environments. This review details the requirements for trace metals in core biological processes and describes how metal exchanges among holobiont partners are key to sustaining complex nutritional symbioses in oligotrophic environments. Specifically, we discuss how trace metals contribute to partner compatibility, ability to cope with stress, and thereby to organismal fitness and distribution. Beyond holobiont trace metal cycling, we outline how the dynamic nature of the availability of environmental trace metal supplies can be influenced by a variability of abiotic factors (e.g. temperature, light, pH, etc.). Climate change will have profound consequences on the availability of trace metals and further intensify the myriad stressors that influence coral survival. Lastly, we suggest future research directions necessary for understanding the impacts of trace metals on the coral holobiont symbioses spanning subcellular to organismal levels, which will inform nutrient cycling in coral ecosystems more broadly. Collectively, this cross-scale elucidation of the role of trace metals for the coral holobiont will allow us to improve forecasts of future coral reef function.}, }
@article {pmid36891392, year = {2023}, author = {Fieschi-Méric, L and Van Leeuwen, P and Hopkins, K and Bournonville, M and Denoël, M and Lesbarrères, D}, title = {Strong restructuration of skin microbiota during captivity challenges ex-situ conservation of amphibians.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1111018}, pmid = {36891392}, issn = {1664-302X}, abstract = {In response to the current worldwide amphibian extinction crisis, conservation instances have encouraged the establishment of ex-situ collections for endangered species. The resulting assurance populations are managed under strict biosecure protocols, often involving artificial cycles of temperature and humidity to induce active and overwintering phases, which likely affect the bacterial symbionts living on the amphibian skin. However, the skin microbiota is an important first line of defense against pathogens that can cause amphibian declines, such as the chytrid Batrachochytrium dendrobatidis (Bd). Determining whether current husbandry practices for assurance populations might deplete amphibians from their symbionts is therefore essential to conservation success. Here, we characterize the effect of the transitions from the wild to captivity, and between aquatic and overwintering phases, on the skin microbiota of two newt species. While our results confirm differential selectivity of skin microbiota between species, they underscore that captivity and phase-shifts similarly affect their community structure. More specifically, the translocation ex-situ is associated with rapid impoverishment, decrease in alpha diversity and strong species turnover of bacterial communities. Shifts between active and overwintering phases also cause changes in the diversity and composition of the microbiota, and on the prevalence of Bd-inhibitory phylotypes. Altogether, our results suggest that current husbandry practices strongly restructure the amphibian skin microbiota. Although it remains to be determined whether these changes are reversible or have deleterious effects on their hosts, we discuss methods to limit microbial diversity loss ex-situ and emphasize the importance of integrating bacterial communities to applied amphibian conservation.}, }
@article {pmid36882766, year = {2023}, author = {Guo, Y and Meng, L and Wang, M and Zhong, Z and Li, D and Zhang, Y and Li, H and Zhang, H and Seim, I and Li, Y and Jiang, A and Ji, Q and Su, X and Chen, J and Fan, G and Li, C and Liu, S}, title = {Hologenome analysis reveals independent evolution to chemosymbiosis by deep-sea bivalves.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {51}, pmid = {36882766}, issn = {1741-7007}, support = {42030407//National Natural Science Foundation of China/ ; No.2022QNLM030004//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratory for Marine Science and Technology (Qingdao)/ ; 42076091//National Natural Science Foundation of China/ ; 42106100//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Bivalvia/genetics ; Biological Transport ; Genome, Bacterial ; Inhibitor of Apoptosis Proteins ; Lipopolysaccharides ; }, abstract = {BACKGROUND: Bivalves have independently evolved a variety of symbiotic relationships with chemosynthetic bacteria. These relationships range from endo- to extracellular interactions, making them ideal for studies on symbiosis-related evolution. It is still unclear whether there are universal patterns to symbiosis across bivalves. Here, we investigate the hologenome of an extracellular symbiotic thyasirid clam that represents the early stages of symbiosis evolution.<br><br>RESULTS: We present a hologenome of Conchocele bisecta (Bivalvia: Thyasiridae) collected from deep-sea hydrothermal vents with extracellular symbionts, along with related ultrastructural evidence and expression data. Based on ultrastructural and sequencing evidence, only one dominant Thioglobaceae bacteria was densely aggregated in the large bacterial chambers of C. bisecta, and the bacterial genome shows nutritional complementarity and immune interactions with the host. Overall, gene family expansions may contribute to the symbiosis-related phenotypic variations in different bivalves. For instance, convergent expansions of gaseous substrate transport families in the endosymbiotic bivalves are absent in C. bisecta. Compared to endosymbiotic relatives, the thyasirid genome exhibits large-scale expansion in phagocytosis, which may facilitate symbiont digestion and account for extracellular symbiotic phenotypes. We also reveal that distinct immune system evolution, including expansion in lipopolysaccharide scavenging and contraction of IAP (inhibitor of apoptosis protein), may contribute to the different manners of bacterial virulence resistance in C. bisecta.<br><br>CONCLUSIONS: Thus, bivalves employ different pathways to adapt to the long-term co-existence with their bacterial symbionts, further highlighting the contribution of stochastic evolution to the independent gain of a symbiotic lifestyle in the lineage.}, }
@article {pmid36882224, year = {2023}, author = {Mohamed, AR and Ochsenkühn, MA and Kazlak, AM and Moustafa, A and Amin, SA}, title = {The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, pmid = {36882224}, issn = {1574-6976}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; *Microbiota ; Bacteria/genetics ; Biological Evolution ; Symbiosis ; }, abstract = {Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.}, }
@article {pmid36872055, year = {2023}, author = {Fieschi-Méric, L and van Leeuwen, P and Denoël, M and Lesbarrères, D}, title = {Encouraging news for in situ conservation: Translocation of salamander larvae has limited impacts on their skin microbiota.}, journal = {Molecular ecology}, volume = {32}, number = {12}, pages = {3276-3289}, doi = {10.1111/mec.16914}, pmid = {36872055}, issn = {1365-294X}, mesh = {Animals ; Caudata/genetics/microbiology ; *Chytridiomycota/genetics ; Skin/microbiology ; Amphibians ; *Microbiota/genetics ; Bacteria/genetics ; Translocation, Genetic ; }, abstract = {The key role of symbiotic skin bacteria communities in amphibian resistance to emerging pathogens is well recognized, but factors leading to their dysbiosis are not fully understood. In particular, the potential effects of population translocations on the composition and diversity of hosts' skin microbiota have received little attention, although such transfers are widely carried out as a strategy for amphibian conservation. To characterize the potential reorganization of the microbiota over such a sudden environmental change, we conducted a common-garden experiment simulating reciprocal translocations of yellow-spotted salamander larvae across three lakes. We sequenced skin microbiota samples collected before and 15 days after the transfer. Using a database of antifungal isolates, we identified symbionts with known function against the pathogen Batrachochytrium dendrobatidis, a major driver of amphibian declines. Our results indicate an important reorganization of bacterial assemblages throughout ontogeny, with strong changes in composition, diversity and structure of the skin microbiota in both control and translocated individuals over the 15 days of monitoring. Unexpectedly, the diversity and community structure of the microbiota were not significantly affected by the translocation event, thus suggesting a strong resilience of skin bacterial communities to environmental change-at least across the time-window studied here. A few phylotypes were more abundant in the microbiota of translocated larvae, but no differences were found among pathogen-inhibiting symbionts. Taken together, our results support amphibian translocations as a promising strategy for this endangered animal class, with limited impact on their skin microbiota.}, }
@article {pmid36869609, year = {2023}, author = {Buitrago-López, C and Cárdenas, A and Hume, BCC and Gosselin, T and Staubach, F and Aranda, M and Barshis, DJ and Sawall, Y and Voolstra, CR}, title = {Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2151-2173}, doi = {10.1111/mec.16871}, pmid = {36869609}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/physiology ; Ecosystem ; Indian Ocean ; Biological Evolution ; Biota ; Coral Reefs ; Symbiosis/genetics ; }, abstract = {Global habitat degradation heightens the need to better understand patterns of genetic connectivity and diversity of marine biota across geographical ranges to guide conservation efforts. Corals across the Red Sea are subject to pronounced environmental differences, but studies so far suggest that animal populations are largely connected, excepting evidence for a genetic break between the northern-central and southern regions. Here, we investigated population structure and holobiont assemblage of two common pocilloporid corals, Pocillopora verrucosa and Stylophora pistillata, across the Red Sea. We found little evidence for population differentiation in P. verrucosa, except for the southernmost site. Conversely, S. pistillata exhibited a complex population structure with evidence for within-reef and regional genetic differentiation, in line with differences in their reproductive mode (P. verrucosa is a broadcast spawner and S. pistillata is a brooder). Analysis for genomic loci under positive selection identified 85 sites (18 of which were in coding sequences) that distinguished the southern P. verrucosa population from the remainder of the Red Sea population. By comparison, we found 128 loci (24 of which were residing in coding sequences) in S. pistillata with evidence for local adaptation at various sites. Functional annotation of the underlying proteins revealed putative roles in the response to stress, lipid metabolism, transport, cytoskeletal rearrangement, and ciliary function (among others). Microbial assemblages of both coral species showed pervasive association with microalgal symbionts from the genus Symbiodinium (former clade A) and bacteria from the genus Endozoicomonas that exhibited significant differences according to host genotype and environment. The disparity of population genetic and holobiont assemblage patterns even between closely related species (family Pocilloporidae) highlights the need for multispecies investigations to better understand the role of the environment in shaping evolutionary trajectories. It further emphasizes the importance of networks of reef reserves to achieve conservation of genetic variants critical to the future survival of coral ecosystems.}, }
@article {pmid36859541, year = {2023}, author = {Bergeron, LA and Besenbacher, S and Zheng, J and Li, P and Bertelsen, MF and Quintard, B and Hoffman, JI and Li, Z and St Leger, J and Shao, C and Stiller, J and Gilbert, MTP and Schierup, MH and Zhang, G}, title = {Evolution of the germline mutation rate across vertebrates.}, journal = {Nature}, volume = {615}, number = {7951}, pages = {285-291}, pmid = {36859541}, issn = {1476-4687}, mesh = {Animals ; Female ; Male ; Birds/genetics ; *Evolution, Molecular ; Fishes/genetics ; *Germ-Line Mutation/genetics ; Mammals/genetics ; *Mutation Rate ; Reptiles/genetics ; *Vertebrates/genetics ; }, abstract = {The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself[1]. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies[2]. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles. We show that the per-generation mutation rate varies among species by a factor of 40, with mutation rates being higher for males than for females in mammals and birds, but not in reptiles and fishes. The generation time, age at maturity and species-level fecundity are the key life-history traits affecting this variation among species. Furthermore, species with higher long-term effective population sizes tend to have lower mutation rates per generation, providing support for the drift barrier hypothesis[3]. The exceptionally high yearly mutation rates of domesticated animals, which have been continually selected on fecundity traits including shorter generation times, further support the importance of generation time in the evolution of mutation rates. Overall, our comparative analysis of pedigree-based mutation rates provides ecological insights on the mutation rate evolution in vertebrates.}, }
@article {pmid36853427, year = {2023}, author = {Johnson, NC and Marín, C}, title = {Microbial villages in the geography of arbuscular mycorrhizal symbioses.}, journal = {The New phytologist}, volume = {238}, number = {2}, pages = {461-463}, doi = {10.1111/nph.18803}, pmid = {36853427}, issn = {1469-8137}, mesh = {*Mycorrhizae ; Plant Roots ; Geography ; Hyphae ; }, }
@article {pmid36848579, year = {2023}, author = {Chevrier, DM and Juhin, A and Menguy, N and Bolzoni, R and Soto-Rodriguez, PED and Kojadinovic-Sirinelli, M and Paterson, GA and Belkhou, R and Williams, W and Skouri-Panet, F and Kosta, A and Le Guenno, H and Pereiro, E and Faivre, D and Benzerara, K and Monteil, CL and Lefevre, CT}, title = {Collective magnetotaxis of microbial holobionts is optimized by the three-dimensional organization and magnetic properties of ectosymbionts.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2216975120}, pmid = {36848579}, issn = {1091-6490}, support = {21-CE02-0034-01//Agence Nationale de la Recherche (ANR)/ ; 797431//european union Marie Sklodowska Curie fellowship/ ; NE/V001233/1//UKRI | Natural Environment Research Council (NERC)/ ; NE/S011978/1//UKRI | Natural Environment Research Council (NERC)/ ; }, mesh = {Physical Phenomena ; *Biomineralization ; Biophysics ; *Electrons ; }, abstract = {Over the last few decades, symbiosis and the concept of holobiont-a host entity with a population of symbionts-have gained a central role in our understanding of life functioning and diversification. Regardless of the type of partner interactions, understanding how the biophysical properties of each individual symbiont and their assembly may generate collective behaviors at the holobiont scale remains a fundamental challenge. This is particularly intriguing in the case of the newly discovered magnetotactic holobionts (MHB) whose motility relies on a collective magnetotaxis (i.e., a magnetic field-assisted motility guided by a chemoaerotaxis system). This complex behavior raises many questions regarding how magnetic properties of symbionts determine holobiont magnetism and motility. Here, a suite of light-, electron- and X-ray-based microscopy techniques [including X-ray magnetic circular dichroism (XMCD)] reveals that symbionts optimize the motility, the ultrastructure, and the magnetic properties of MHBs from the microscale to the nanoscale. In the case of these magnetic symbionts, the magnetic moment transferred to the host cell is in excess (10[2] to 10[3] times stronger than free-living magnetotactic bacteria), well above the threshold for the host cell to gain a magnetotactic advantage. The surface organization of symbionts is explicitly presented herein, depicting bacterial membrane structures that ensure longitudinal alignment of cells. Magnetic dipole and nanocrystalline orientations of magnetosomes were also shown to be consistently oriented in the longitudinal direction, maximizing the magnetic moment of each symbiont. With an excessive magnetic moment given to the host cell, the benefit provided by magnetosome biomineralization beyond magnetotaxis can be questioned.}, }
@article {pmid36848561, year = {2023}, author = {Di Lelio, I and Forni, G and Magoga, G and Brunetti, M and Bruno, D and Becchimanzi, A and De Luca, MG and Sinno, M and Barra, E and Bonelli, M and Frusciante, S and Diretto, G and Digilio, MC and Woo, SL and Tettamanti, G and Rao, R and Lorito, M and Casartelli, M and Montagna, M and Pennacchio, F}, title = {A soil fungus confers plant resistance against a phytophagous insect by disrupting the symbiotic role of its gut microbiota.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {10}, pages = {e2216922120}, pmid = {36848561}, issn = {1091-6490}, support = {773554//EC | Horizon 2020 Framework Programme (H2020)/ ; 2017JLN833//Ministero dell'Universit&#xe0; e della Ricerca (MUR)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Soil ; *Microbiota ; Insecta ; Agriculture ; *Solanum lycopersicum ; }, abstract = {Plants generate energy flows through natural food webs, driven by competition for resources among organisms, which are part of a complex network of multitrophic interactions. Here, we demonstrate that the interaction between tomato plants and a phytophagous insect is driven by a hidden interplay between their respective microbiotas. Tomato plants colonized by the soil fungus Trichoderma afroharzianum, a beneficial microorganism widely used in agriculture as a biocontrol agent, negatively affects the development and survival of the lepidopteran pest Spodoptera littoralis by altering the larval gut microbiota and its nutritional support to the host. Indeed, experiments aimed to restore the functional microbial community in the gut allow a complete rescue. Our results shed light on a novel role played by a soil microorganism in the modulation of plant-insect interaction, setting the stage for a more comprehensive analysis of the impact that biocontrol agents may have on ecological sustainability of agricultural systems.}, }
@article {pmid36840260, year = {2023}, author = {Anguita-Maeso, M and Navas-Cortés, JA and Landa, BB}, title = {Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840260}, issn = {2223-7747}, support = {AGL2016-75606-R and PID2020-114917RB-I00//Programa Estatal de I+D Orientado a los Retos de la Sociedad from Spanish Government, the Spanish State Research Agency and FEDER-EU/ ; TED2021-130110B-C41//Proyectos Orientados a la Transici&#xf3;n Ecol&#xf3;gica y a la Transici&#xf3;n Digital-Plan de Recuperaci&#xf3;n, Transformaci&#xf3;n y Resiliencia from Spanish Government, the Spanish State Research Agency/ ; grant 727987//XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary Oriented Research Strategy; from the European Union's Horizon 2020 Framework Research Programme/ ; }, abstract = {Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.}, }
@article {pmid36838257, year = {2023}, author = {Mashini, AG and Oakley, CA and Beepat, SS and Peng, L and Grossman, AR and Weis, VM and Davy, SK}, title = {The Influence of Symbiosis on the Proteome of the Exaiptasia Endosymbiont Breviolum minutum.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838257}, issn = {2076-2607}, support = {VUW1601//Royal Society of New Zealand/ ; PhD Scholarship awarded to AGM//Victoria University of Wellington/ ; }, abstract = {The cellular mechanisms responsible for the regulation of nutrient exchange, immune response, and symbiont population growth in the cnidarian-dinoflagellate symbiosis are poorly resolved. Here, we employed liquid chromatography-mass spectrometry to elucidate proteomic changes associated with symbiosis in Breviolum minutum, a native symbiont of the sea anemone Exaiptasia diaphana ('Aiptasia'). We manipulated nutrients available to the algae in culture and to the holobiont in hospite (i.e., in symbiosis) and then monitored the impacts of our treatments on host-endosymbiont interactions. Both the symbiotic and nutritional states had significant impacts on the B. minutum proteome. B. minutum in hospite showed an increased abundance of proteins involved in phosphoinositol metabolism (e.g., glycerophosphoinositol permease 1 and phosphatidylinositol phosphatase) relative to the free-living alga, potentially reflecting inter-partner signalling that promotes the stability of the symbiosis. Proteins potentially involved in concentrating and fixing inorganic carbon (e.g., carbonic anhydrase, V-type ATPase) and in the assimilation of nitrogen (e.g., glutamine synthase) were more abundant in free-living B. minutum than in hospite, possibly due to host-facilitated access to inorganic carbon and nitrogen limitation by the host when in hospite. Photosystem proteins increased in abundance at high nutrient levels irrespective of the symbiotic state, as did proteins involved in antioxidant defences (e.g., superoxide dismutase, glutathione s-transferase). Proteins involved in iron metabolism were also affected by the nutritional state, with an increased iron demand and uptake under low nutrient treatments. These results detail the changes in symbiont physiology in response to the host microenvironment and nutrient availability and indicate potential symbiont-driven mechanisms that regulate the cnidarian-dinoflagellate symbiosis.}, }
@article {pmid36835084, year = {2023}, author = {Mutusamy, P and Banga Singh, KK and Su Yin, L and Petersen, B and Sicheritz-Ponten, T and Clokie, MRJ and Loke, S and Millard, A and Parimannan, S and Rajandas, H}, title = {Phenotypic Characterization and Comparative Genomic Analysis of Novel Salmonella Bacteriophages Isolated from a Tropical Rainforest.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835084}, issn = {1422-0067}, support = {JPT(BKPI)1000/016/018/25 (60)//Ministry of Higher Education Malaysia/ ; }, mesh = {Humans ; *Salmonella Phages/genetics ; Rainforest ; Salmonella/genetics ; *Bacteriophages/genetics ; *Salmonella Infections/genetics ; Phenotype ; Genomics ; Genome, Viral ; }, abstract = {Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.}, }
@article {pmid36824281, year = {2023}, author = {Biget, M and Wang, T and Mony, C and Xu, Q and Lecoq, L and Chable, V and Theis, KR and Ling, N and Vandenkoornhuyse, P}, title = {Evaluating the hologenome concept by analyzing the root-endosphere microbiota of chimeric plants.}, journal = {iScience}, volume = {26}, number = {2}, pages = {106031}, pmid = {36824281}, issn = {2589-0042}, abstract = {The hologenome concept considers the entity formed by a host and its microbiota, the holobiont, as new level of hierarchical organization subject to neutral and selective forces. We used grafted plants to formally evaluate the hologenome concept. We analyzed the root-endosphere microbiota of two independent watermelon and grapevine plant systems, including ungrafted and reciprocal-grafting combinations. Grafted and ungrafted hosts harbor markedly different microbiota compositions. Furthermore, the results indicate a non-random assembly of bacterial communities inhabiting the root endosphere of chimeric plants with interactive effect of both the rootstock and scion on the recruitment of microorganisms. Because chimeric plants did not have a random microbiota, the null hypothesis that holobionts assemble randomly and hologenome concept is an intellectual construction only can be rejected. The study supports the relevance of hologenome as biological level of organization and opens new avenues for a better fundamental understanding of plants as holobionts.}, }
@article {pmid36819038, year = {2023}, author = {Sun, X and Li, Y and Yang, Q and Zhang, H and Xu, N and Tang, Z and Wu, S and Jiang, Y and Mohamed, HF and Ou, D and Zheng, X}, title = {Identification of quorum sensing-regulated Vibrio fortis as potential pathogenic bacteria for coral bleaching and the effects on the microbial shift.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1116737}, pmid = {36819038}, issn = {1664-302X}, abstract = {Coastal pollution, global warming, ocean acidification, and other reasons lead to the imbalance of the coral reef ecosystem, resulting in the increasingly serious problem of coral degradation. Coral bleaching is often accompanied by structural abnormalities of coral symbiotic microbiota, among which Vibrio is highly concerned. In this study, Vibrio fortis S10-1 (MCCC 1H00104), isolated from sea cucumber, was used for the bacterial infection on coral Seriatopora guttatus and Pocillopora damicornis. The infection of S10-1 led to coral bleaching and a significant reduction of photosynthetic function in coral holobiont, and the pathogenicity of V. fortis was regulated by quorum sensing. Meanwhile, Vibrio infection also caused a shift of coral symbiotic microbial community, with significantly increased abundant Proteobacteria and Actinobacteria and significantly reduced abundant Firmicutes; on genus level, the abundance of Bacillus decreased significantly and the abundance of Rhodococcus, Ralstonia, and Burkholderia-Caballeronia-Paraburkholderia increased significantly; S10-1 infection also significantly impacted the water quality in the micro-ecosystem. In contrast, S10-1 infection showed less effect on the microbial community of the live stone, which reflected that the microbes in the epiphytic environment of the live stone might have a stronger ability of self-regulation; the algal symbionts mainly consisted of Cladocopium sp. and showed no significant effect by the Vibrio infection. This study verified that V. fortis is the primary pathogenic bacterium causing coral bleaching, revealed changes in the microbial community caused by its infection, provided strong evidence for the "bacterial bleaching" hypothesis, and provided an experimental experience for the exploration of the interaction mechanism among microbial communities, especially coral-associated Vibrio in the coral ecosystem, and potential probiotic strategy or QS regulation on further coral disease control.}, }
@article {pmid36815841, year = {2023}, author = {Jin, X and Zhu, H and Shi, Y and Chen, Z and Wang, Y and Gui, JF and Zhao, Z}, title = {Host Hybridization Dominates over Cohabitation in Affecting Gut Microbiota of Intrageneric Hybrid Takifugu Pufferfish.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0118122}, pmid = {36815841}, issn = {2379-5077}, mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Takifugu/genetics ; *Microbiota ; Fishes ; Hybridization, Genetic ; }, abstract = {Microbial symbionts are of great importance for macroscopic life, including fish, and both collectively comprise an integrated biological entity known as the holobiont. Yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to biotic and/or abiotic influences. Here, through amplicon profiling, the genealogical relationship between artificial F1 hybrid pufferfish with growth heterosis, produced from crossing female Takifugu obscurus with male Takifugu rubripes and its maternal halfsibling purebred, was well recapitulated by their gut microbial community similarities, indicating an evident parallelism between host phylogeny (hybridity) and microbiota relationships therein. Interestingly, modest yet significant fish growth promotion and gut microbiota alteration mediated by hybrid-purebred cohabitation were observed, in comparison with their respective monoculture cohorts that share common genetic makeups, implying a certain degree of environmental influences. Moreover, the underlying assemblage patterns of gut microbial communities were found associated with a trade-off between variable selection and dispersal limitation, which are plausibly driven by the augmented social interactions between hybrid and purebred cohabitants differing in behaviors. Results from this study not only can enrich, from a microbial perspective, the sophisticated understanding of complex and dynamic assemblage of the fish holobiont, but will also provide deeper insights into the ecophysiological factors imposed on the diversity-function relationships thereof. Our findings emphasize the intimate associations of gut microbiota in host genetics-environmental interactions and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve the production of farmed fishes. IMPORTANCE Microbial symbionts are of great importance for macroscopic life, including fish, and yet little is known as to how the normal balance within the fish holobiont is maintained and how it responds to the biotic and/or abiotic influences. Through gut microbiota profiling, we show that host intrageneric hybridization and cohabitation can impose a strong disturbance upon pufferfish gut microbiota. Moreover, marked alterations in the composition and function of gut microbiota in both hybrid and purebred pufferfish cohabitants were observed, which are potentially correlated with different metabolic priorities and behaviors between host genealogy. These results can enrich, from a microbial perspective, the sophisticated understanding of the complex and dynamic assemblage of the fish holobiont and would have deeper practical implications for microbial contributions to optimize performance prediction and to improve farmed fish production.}, }
@article {pmid36807754, year = {2023}, author = {Lindner, M and Radke, DI and Elke, G}, title = {[Bacterial gut microbiota-key player in sepsis].}, journal = {Medizinische Klinik, Intensivmedizin und Notfallmedizin}, volume = {118}, number = {2}, pages = {107-113}, pmid = {36807754}, issn = {2193-6226}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Bacteria ; *Sepsis ; Dysbiosis/complications/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The gut microbiota is comprised of over 1200 different bacteria and forms a symbiotic community with the human organism, the holobiont. It plays an important role in the maintenance of homeostasis, e.g., of the immune system and essential metabolic processes. Disturbances in the balance of this reciprocal relationship are called dysbiosis and, in the field of sepsis, are associated with incidence of disease, extent of the systemic inflammatory response, severity of organ dysfunction, and mortality. In addition to providing guiding principles in the fascinating relationship between "human and microbe," this article summarizes recent findings regarding the role of the bacterial gut microbiota in sepsis, which is one a very relevant in intensive care medicine.}, }
@article {pmid36807409, year = {2023}, author = {Rasmussen, JA and Kiilerich, P and Madhun, AS and Waagbø, R and Lock, ER and Madsen, L and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Co-diversification of an intestinal Mycoplasma and its salmonid host.}, journal = {The ISME journal}, volume = {17}, number = {5}, pages = {682-692}, pmid = {36807409}, issn = {1751-7370}, mesh = {Animals ; *Salmonidae ; Bacteria ; *Gastrointestinal Microbiome ; *Salmo salar ; }, abstract = {Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.}, }
@article {pmid36803555, year = {2023}, author = {Poupin, MJ and Ledger, T and Roselló-Móra, R and González, B}, title = {The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {9}, pmid = {36803555}, issn = {2524-6372}, support = {PIA/BASAL FB0002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; PIA/BASAL FB0002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; PIA/BASAL FB0002//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; PGC2018-096956-B-C41//European Regional Development Fund/ ; }, abstract = {As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.}, }
@article {pmid36801111, year = {2023}, author = {Theissinger, K and Fernandes, C and Formenti, G and Bista, I and Berg, PR and Bleidorn, C and Bombarely, A and Crottini, A and Gallo, GR and Godoy, JA and Jentoft, S and Malukiewicz, J and Mouton, A and Oomen, RA and Paez, S and Palsbøll, PJ and Pampoulie, C and Ruiz-López, MJ and Secomandi, S and Svardal, H and Theofanopoulou, C and de Vries, J and Waldvogel, AM and Zhang, G and Jarvis, ED and Bálint, M and Ciofi, C and Waterhouse, RM and Mazzoni, CJ and Höglund, J and , }, title = {How genomics can help biodiversity conservation.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {7}, pages = {545-559}, doi = {10.1016/j.tig.2023.01.005}, pmid = {36801111}, issn = {0168-9525}, mesh = {*Conservation of Natural Resources ; *Biodiversity ; Genomics ; Genome ; }, abstract = {The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.}, }
@article {pmid36797336, year = {2023}, author = {Eisenhofer, R and Odriozola, I and Alberdi, A}, title = {Impact of microbial genome completeness on metagenomic functional inference.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {12}, pmid = {36797336}, issn = {2730-6151}, support = {817729//European Commission (EC)/ ; DNRF143//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; CF20-0460//Carlsbergfondet (Carlsberg Foundation)/ ; }, abstract = {Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this overlooked bias in metagenomic functional inference.}, }
@article {pmid36795564, year = {2023}, author = {Zhang, P and Zhu, Y and Guo, Q and Li, J and Zhan, X and Yu, H and Xie, N and Tan, H and Lundholm, N and Garcia-Cuetos, L and Martin, MD and Subirats, MA and Su, YH and Ruiz-Trillo, I and Martindale, MQ and Yu, JK and Gilbert, MTP and Zhang, G and Li, Q}, title = {On the origin and evolution of RNA editing in metazoans.}, journal = {Cell reports}, volume = {42}, number = {2}, pages = {112112}, pmid = {36795564}, issn = {2211-1247}, mesh = {Animals ; *RNA Editing/genetics ; *RNA, Double-Stranded/genetics ; RNA, Messenger ; Adenosine Deaminase/metabolism ; Inosine/genetics ; }, abstract = {Extensive adenosine-to-inosine (A-to-I) editing of nuclear-transcribed mRNAs is the hallmark of metazoan transcriptional regulation. Here, by profiling the RNA editomes of 22 species that cover major groups of Holozoa, we provide substantial evidence supporting A-to-I mRNA editing as a regulatory innovation originating in the last common ancestor of extant metazoans. This ancient biochemistry process is preserved in most extant metazoan phyla and primarily targets endogenous double-stranded RNA (dsRNA) formed by evolutionarily young repeats. We also find intermolecular pairing of sense-antisense transcripts as an important mechanism for forming dsRNA substrates for A-to-I editing in some but not all lineages. Likewise, recoding editing is rarely shared across lineages but preferentially targets genes involved in neural and cytoskeleton systems in bilaterians. We conclude that metazoan A-to-I editing might first emerge as a safeguard mechanism against repeat-derived dsRNA and was later co-opted into diverse biological processes due to its mutagenic nature.}, }
@article {pmid36793883, year = {2022}, author = {Clokie, M and Sicheritz-Pontén, T}, title = {Reflections on 2022: A Progressive Year for Phage Therapy.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {4}, pages = {181-182}, doi = {10.1089/phage.2022.29038.editorial}, pmid = {36793883}, issn = {2641-6549}, }
@article {pmid36793689, year = {2023}, author = {Matias, AMA and Popovic, I and Thia, JA and Cooke, IR and Torda, G and Lukoschek, V and Bay, LK and Kim, SW and Riginos, C}, title = {Cryptic diversity and spatial genetic variation in the coral Acropora tenuis and its endosymbionts across the Great Barrier Reef.}, journal = {Evolutionary applications}, volume = {16}, number = {2}, pages = {293-310}, pmid = {36793689}, issn = {1752-4571}, abstract = {Genomic studies are uncovering extensive cryptic diversity within reef-building corals, suggesting that evolutionarily and ecologically relevant diversity is highly underestimated in the very organisms that structure coral reefs. Furthermore, endosymbiotic algae within coral host species can confer adaptive responses to environmental stress and may represent additional axes of coral genetic variation that are not constrained by taxonomic divergence of the cnidarian host. Here, we examine genetic variation in a common and widespread, reef-building coral, Acropora tenuis, and its associated endosymbiotic algae along the entire expanse of the Great Barrier Reef (GBR). We use SNPs derived from genome-wide sequencing to characterize the cnidarian coral host and organelles from zooxanthellate endosymbionts (genus Cladocopium). We discover three distinct and sympatric genetic clusters of coral hosts, whose distributions appear associated with latitude and inshore-offshore reef position. Demographic modelling suggests that the divergence history of the three distinct host taxa ranges from 0.5 to 1.5 million years ago, preceding the GBR's formation, and has been characterized by low-to-moderate ongoing inter-taxon gene flow, consistent with occasional hybridization and introgression typifying coral evolution. Despite this differentiation in the cnidarian host, A. tenuis taxa share a common symbiont pool, dominated by the genus Cladocopium (Clade C). Cladocopium plastid diversity is not strongly associated with host identity but varies with reef location relative to shore: inshore colonies contain lower symbiont diversity on average but have greater differences between colonies as compared with symbiont communities from offshore colonies. Spatial genetic patterns of symbiont communities could reflect local selective pressures maintaining coral holobiont differentiation across an inshore-offshore environmental gradient. The strong influence of environment (but not host identity) on symbiont community composition supports the notion that symbiont community composition responds to habitat and may assist in the adaptation of corals to future environmental change.}, }
@article {pmid36756199, year = {2022}, author = {Choudhary, DK and Vaishnav, A and Jain, S and Mandal, MK and Prasad, R}, title = {Editorial: Climate impact on plant holobiont: Mitigation strategies and sustainability.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1040876}, doi = {10.3389/fmicb.2022.1040876}, pmid = {36756199}, issn = {1664-302X}, }
@article {pmid36750176, year = {2023}, author = {Woltyńska, A and Gawor, J and Olech, MA and Górniak, D and Grzesiak, J}, title = {Bacterial communities of Antarctic lichens explored by gDNA and cDNA 16S rRNA gene amplicon sequencing.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {3}, pages = {}, pmid = {36750176}, issn = {1574-6941}, mesh = {*Lichens/genetics ; RNA, Ribosomal, 16S/genetics ; DNA, Complementary ; Genes, rRNA ; Phylogeny ; Bacteria/genetics ; Antarctic Regions ; }, abstract = {Recently, lichens came once more into the scientific spotlight due to their unique relations with prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper, we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the nonactive part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.}, }
@article {pmid36750093, year = {2023}, author = {Kazmi, SA and Hsiao, EY}, title = {Extending genetic risk for Alzheimer's disease from host to holobiont.}, journal = {Cell}, volume = {186}, number = {4}, pages = {690-692}, doi = {10.1016/j.cell.2023.01.004}, pmid = {36750093}, issn = {1097-4172}, mesh = {Mice ; Animals ; *Alzheimer Disease/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Bacteria/metabolism ; }, abstract = {The gut microbiota is implicated in risk for Alzheimer's disease (AD). A study in Science reports that depleting gut bacteria in mice with genetic risk for AD reduces neuropathology in a sex-dependent manner. This is reversed by administering short-chain fatty acids, suggesting that specific bacterial metabolites increase susceptibility to AD.}, }
@article {pmid36748430, year = {2022}, author = {Izraeli, Y and Lepetit, D and Atias, S and Mozes-Daube, N and Wodowski, G and Lachman, O and Luria, N and Steinberg, S and Varaldi, J and Zchori-Fein, E and Chiel, E}, title = {Genomic characterization of viruses associated with the parasitoid Anagyrus vladimiri (Hymenoptera: Encyrtidae).}, journal = {The Journal of general virology}, volume = {103}, number = {12}, pages = {}, doi = {10.1099/jgv.0.001810}, pmid = {36748430}, issn = {1465-2099}, mesh = {Humans ; Female ; Animals ; Phylogeny ; *Wasps ; *Viruses ; Genomics ; *Reoviridae/genetics ; }, abstract = {Knowledge on symbiotic microorganisms of insects has increased dramatically in recent years, yet relatively little data are available regarding non-pathogenic viruses. Here we studied the virome of the parasitoid wasp Anagyrus vladimiri Triapitsyn (Hymenoptera: Encyrtidae), a biocontrol agent of mealybugs. By high-throughput sequencing of viral nucleic acids, we revealed three novel viruses, belonging to the families Reoviridae [provisionally termed AnvRV (Anagyrus vladimiri reovirus)], Iflaviridae (AnvIFV) and Dicistroviridae (AnvDV). Phylogenetic analysis further classified AnvRV in the genus Idnoreovirus, and AnvDV in the genus Triatovirus. The genome of AnvRV comprises 10 distinct genomic segments ranging in length from 1.5 to 4.2 kb, but only two out of the 10 ORFs have a known function. AnvIFV and AnvDV each have one polypeptide ORF, which is typical of iflaviruses but very un-common among dicistroviruses. Five conserved domains were found along both the ORFs of those two viruses. AnvRV was found to be fixed in an A. vladimiri population that was obtained from a mass rearing facility, whereas its prevalence in field-collected A. vladimiri was ~15 %. Similarly, the prevalence of AnvIFV and AnvDV was much higher in the mass rearing population than in the field population. The presence of AnvDV was positively correlated with the presence of Wolbachia in the same individuals. Transmission electron micrographs of females' ovaries revealed clusters and viroplasms of reovirus-like particles in follicle cells, suggesting that AnvRV is vertically transmitted from mother to offspring. AnvRV was not detected in the mealybugs, supporting the assumption that this virus is truly associated with the wasps. The possible effects of these viruses on A. vladimiri's biology, and on biocontrol agents in general, are discussed. Our findings identify RNA viruses as potentially involved in the multitrophic system of mealybugs, their parasitoids and other members of the holobiont.}, }
@article {pmid36745783, year = {2023}, author = {Germain, RR and Feng, S and Buffan, L and Carmona, CP and Chen, G and Graves, GR and Tobias, JA and Rahbek, C and Lei, F and Fjeldså, J and Hosner, PA and Gilbert, MTP and Zhang, G and Nogués-Bravo, D}, title = {Changes in the functional diversity of modern bird species over the last million years.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {7}, pages = {e2201945119}, pmid = {36745783}, issn = {1091-6490}, mesh = {Humans ; Animals ; *Biodiversity ; *Biota ; Time Factors ; Birds/genetics ; Climate Change ; Ecosystem ; }, abstract = {Despite evidence of declining biosphere integrity, we currently lack understanding of how the functional diversity associated with changes in abundance among ecological communities has varied over time and before widespread human disturbances. We combine morphological, ecological, and life-history trait data for >260 extant bird species with genomic-based estimates of changing effective population size (Ne) to quantify demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. We show that functional diversity was relatively stable over this period, but underwent significant changes in some key areas of trait space due to changing species abundances. Our results suggest that patterns of population decline over the Pleistocene have been concentrated in particular regions of trait space associated with extreme reproductive strategies and low dispersal ability, consistent with an overall erosion of functional diversity. Further, species most sensitive to climate warming occupied a relatively narrow region of functional space, indicating that the largest potential population increases and decreases under climate change will occur among species with relatively similar trait sets. Overall, our results identify fluctuations in functional space of extant species over evolutionary timescales and represent the demographic-based vulnerability of different regions of functional space among these taxa. The integration of paleodemographic dynamics with functional trait data enhances our ability to quantify losses of biosphere integrity before anthropogenic disturbances and attribute contemporary biodiversity loss to different drivers over time.}, }
@article {pmid36736005, year = {2023}, author = {Fujiyoshi, S and Yarimizu, K and Perera, I and Abanto, M and Jorquera, M and Maruyama, F}, title = {Learning from mistakes: challenges in finding holobiont factors from environmental samples and the importance of methodological consistency.}, journal = {Current opinion in biotechnology}, volume = {80}, number = {}, pages = {102897}, doi = {10.1016/j.copbio.2023.102897}, pmid = {36736005}, issn = {1879-0429}, mesh = {Humans ; *Harmful Algal Bloom ; *Bacteria ; Environmental Monitoring ; }, abstract = {The cause of harmful algal blooms has been a mystery, but research to elucidate its mechanism has progressed over the years thanks to genetic technologies. We have monitored toxic algae and its associated bacteria as a community, the so-called 'holobiont' in Chilean coastal waters for years from the perspective of bacteria as an algal bloom driver. This review describes the challenges of holobiont monitoring, specifically with respect to standardizing and compliance with the monitoring protocols to collect reliable and sustainable data. Further, we suggest adopting the high-throughput sequencing (HTS) standard operating procedure (SOP) by the International Human Microbiome to improve the quality and consistency of holobiont monitoring in the harmful algal world.}, }
@article {pmid36731191, year = {2023}, author = {Zhu, W and Wang, H and Li, X and Liu, X and Zhu, M and Wang, A and Li, X}, title = {Consistent responses of coral microbiome to acute and chronic heat stress exposures.}, journal = {Marine environmental research}, volume = {185}, number = {}, pages = {105900}, doi = {10.1016/j.marenvres.2023.105900}, pmid = {36731191}, issn = {1879-0291}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota/genetics ; Heat-Shock Response ; Bacteria ; Symbiosis ; }, abstract = {Frequent and intense heat waves lead to bleaching and even death of reef-building corals, and the thermal tolerance ultimately depends on the genetic composition of the holobiont. Here, we compared the effects of acute and chronic heat stress exposures on coral Porites cylindrica holobiont. Regardless of the temperature treatment, corals at 33 °C showed signs of bleaching and a significant decrease in photochemical efficiency (Fv/Fm). However, Symbiodiniaceae communities were relatively stable and all dominated by the same genus Cladocopium (C15). The relative abundanbce of core microbiome varied significantly, and they may provide several functions important to holobiont fitness. Both heat stress exposures induced the significant structural reorganization of coral-associated bacteria, with bacterial diversity and community heterogeneity significantly increasing with the temperature treatment. The modified stochasticity ratio (MST) revealed that stochastic processes dominated bacterial community assembly in thermally stressed corals. Certain core bacterial members that were hypothesized to fulfil functional niche decreased significantly, with the enrichment of potentially pathogenic and opportunistic bacteria in heat stress exposures. Thermally stressed corals had more positive correlation, higher network complexity and tighter associations among microbial taxa, relative to healthy corals. Overall, the coral microbiome exhibits similar responses to acute and chronic heat stress, and our study provides new insights about the deleterious impacts of complex warming oceans on coral holobiont.}, }
@article {pmid36719456, year = {2023}, author = {Lin, Z and Zheng, X and Chen, J}, title = {Deciphering pH-dependent microbial taxa and functional gene co-occurrence in the coral Galaxea fascicularis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1856-1868}, pmid = {36719456}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Seawater/microbiology ; Hydrogen-Ion Concentration ; Bacteria/genetics ; *Microbiota/genetics ; Carbon ; Coral Reefs ; }, abstract = {How the coral microbiome responds to oceanic pH changes due to anthropogenic climate change, including ocean acidification and deliberate artificial alkalization, remains an open question. Here, we applied a 16S profile and GeoChip approach to microbial taxonomic and gene functional landscapes in the coral Galaxea fascicularis under three pH levels (7.85, 8.15, and 8.45) and tested the influence of pH changes on the cell growth of several coral-associated strains and bacterial populations. Statistical analysis of GeoChip-based data suggested that both ocean acidification and alkalization destabilized functional cores related to aromatic degradation, carbon degradation, carbon fixation, stress response, and antibiotic biosynthesis in the microbiome, which are related to holobiont carbon cycling and health. The taxonomic analysis revealed that bacterial species richness was not significantly different among the three pH treatments, but the community compositions were significantly distinct. Acute seawater alkalization leads to an increase in pathogens as well as a stronger taxonomic shift than acidification, which is worth considering when using artificial ocean alkalization to protect coral ecosystems from ocean acidification. In addition, our co-occurrence network analysis reflected microbial community and functional shifts in response to pH change cues, which will further help to understand the functional ecological role of the microbiome in coral resilience.}, }
@article {pmid36713485, year = {2023}, author = {Bonthond, G and Neu, AK and Bayer, T and Krueger-Hadfield, SA and Künzel, S and Weinberger, F}, title = {Non-native hosts of an invasive seaweed holobiont have more stable microbial communities compared to native hosts in response to thermal stress.}, journal = {Ecology and evolution}, volume = {13}, number = {1}, pages = {e9753}, pmid = {36713485}, issn = {2045-7758}, abstract = {Seaweeds are colonized by a microbial community, which can be directly linked to their performance. This community is shaped by an interplay of stochastic and deterministic processes, including mechanisms which the holobiont host deploys to manipulate its associated microbiota. The Anna Karenina principle predicts that when a holobiont is exposed to suboptimal or stressful conditions, these host mechanisms may be compromised. This leads to a relative increase of stochastic processes that may potentially result in the succession of a microbial community harmful to the host. Based on this principle, we used the variability in microbial communities (i.e., beta diversity) as a proxy for stability within the invasive holobiont Gracilaria vermiculophylla during a simulated invasion in a common garden experiment. Independent of host range, host performance declined at elevated temperature (22°C) and disease incidence and beta diversity increased. Under thermally stressful conditions, beta diversity increased more in epibiota from native populations, suggesting that epibiota from non-native holobionts are thermally more stable. This pattern reflects an increase in deterministic processes acting on epibiota associated with non-native hosts, which in the setting of a common garden can be assumed to originate from the host itself. Therefore, these experimental data suggest that the invasion process may have selected for hosts better able to maintain stable microbiota during stress. Future studies are needed to identify the underlying host mechanisms.}, }
@article {pmid36702670, year = {2023}, author = {Li, JH and Muhammad Aslam, M and Gao, YY and Dai, L and Hao, GF and Wei, Z and Chen, MX and Dini-Andreote, F}, title = {Microbiome-mediated signal transduction within the plant holobiont.}, journal = {Trends in microbiology}, volume = {31}, number = {6}, pages = {616-628}, doi = {10.1016/j.tim.2022.12.005}, pmid = {36702670}, issn = {1878-4380}, mesh = {*Plants ; Rhizosphere ; Symbiosis ; *Microbiota ; Signal Transduction ; Plant Roots ; Soil Microbiology ; }, abstract = {Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.}, }
@article {pmid36699263, year = {2023}, author = {Bolt Botnen, A and Bjørnsen, MB and Alberdi, A and Gilbert, MTP and Aizpurua, O}, title = {A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12861}, pmid = {36699263}, issn = {2405-8440}, abstract = {As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.}, }
@article {pmid36688656, year = {2023}, author = {Rosado, PM and Cardoso, PM and Rosado, JG and Schultz, J and Nunes da Rocha, U and Keller-Costa, T and Peixoto, RS}, title = {Exploring the Potential Molecular Mechanisms of Interactions between a Probiotic Consortium and Its Coral Host.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0092122}, pmid = {36688656}, issn = {2379-5077}, mesh = {Animals ; *Anthozoa/genetics ; Bacteria/genetics ; *Probiotics/pharmacology ; Coral Bleaching ; }, abstract = {Beneficial microorganisms for corals (BMCs) have been demonstrated to be effective probiotics to alleviate bleaching and mitigate coral mortality in vivo. The selection of putative BMCs is traditionally performed manually, using an array of biochemical and molecular tests for putative BMC traits. We present a comprehensive genetic survey of BMC traits using a genome-based framework for the identification of alternative mechanisms that can be used for future in silico selection of BMC strains. We identify exclusive BMC traits associated with specific strains and propose new BMC mechanisms, such as the synthesis of glycine betaine and ectoines. Our roadmap facilitates the selection of BMC strains while increasing the array of genetic targets that can be included in the selection of putative BMC strains to be tested as coral probiotics. IMPORTANCE Probiotics are currently the main hope as a potential medicine for corals, organisms that are considered the marine "canaries of the coal mine" and that are threatened with extinction. Our experiments have proved the concept that probiotics mitigate coral bleaching and can also prevent coral mortality. Here, we present a comprehensive genetic survey of probiotic traits using a genome-based framework. The main outcomes are a roadmap that facilitates the selection of coral probiotic strains while increasing the array of mechanisms that can be included in the selection of coral probiotics.}, }
@article {pmid36687663, year = {2022}, author = {Burgunter-Delamare, B and Rousvoal, S and Legeay, E and Tanguy, G and Fredriksen, S and Boyen, C and Dittami, SM}, title = {The Saccharina latissima microbiome: Effects of region, season, and physiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1050939}, pmid = {36687663}, issn = {1664-302X}, abstract = {INTRODUCTION: Saccharina latissima is a canopy-forming species of brown algae and, as such, is considered an ecosystem engineer. Several populations of this alga are exploited worldwide, and a decrease in the abundance of S. latissima at its southern distributional range limits has been observed. Despite its economic and ecological interest, only a few data are available on the composition of microbiota associated with S. latissima and its role in algal physiologyn.<br><br>METHODS: We studied the whole bacterial community composition associated with S. latissima samples from three locations (Brittany, Helgoland, and Skagerrak) by 16S metabarcoding analyses at different scales: algal blade part, regions, season (at one site), and algal physiologic state.<br><br>RESULTS AND DISCUSSION: We have shown that the difference in bacterial composition is driven by factors of decreasing importance: (i) the algal tissues (apex/meristem), (ii) the geographical area, (iii) the seasons (at the Roscoff site), and (iv) the algal host's condition (healthy vs. symptoms). Overall, Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia dominated the general bacterial communities. Almost all individuals hosted bacteria of the genus Granulosicoccus, accounting for 12% of the total sequences, and eight additional core genera were identified. Our results also highlight a microbial signature characteristic for algae in poor health independent of the disease symptoms. Thus, our study provides a comprehensive overview of the S. latissima microbiome, forming a basis for understanding holobiont functioning.}, }
@article {pmid36683362, year = {2022}, author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H}, title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36683362}, issn = {2047-217X}, support = {DP200101613//Australian Research Council/ ; //University of Melbourne/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Archaea/genetics ; Coral Reefs ; Bacteria/genetics ; Metagenome ; Genomics ; }, abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.}, }
@article {pmid36680370, year = {2023}, author = {Hansen, CCR and Láruson, &#xc1;J and Rasmussen, JA and Ballesteros, JAC and Sinding, MS and Hallgrimsson, GT and von Schmalensee, M and Stefansson, RA and Skarphédinsson, KH and Labansen, AL and Leivits, M and Sonne, C and Dietz, R and Skelmose, K and Boertmann, D and Eulaers, I and Martin, MD and Helgason, AS and Gilbert, MTP and Pálsson, S}, title = {Genomic diversity and differentiation between island and mainland populations of white-tailed eagles (Haliaeetus albicilla).}, journal = {Molecular ecology}, volume = {32}, number = {8}, pages = {1925-1942}, doi = {10.1111/mec.16858}, pmid = {36680370}, issn = {1365-294X}, support = {185280-052//Icelandic Centre for Research/ ; }, mesh = {Animals ; Humans ; *Eagles/genetics ; Europe ; Norway ; Genomics ; *Environmental Pollutants ; Genetic Variation/genetics ; }, abstract = {Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: (1) Isolation of refugia during the last glacial period 110-115,000 years ago, (2) population divergence following the colonization of the deglaciated areas ~10,000 years ago, (3) human population expansion, which led to the settlement in Iceland ~1100 years ago, and (4) human persecution and exposure to toxic pollutants during the last two centuries.}, }
@article {pmid36679063, year = {2023}, author = {Conte, C and Apostolaki, ET and Vizzini, S and Migliore, L}, title = {A Tight Interaction between the Native Seagrass Cymodocea nodosa and the Exotic Halophila stipulacea in the Aegean Sea Highlights Seagrass Holobiont Variations.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36679063}, issn = {2223-7747}, abstract = {Seagrasses harbour bacterial communities with which they constitute a functional unit called holobiont that responds as a whole to environmental changes. Epiphytic bacterial communities rapidly respond to both biotic and abiotic factors, potentially contributing to the host fitness. The Lessepsian migrant Halophila stipulacea has a high phenotypical plasticity and harbours a highly diverse epiphytic bacterial community, which could support its invasiveness in the Mediterranean Sea. The current study aimed to evaluate the Halophila/Cymodocea competition in the Aegean Sea by analysing each of the two seagrasses in a meadow zone where these intermingled, as well as in their monospecific zones, at two depths. Differences in holobionts were evaluated using seagrass descriptors (morphometric, biochemical, elemental, and isotopic composition) to assess host changes, and 16S rRNA gene to identify bacterial community structure and composition. An Indicator Species Index was used to identify bacteria significantly associated with each host. In mixed meadows, native C. nodosa was shown to be affected by the presence of exotic H. stipulacea, in terms of both plant descriptors and bacterial communities, while H. stipulacea responded only to environmental factors rather than C. nodosa proximity. This study provided evidence of the competitive advantage of H. stipulacea on C. nodosa in the Aegean Sea and suggests the possible use of associated bacterial communities as an ecological seagrass descriptor.}, }
@article {pmid36675911, year = {2023}, author = {Mathew, SA and Helander, M and Saikkonen, K and Vankova, R and Dobrev, PI and Dirihan, S and Fuchs, B}, title = {Epichloë Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, pmid = {36675911}, issn = {2309-608X}, support = {311077//Academy of Finland/ ; 326226//Academy of Finland/ ; 324523//Academy of Finland/ ; }, abstract = {Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloë uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloë-symbiotic (E+) and Epichloë-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloë symbiosis, while the fungal community was different in the leaves of Epichloë-symbiotic and Epichloë-free plants in both cultivars. At the same time, Epichloë symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloë-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloë symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloë endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloë endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.}, }
@article {pmid36662226, year = {2023}, author = {Deutsch, JM and Green, MO and Akavaram, P and Davis, AC and Diskalkar, SS and Du Plessis, IA and Fallon, HA and Grason, EM and Kauf, EG and Kim, ZM and Miller, JR and Neal, AL and Riera, T and Stroeva, SE and Tran, J and Tran, V and Coronado, AV and Coronado, VV and Wall, BT and Yang, CM and Mohanty, I and Abrahamse, NH and Freeman, CJ and Easson, CG and Fiore, CL and Onstine, AE and Djeddar, N and Biliya, S and Bryksin, AV and Garg, N and Agarwal, V}, title = {Limited Metabolomic Overlap between Commensal Bacteria and Marine Sponge Holobionts Revealed by Large Scale Culturing and Mass Spectrometry-Based Metabolomics: An Undergraduate Laboratory Pedagogical Effort at Georgia Tech.}, journal = {Marine drugs}, volume = {21}, number = {1}, pages = {}, pmid = {36662226}, issn = {1660-3397}, mesh = {Animals ; Humans ; Phylogeny ; Georgia ; *Porifera/microbiology ; Bacteria ; Metabolomics ; Students ; *Biological Products/chemistry ; }, abstract = {Sponges are the richest source of bioactive organic small molecules, referred to as natural products, in the marine environment. It is well established that laboratory culturing-resistant symbiotic bacteria residing within the eukaryotic sponge host matrix often synthesize the natural products that are detected in the sponge tissue extracts. However, the contributions of the culturing-amenable commensal bacteria that are also associated with the sponge host to the overall metabolome of the sponge holobiont are not well defined. In this study, we cultured a large library of bacteria from three marine sponges commonly found in the Florida Keys. Metabolomes of isolated bacterial strains and that of the sponge holobiont were compared using mass spectrometry to reveal minimal metabolomic overlap between commensal bacteria and the sponge hosts. We also find that the phylogenetic overlap between cultured commensal bacteria and that of the sponge microbiome is minimal. Despite these observations, the commensal bacteria were found to be a rich resource for novel natural product discovery. Mass spectrometry-based metabolomics provided structural insights into these cryptic natural products. Pedagogic innovation in the form of laboratory curricula development is described which provided undergraduate students with hands-on instruction in microbiology and natural product discovery using metabolomic data mining strategies.}, }
@article {pmid36653630, year = {2023}, author = {Mayfield, AB}, title = {Multi-macromolecular Extraction from Endosymbiotic Anthozoans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2625}, number = {}, pages = {17-56}, pmid = {36653630}, issn = {1940-6029}, mesh = {Animals ; Ecosystem ; *Anthozoa ; *Sea Anemones ; *Dinoflagellida/physiology ; Symbiosis ; }, abstract = {Obligately symbiotic associations between reef-building corals (anthozoan cnidarians) and photosynthetically active dinoflagellates of the family Symbiodiniaceae comprise the functional basis of all coral reef ecosystems. Given the existential threats of global climate change toward these thermo-sensitive entities, there is an urgent need to better understand the physiological implications of changes in the abiotic milieu of scleractinian corals and their mutualistic algal endosymbionts. Although initially slow to leverage the immense breakthroughs in molecular biotechnology that have benefited humankind, coral biologists are making up for lost time in exploiting an array of ever-advancing molecular tools for answering key questions pertaining to the survival of corals in an ever-changing world. In order to comprehensively characterize the multi-omic landscape of the coral holobiont-the cnidarian host, its intracellular dinoflagellates, and a plethora of other microbial constituents-I introduce a series of protocols herein that yield large quantities of high-quality RNA, DNA, protein, lipids, and polar metabolites from a diverse array of reef corals and endosymbiotic sea anemones. Although numerous published articles in the invertebrate zoology field feature protocols that lead to sufficiently high yield of intact host coral macromolecules, through using the approach outlined herein one may simultaneously acquire a rich, multi-compartmental biochemical pool that truly reflects the complex and dynamic nature of these animal-plant chimeras.}, }
@article {pmid36651852, year = {2023}, author = {Takagi, T and Aoyama, K and Motone, K and Aburaya, S and Yamashiro, H and Miura, N and Inoue, K}, title = {Mutualistic Interactions between Dinoflagellates and Pigmented Bacteria Mitigate Environmental Stress.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0246422}, pmid = {36651852}, issn = {2165-0497}, mesh = {Animals ; *Dinoflagellida/genetics ; RNA, Ribosomal, 16S/genetics ; Coral Reefs ; *Anthozoa/genetics/microbiology ; Bacteria ; Symbiosis ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Scleractinian corals form symbiotic relationships with a variety of microorganisms, including endosymbiotic dinoflagellates of the family Symbiodiniaceae, and with bacteria, which are collectively termed coral holobionts. Interactions between hosts and their symbionts are critical to the physiological status of corals. Coral-microorganism interactions have been studied extensively, but dinoflagellate-bacterial interactions remain largely unexplored. Here, we developed a microbiome manipulation method employing KAS-antibiotic treatment (kanamycin, ampicillin, and streptomycin) to favor pigmented bacteria residing on cultured Cladocopium and Durusdinium, major endosymbionts of corals, and isolated several carotenoid-producing bacteria from cell surfaces of the microalgae. Following KAS-antibiotic treatment of Cladocopium sp. strain NIES-4077, pigmented bacteria increased 8-fold based on colony-forming assays from the parental strain, and 100% of bacterial sequences retrieved through 16S rRNA amplicon sequencing were affiliated with the genus Maribacter. Microbiome manipulation enabled host microalgae to maintain higher maximum quantum yield of photosystem II (variable fluorescence divided by maximum fluorescence [Fv/Fm]) under light-stress conditions, compared to the parental strain. Furthermore, by combining culture-dependent and -independent techniques, we demonstrated that species of the family Symbiodiniaceae and pigmented bacteria form strong interactions. Dinoflagellates protected bacteria from antibiotics, while pigmented bacteria protected microalgal cells from light stress via carotenoid production. Here, we describe for the first time a symbiotic relationship in which dinoflagellates and bacteria mutually reduce environmental stress. Investigations of microalgal-bacterial interactions further document bacterial contributions to coral holobionts and may facilitate development of novel techniques for microbiome-mediated coral reef conservation. IMPORTANCE Coral reefs cover less than 0.1% of the ocean floor, but about 25% of all marine species depend on coral reefs at some point in their life cycles. However, rising ocean temperatures associated with global climate change are a serious threat to coral reefs, causing dysfunction of the photosynthetic apparatus of endosymbiotic microalgae of corals, and overproducing reactive oxygen species harmful to corals. We manipulated the microbiome using an antibiotic treatment to favor pigmented bacteria, enabling their symbiotic microalgal partners to maintain higher photosynthetic function under insolation stress. Furthermore, we investigated mechanisms underlying microalgal-bacterial interactions, describing for the first time a symbiotic relationship in which the two symbionts mutually reduce environmental stress. Our findings extend current insights about microalgal-bacterial interactions, enabling better understanding of bacterial contributions to coral holobionts under stressful conditions and offering hope of reducing the adverse impacts of global warming on coral reefs.}, }
@article {pmid36647171, year = {2023}, author = {Pirolo, M and Espinosa-Gongora, C and Alberdi, A and Eisenhofer, R and Soverini, M and Eriksen, E&#xd8; and Pedersen, KS and Guardabassi, L}, title = {Bacterial topography of the upper and lower respiratory tract in pigs.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {5}, pmid = {36647171}, issn = {2524-4671}, support = {ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; }, abstract = {BACKGROUND: Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing.<br><br>RESULTS: The bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT.<br><br>CONCLUSION: We provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.}, }
@article {pmid36637211, year = {2023}, author = {Feldner-Busztin, D and Firbas Nisantzis, P and Edmunds, SJ and Boza, G and Racimo, F and Gopalakrishnan, S and Limborg, MT and Lahti, L and de Polavieja, GG}, title = {Dealing with dimensionality: the application of machine learning to multi-omics data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36637211}, issn = {1367-4811}, support = {//European Union's Horizon 2020 research and innovation programme/ ; CEH-DNRF143//Danish National Research Foundation/ ; }, mesh = {Humans ; *Multiomics ; *Neoplasms/genetics ; Machine Learning ; Genome ; }, abstract = {MOTIVATION: Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.<br><br>RESULTS: Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.<br><br>All data and processing scripts are available at this GitLab repository: https://gitlab.com/polavieja_lab/ml_multi-omics_review/ or in Zenodo: https://doi.org/10.5281/zenodo.7361807.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid36629441, year = {2023}, author = {Šigutová, H and Šigut, M and Pyszko, P and Kostovčík, M and Kolařík, M and Drozd, P}, title = {Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0316022}, pmid = {36629441}, issn = {2165-0497}, mesh = {Animals ; *Mycobiome ; Larva ; Seasons ; Bacteria/genetics ; Diet ; }, abstract = {Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.}, }
@article {pmid36629118, year = {2023}, author = {Chou, PH and Hu, MY and Guh, YJ and Wu, GC and Yang, SH and Tandon, K and Shao, YT and Lin, LY and Chen, C and Tseng, KY and Wang, MC and Zhang, CM and Han, BC and Lin, CC and Tang, SL and Jeng, MS and Chang, CF and Tseng, YC}, title = {Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1990}, pages = {20221973}, pmid = {36629118}, issn = {1471-2954}, mesh = {Animals ; *Hydrothermal Vents ; Thiosulfates ; Sulfides/toxicity ; *Brachyura/physiology ; Bacteria ; }, abstract = {The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.}, }
@article {pmid36627918, year = {2023}, author = {Singh, T and Sakai, K and Ishida-Castañeda, J and Iguchi, A}, title = {Short-term improvement of heat tolerance in naturally growing Acropora corals in Okinawa.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14629}, pmid = {36627918}, issn = {2167-8359}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Thermotolerance ; Temperature ; Heat-Shock Response ; }, abstract = {Mass bleaching and subsequent mortality of reef corals by heat stress has increased globally since the late 20th century, due to global warming. Some experimental studies have reported that corals may increase heat tolerance for short periods, but only a few such studies have monitored naturally-growing colonies. Therefore, we monitored the survival, growth, and bleaching status of Acropora corals in fixed plots by distinguishing individual colonies on a heat-sensitive reef flat in Okinawa, Japan. The level of heat stress, assessed by the modified version of degree heating week duration in July and August, when the seawater temperature was the highest, was minimally but significantly higher in 2017 than in 2016; however, the same colonies exhibited less bleaching and mortality in 2017 than in 2016. Another study conducted at the same site showed that the dominant unicellular endosymbiotic algal species did not change before and after the 2016 bleaching, indicating that shifting and switching of the Symbiodiniaceae community did not contribute to improved heat tolerance. Colonies that suffered from partial mortality in 2016 were completely bleached at higher rates in 2017 than those without partial mortality in 2016. The present results suggest that either genetic or epigenetic changes in coral hosts and/or algal symbionts, or the shifting or switching of microbes other than endosymbionts, may have improved coral holobiont heat tolerance.}, }
@article {pmid36621484, year = {2023}, author = {Jiang, M and Li, S and Li, H and Jian, S and Liu, F and Li, X}, title = {Reprogramming of microbial community in barley root endosphere and rhizosphere soil by polystyrene plastics with different particle sizes.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161420}, doi = {10.1016/j.scitotenv.2023.161420}, pmid = {36621484}, issn = {1879-1026}, mesh = {Soil/chemistry ; Plastics ; Polystyrenes ; Microplastics ; *Hordeum ; Rhizosphere ; Particle Size ; *Microbiota ; Bacteria ; Plants ; Fungi ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Polystyrene plastics is an emerging pollutant affecting plant performance and soil functioning. However, little information is available on the effects of microplastics and nanoplastics on plant root endophytic and rhizospheric soil microbial communities. Here, barley plants were grown in microplastics/nanoplastics -treated soil and the diversity, composition and function of bacteria and fungi in the root and rhizosphere soil were examined. At the seedling stage, greater changes of root endophytes were found compared with rhizosphere microorganisms under the plastic treatments. Nanoplastics decreased the richness and diversity of the fungal community, while microplastics increased the diversity of the root endophytic bacterial community. The network of the bacterial community under nanoplastics showed higher vulnerability while lower complexity than that under the control. However, the bacterial community under microplastics had a relatively higher resistance than the control. For the rhizosphere microbial community, no significant effect of plastics was found on the α-diversity index at the seedling stage. In addition, the nanoplastics resulted in higher sensitivity in the relative abundance and function of rhizosphere soil microbes than root endophytic microbes at the mature stage. Treatments of polystyrene plastics with different particle sizes reprogramed the rhizosphere and root endophytic microbial communities. Different effects of microplastics and nanoplastics were found on the diversity, composition, network structure and function of bacteria and fungi, which might be due to the variation in particle sizes. These results lay a foundation for learning the effects of polystyrene plastics with different particle sizes on the microorganisms in rhizosphere soil and plant roots, which may have important implications for the adaptation of plant-microbial holobiont in polystyrene plastics-polluted soils.}, }
@article {pmid36620745, year = {2023}, author = {Baldo, L and Tavecchia, G and Rotger, A and Igual, JM and Riera, JL}, title = {Insular holobionts: persistence and seasonal plasticity of the Balearic wall lizard (Podarcis lilfordi) gut microbiota.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14511}, pmid = {36620745}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Seasons ; *Microbiota ; Feces ; *Lizards/microbiology ; }, abstract = {BACKGROUND: Integrative studies of animals and associated microbial assemblages (i.e., the holobiont) are rapidly changing our perspectives on organismal ecology and evolution. Insular vertebrates provide ideal natural systems to understand patterns of host-gut microbiota coevolution, the resilience and plasticity these microbial communities over temporal and spatial scales, and ultimately their role in the host ecological adaptation.<br><br>METHODS: Here we used the endemic Balearic wall lizard Podarcis lilfordi to dissect the drivers of the microbial diversity within and across host allopatric populations/islets. By focusing on three extensively studied populations/islets of Mallorca (Spain) and fecal sampling from individually identified lizards along two years (both in spring and autumn), we sorted out the effect of islet, sex, life stage, year and season on the microbiota composition. We further related microbiota diversity to host genetics, trophic ecology and expected annual metabolic changes.<br><br>RESULTS: All the three populations showed a remarkable conservation of the major microbial taxonomic profile, while carrying their unique microbial signature at finer level of taxonomic resolution (Amplicon Sequence Variants (ASVs)). Microbiota distances across populations were compatible with both host genetics (based on microsatellites) and trophic niche distances (based on stable isotopes and fecal content). Within populations, a large proportion of ASVs (30-50%) were recurrently found along the four sampling dates. The microbial diversity was strongly marked by seasonality, with no sex effect and a marginal life stage and annual effect. The microbiota showed seasonal fluctuations along the two sampled years, primarily due to changes in the relative abundances of fermentative bacteria (mostly families Lachnospiraceae and Ruminococcaceae), without any major compositional turnover.<br><br>CONCLUSIONS: These results support a large resilience of the major compositional aspects of the P. lilfordi gut microbiota over the short-term evolutionary divergence of their host allopatric populations (<10,000 years), but also indicate an undergoing process of parallel diversification of the both host and associated gut microbes. Predictable seasonal dynamics in microbiota diversity suggests a role of microbiota plasticity in the lizards' metabolic adaptation to their resource-constrained insular environments. Overall, our study supports the need for longitudinal and integrative studies of host and associated microbes in natural systems.}, }
@article {pmid36620197, year = {2022}, author = {Marcos, S and Parejo, M and Estonba, A and Alberdi, A}, title = {Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {3}, number = {3}, pages = {2100065}, pmid = {36620197}, issn = {2641-6573}, abstract = {Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.}, }
@article {pmid36618624, year = {2022}, author = {Lyu, D and Smith, DL}, title = {The root signals in rhizospheric inter-organismal communications.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1064058}, pmid = {36618624}, issn = {1664-462X}, abstract = {Root exudates play a key role in mediating plant-plant and plant-rhizomicrobiome interactions, including regulating biochemical/physiological aspects of plant-associated microorganisms, to enhance host plant growth and resilience. Root exudates can act as signals to reduce the competition from neighboring plants and recruiting/choreographing a wide range of diverse rhizomicrobiome members to make the host plant a good fit with its immediate environment. Root exudate production is a dynamic and key process, but there is a limited understanding of the metabolites or metabolic pathways involved in the inter-organismal communications facilitated by them. Given the well-known symbiotic relationships between plants and associated rhizomicrobiome members, adding root exudates to microbial isolation media may allow some of the large segments of rhizomicrobiome members that are not currently culturable to be grown in vitro. This will provide new insights into how root signals orchestrate associated microbes, will benefit agricultural production in the face of challenges posed by climate change, and will help to sustainably provide food for a growing global human population.}, }
@article {pmid36608656, year = {2023}, author = {Rodríguez-Varela, R and Moore, KHS and Ebenesersdóttir, SS and Kilinc, GM and Kjellström, A and Papmehl-Dufay, L and Alfsdotter, C and Berglund, B and Alrawi, L and Kashuba, N and Sobrado, V and Lagerholm, VK and Gilbert, E and Cavalleri, GL and Hovig, E and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Munters, AR and Bernhardsson, C and Skar, B and Christophersen, A and Turner-Walker, G and Gopalakrishnan, S and Daskalaki, E and Omrak, A and Pérez-Ramallo, P and Skoglund, P and Girdland-Flink, L and Gunnarsson, F and Hedenstierna-Jonson, C and Gilbert, MTP and Lidén, K and Jakobsson, M and Einarsson, L and Victor, H and Krzewińska, M and Zachrisson, T and Storå, J and Stefánsson, K and Helgason, A and Götherström, A}, title = {The genetic history of Scandinavia from the Roman Iron Age to the present.}, journal = {Cell}, volume = {186}, number = {1}, pages = {32-46.e19}, doi = {10.1016/j.cell.2022.11.024}, pmid = {36608656}, issn = {1097-4172}, mesh = {Humans ; Europe ; Genetic Variation ; Scandinavian and Nordic Countries ; United Kingdom ; White People/genetics/history ; *Genome, Human ; Human Migration ; }, abstract = {We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.}, }
@article {pmid36596505, year = {2023}, author = {Wakimoto, T}, title = {Biosynthesis of Bioactive Natural Products Derived from Theonellidae Family Marine Sponges.}, journal = {Chemical &amp; pharmaceutical bulletin}, volume = {71}, number = {1}, pages = {1-8}, doi = {10.1248/cpb.c22-00715}, pmid = {36596505}, issn = {1347-5223}, mesh = {Animals ; *Biological Products/chemistry ; *Porifera/chemistry ; Bacteria/metabolism ; Peptides/metabolism ; *Polyketides/pharmacology ; *Antineoplastic Agents/pharmacology/metabolism ; }, abstract = {Marine sponges are among the most primitive animals and often contain unique, biologically active compounds. Several of these compounds have played an important roles as pharmaceutical leads for anti-cancer drugs, such as halichondrin B, which led to the development of an anti-breast cancer drug. Some compounds with remarkable biological activities are accumulated in significantly high concentrations in the sponge. How and why the marine sponges produce and accumulate bioactive natural products are long-standing questions with both biochemical and ecological implications, since in sponges, the animal-microbe symbioses are presumed to be responsible for the biosynthetic machinery, consisting of efficient enzymes and regulatory systems for the specific biological activities of medicinally relevant natural products. In this review, I focus on the chemically rich Theonellidae family sponges and discuss the biosynthesis of bioactive peptides and polyketides. In particular, the biosynthetic pathway of calyculin A suggests that crosstalk between the sponge host and bacterial symbiont confers a chemical defense system on the immobile animal-microbe holobiont.}, }
@article {pmid36581277, year = {2023}, author = {Cheng, K and Tong, M and Cai, Z and Jong, MC and Zhou, J and Xiao, B}, title = {Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea.}, journal = {The Science of the total environment}, volume = {867}, number = {}, pages = {161185}, doi = {10.1016/j.scitotenv.2022.161185}, pmid = {36581277}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Host Specificity ; Bacteria ; *Microbiota ; Symbiosis ; Coral Reefs ; }, abstract = {Reef-building corals are well known for their obligate association with Symbiodiniaceae, and an array of other microbes, including bacteria, fungi, and symbiotic algae (i.e., total microbiome), which together form the coral holobiont. The total microbiome plays an intricate part in maintaining the homeostasis of the coral holobiont and is closely associated with host health. However, the composition of the coral associated microbiome and interaction between its different members remains elusive because few analyses have bridged taxonomically disparate groups. This research gaps have prevented a holistic understanding of the total microbiome. Thus, to simultaneously characterize the bacterial, fungal and symbiotic algal communities associated with different coral species, and explore the relationship between these symbionts and coral health, healthy and bleached tissues from four coral species, Acropora muricata, Galaxea fascicularis, Platygyra daedalea, and Pavona explanulata, were collected from the Xisha Islands of the South China Sea. Using high throughput sequencing, a high degree of host-specificity was observed among bacterial, fungal, and algal groups across coral species. There were no obvious changes in the microbial community structure of apparently healthy and bleached corals, but host bleaching allowed colonization of the holobionts by diverse opportunistic microbes, resulting in a significant elevation in the α-diversity of microbial communities. In addition, co-occurrence analysis of the coral microbiota also identified more complex microbial interactions in bleached corals than in healthy ones. In summary, this study characterized the structure of coral-associated microbiomes across four coral species, and systematically studied microbiome differences between healthy and bleached corals. The findings improve our understanding of the heterogeneity of symbiotic microorganisms and the impact of coral's physiological status on its associated microbial communities composition.}, }
@article {pmid36561457, year = {2022}, author = {Liu, Y and Morelli, M and Koskimäki, JJ and Qin, S and Zhu, YH and Zhang, XX}, title = {Editorial: Role of endophytic bacteria in improving plant stress resistance.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1106701}, pmid = {36561457}, issn = {1664-462X}, }
@article {pmid36560776, year = {2022}, author = {Nale, JY and Thanki, AM and Rashid, SJ and Shan, J and Vinner, GK and Dowah, ASA and Cheng, JKJ and Sicheritz-Pontén, T and Clokie, MRJ}, title = {Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560776}, issn = {1999-4915}, support = {RM38G0140/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; *Clostridioides difficile ; Clostridioides ; Prophages/genetics ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.}, }
@article {pmid36558520, year = {2022}, author = {Ramos Meyers, G and Samouda, H and Bohn, T}, title = {Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, pmid = {36558520}, issn = {2072-6643}, support = {PRIDE-2019 / 20200838//Fonds National de la Recherche/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Tissue Distribution ; *Microbiota ; Intestinal Mucosa/metabolism ; Dietary Fiber/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.}, }
@article {pmid36557214, year = {2022}, author = {Rhimi, S and Kriaa, A and Mariaule, V and Saidi, A and Drut, A and Jablaoui, A and Akermi, N and Maguin, E and Hernandez, J and Rhimi, M}, title = {The Nexus of Diet, Gut Microbiota and Inflammatory Bowel Diseases in Dogs.}, journal = {Metabolites}, volume = {12}, number = {12}, pages = {}, pmid = {36557214}, issn = {2218-1989}, support = {41786NC//Campus France/ ; MICAfrica 952583//European Commission/ ; No. 19G0819//PS-Com-Pro Project, CMCU-PHC Utique/ ; }, abstract = {Canine inflammatory bowel diseases (IBD) are of increasing interest in veterinary medicine. They refer to complex and debilitating conditions of dogs' gastrointestinal tract. Although little evidence for causal inferences is currently available, it is believed that IBD pathophysiology entails intricate interactions between environmental factors, the intestinal immune system, and the microbial communities that colonize the gut. To better understand the mechanisms underlying these disorders, leveraging factors associated with the development of these diseases is imperative. Of these factors, emerging evidence supports the role of dietary patterns as key players influencing the composition and function of gut microbes, with subsequent effects on health and disease. In this review, we particularly focus on addressing IBD in dogs and discuss how specific nutrients may elicit or relieve gut inflammation. Gaining mechanistic insights into such interplay and the underpinning mechanisms is key to inferring dietary recommendations, and setting up new and promising therapeutics.}, }
@article {pmid36547600, year = {2022}, author = {Schulz, M and Schmitt, I and Weber, D and Dal Grande, F}, title = {Fungal Host Affects Photosynthesis in a Lichen Holobiont.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, pmid = {36547600}, issn = {2309-608X}, abstract = {Corals and lichens are iconic examples of photosynthetic holobionts, i.e., ecological and evolutionary units resulting from the tightly integrated association of algae and prokaryotic microbiota with animal or fungal hosts, respectively. While the role of the coral host in modulating photosynthesis has been clarified to a large extent in coral holobionts, the role of the fungal host in this regard is far less understood. Here, we address this question by taking advantage of the recent discovery of highly specific fungal-algal pairings corresponding to climatically adapted ecotypes of the lichen-forming genus Umbilicaria. Specifically, we compared chlorophyll a fluorescence kinetics among lichen thalli consisting of different fungal-algal combinations. We show that photosynthetic performance in these lichens is not only driven by algal genotype, but also by fungal host species identity and intra-host genotype. These findings shed new light on the closely intertwined physiological processes of fungal and algal partners in the lichen symbiosis. Indeed, the specific combinations of fungal and algal genotypes within a lichen individual-and the resulting combined functional phenotype-can be regarded as a response to the environment. Our findings suggest that characterizing the genetic composition of both eukaryotic partners is an important complimentary step to understand and predict the lichen holobiont's responses to environmental change.}, }
@article {pmid36546449, year = {2023}, author = {Fontaine, SS and Kohl, KD}, title = {The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming.}, journal = {The Journal of experimental biology}, volume = {226}, number = {1}, pages = {}, pmid = {36546449}, issn = {1477-9145}, mesh = {Animals ; Larva ; Host Microbial Interactions ; *Microbiota ; *Thermotolerance ; }, abstract = {Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that 'depleted' tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than 'colonized' tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compared gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.}, }
@article {pmid36539412, year = {2022}, author = {Chen, L and Li, Z and Wu, B and Zhou, B and Heller, R and Zhou, J and Wang, K and Lin, Z and Wu, D and Qiu, Q}, title = {Progressive evolution of secondary aquatic adaptation in hippos and cetaceans.}, journal = {Cell discovery}, volume = {8}, number = {1}, pages = {134}, pmid = {36539412}, issn = {2056-5968}, support = {32000294//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31970392//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020JQ-149//Natural Science Foundation of Shaanxi Province (Shaanxi Province Natural Science Foundation)/ ; }, }
@article {pmid36534288, year = {2023}, author = {Espino-Vázquez, AN and Córdova-López, G and Cabrera-Rangel, JF and Mendoza-Servín, JV and Partida-Martínez, LP}, title = {The Rhizopus Holobiont: A Model to Decipher Fungal-Bacterial-Viral Symbioses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2610}, number = {}, pages = {137-147}, pmid = {36534288}, issn = {1940-6029}, mesh = {Humans ; Symbiosis/genetics ; *Burkholderia/genetics/metabolism ; Reproduction ; Reproduction, Asexual ; Rhizopus/genetics ; *Bacteriophages ; }, abstract = {Rhizopus microsporus is an early-diverging fungal species that inhabits the soil, is used for the fermentation of diverse Asian and African foods, and can be a pathogen of plants, animals, and humans.Toxin-producing strains of R. microsporus live in symbiosis with Gram-negative betaproteobacteria from the genus Mycetohabitans (Burkholderia sensu lato). These bacterial endosymbionts increase the metabolic plasticity of the fungal holobiont by producing the "mycotoxins," control their asexual reproduction, and influence their sexual success. Recently, we identified two viruses of the genus Narnavirus in some R. microsporus strains that harbor Mycetohabitans. By eliminating bacteria and/or viruses from host R. microsporus strains, we have been able to study the role of these symbionts in fungal biology. Remarkably, the absence of these bacterial and viral symbionts decreases sexual reproduction. In this chapter, the method developed to eliminate and genotype the Narnavirus RmNV-20S and RmNV-23S in R. microsporus is described in detail.}, }
@article {pmid36513413, year = {2022}, author = {Sangiorgio, D and Cellini, A and Donati, I and Ferrari, E and Tanunchai, B and Fareed Mohamed Wahdan, S and Sadubsarn, D and Farneti, B and Checcucci, A and Buscot, F and Spinelli, F and Purahong, W}, title = {Taxonomical and functional composition of strawberry microbiome is genotype-dependent.}, journal = {Journal of advanced research}, volume = {42}, number = {}, pages = {189-204}, pmid = {36513413}, issn = {2090-1224}, mesh = {*Fragaria/microbiology ; *Microbiota ; Bacteria/genetics ; Genotype ; Symbiosis ; }, abstract = {INTRODUCTION: Specific microbial communities are associated to host plants, influencing their phenotype and fitness.Despite the rising interest in plant microbiome, the role of microbial communities associated with perennial fruit plants remains overlooked.<br><br>OBJECTIVES: This work provides the first comprehensive descriptionof the taxonomical and functional bacterial and fungal microbiota of below- and above-ground organsof three commercially important strawberry genotypes under cultural conditions.<br><br>METHODS: Strawberry-associatedfungal and bacterial microbiomes were characterised by Next-Generation Sequencing and the potential functions expressed by the bacterial microbiome were analysed by both in silico and in vitro characterisation of plant growth-promoting abilities of native bacteria. Additionally, the association between the strawberry microbiome, plant disease tolerance, plant mineral nutrient content, and fruit quality was investigated.<br><br>RESULTS: Results showed that thestrawberry core microbiome included 24 bacteria and 15 fungal operational taxonomicunits (OTUs).However, plant organ and genotype had a significant role in determining the taxonomical and functional composition of microbial communities. Interestingly, the cultivar with the highesttolerance against powdery mildew and leaf spot and the highest fruit productivity was the only one able to ubiquitously recruit the beneficial bacterium, Pseudomonasfluorescens, and to establish a mutualistic symbiosis with the arbuscular mycorrhizaRhizophagus irregularis.<br><br>CONCLUSION: This work sheds light on the interaction of cultivated strawberry genotypes with a variety of microbes and highlights the importance of their applications to increase the sustainability of fruit crop production.}, }
@article {pmid36510852, year = {2023}, author = {Biggs, E and Taylor, MW and Middleton, DMRL}, title = {Beyond the theory: From holobiont concept to microbiome engineering.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {832-835}, doi = {10.1111/1462-2920.16308}, pmid = {36510852}, issn = {1462-2920}, mesh = {*Microbiota/genetics ; Biological Evolution ; Symbiosis ; Biotechnology ; }, abstract = {Holobiont research has increasingly moved from descriptive studies to sophisticated field- and laboratory-based manipulations; however, the extent to which changes in the holobiont persist remains largely unknown. In this Burning Question, we ask whether the underlying principles of the holobiont concept, whereby an externally applied evolutionary pressure can lead to a beneficial change in host-associated microbial community composition, could be used to facilitate microbiome engineering and thereby addition of a new ecosystem service that persists across generations. The answer to this question has potential implications for diverse fields including symbiosis, conservation and biotechnology.}, }
@article {pmid36504779, year = {2022}, author = {Liberman, R and Benayahu, Y and Huchon, D}, title = {Octocorals in the Gulf of Aqaba exhibit high photosymbiont fidelity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1005471}, pmid = {36504779}, issn = {1664-302X}, abstract = {Symbiotic associations, widespread in terrestrial and marine ecosystems, are of considerable ecological importance. Many tropical coral species are holobionts, formed by the obligate association between a cnidarian host and endosymbiotic dinoflagellates of the family Symbiodiniaceae. The latter are abundant on coral reefs from very shallow water down to the upper mesophotic zone (30-70 m). The research on scleractinians has revealed that the photosymbiont lineages present in the cnidarian host play an important role in the coral's ability to thrive under different environmental conditions, such as light regime and temperature. However, little is known regarding octocoral photosymbionts, and in particular regarding those found deeper than 30 m. Here, we used ribosomal (ITS2) and chloroplast (23S) markers to uncover, for the first time, the dominant Symbiodiniaceae taxa present in 19 mesophotic octocoral species (30-70 m depth) from the Gulf of Aqaba/Eilat (northern Red Sea). In addition, using high-throughput sequencing of the ITS2 region we characterized both the dominant and the rare Symbiodiniaceae lineages found in several species across depth. The phylogenetic analyses of both markers were in agreement and revealed that most of the studied mesophotic octocorals host the genus Cladocopium. Litophyton spp. and Klyxum utinomii were exceptions, as they harbored Symbiodinium and Durusdinium photosymbionts, respectively. While the dominant algal lineage of each coral species did not vary across depth, the endosymbiont community structure significantly differed between host species, as well as between different depths for some host species. The findings from this study contribute to the growing global-catalogue of Cnidaria-Symbiodiniaceae associations. Unravelling the Symbiodiniaceae composition in octocoral holobionts across environmental gradients, depth in particular, may enable a better understanding of how specialized those associations are, and to what extent coral holobionts are able to modify their photosymbionts.}, }
@article {pmid36503639, year = {2023}, author = {Hodžić, A and Dheilly, NM and Cabezas-Cruz, A and Berry, D}, title = {The helminth holobiont: a multidimensional host-parasite-microbiota interaction.}, journal = {Trends in parasitology}, volume = {39}, number = {2}, pages = {91-100}, doi = {10.1016/j.pt.2022.11.012}, pmid = {36503639}, issn = {1471-5007}, mesh = {Animals ; Humans ; *Parasites ; *Helminths/genetics ; *Microbiota ; *Helminthiasis/parasitology ; *Gastrointestinal Microbiome ; }, abstract = {Gastrointestinal helminths have developed multiple mechanisms by which they manipulate the host microbiome to make a favorable environment for their long-term survival. While the impact of helminth infections on vertebrate host immunity and its gut microbiota is relatively well studied, little is known about the structure and functioning of microbial populations supported by metazoan parasites. Here we argue that an integrated understanding of the helminth-associated microbiome and its role in the host disease pathogenesis may facilitate the discovery of specific microbial and/or genetic patterns critical for parasite biology and subsequently pave the way for the development of alternative control strategies against parasites and parasitic disease.}, }
@article {pmid36496327, year = {2023}, author = {Zhu, Z and Liu, Y and Hu, H and Wang, GH}, title = {Nasonia-microbiome associations: a model for evolutionary hologenomics research.}, journal = {Trends in parasitology}, volume = {39}, number = {2}, pages = {101-112}, doi = {10.1016/j.pt.2022.11.005}, pmid = {36496327}, issn = {1471-5007}, mesh = {Animals ; Biological Evolution ; *Wasps/genetics ; Insecta/genetics ; *Microbiota/genetics ; Symbiosis ; }, abstract = {In recent years, with the development of microbial research technologies, microbiota research has received widespread attention. The parasitoid wasp genus Nasonia is a good model organism for studying insect behavior, development, evolutionary genetics, speciation, and symbiosis. This review describes key advances and progress in the field of the Nasonia-microbiome interactions. We provide an overview of the advantages of Nasonia as a model organism for microbiome studies, list research methods to study the Nasonia microbiome, and discuss recent discoveries in Nasonia microbiome research. This summary of the complexities of Nasonia-microbiome relationships will help to contribute to a better understanding of the interactions between animals and their microbiomes and establish a clear research direction for Nasonia-microbiome interactions in the future.}, }
@article {pmid36494920, year = {2023}, author = {Gruet, C and Abrouk, D and Börner, A and Muller, D and Moënne-Loccoz, Y}, title = {Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere.}, journal = {Plant, cell &amp; environment}, volume = {46}, number = {3}, pages = {1018-1032}, doi = {10.1111/pce.14508}, pmid = {36494920}, issn = {1365-3040}, mesh = {*Triticum/genetics ; Rhizosphere ; Polyploidy ; Genome, Plant/genetics ; Biological Evolution ; *Aegilops/genetics ; }, abstract = {Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB {SS} (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.}, }
@article {pmid36482381, year = {2022}, author = {Zhang, X and Ma, YN and Wang, X and Liao, K and He, S and Zhao, X and Guo, H and Zhao, D and Wei, HL}, title = {Dynamics of rice microbiomes reveal core vertically transmitted seed endophytes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {216}, pmid = {36482381}, issn = {2049-2618}, mesh = {*Oryza ; Endophytes/genetics ; Seeds ; }, abstract = {BACKGROUND: Plants and their associated microbiota constitute an assemblage of species known as holobionts. The plant seed microbiome plays an important role in nutrient uptake and stress attenuation. However, the core vertically transmitted endophytes remain largely unexplored.<br><br>RESULTS: To gain valuable insights into the vertical transmission of rice seed core endophytes, we conducted a large-scale analysis of the microbiomes of two generations of six different rice varieties from five microhabitats (bulk soil, rhizosphere, root, stem, and seed) from four geographic locations. We showed that the microhabitat rather than the geographic location and rice variety was the primary driver of the rice microbiome assemblage. The diversity and network complexity of the rice-associated microbiome decreased steadily from far to near the roots, rice exterior to interior, and from belowground to aboveground niches. Remarkably, the microbiomes of the roots, stems, and seeds of the rice interior compartments were not greatly influenced by the external environment. The core bacterial endophytes of rice were primarily comprised of 14 amplicon sequence variants (ASVs), 10 of which, especially ASV_2 (Pantoea) and ASV_48 (Xanthomonas), were identified as potentially vertically transmitted taxa because they existed across generations, were rarely present in exterior rice microhabitats, and were frequently isolated from rice seeds. The genome sequences of Pantoea and Xanthomonas isolated from the parental and offspring seeds showed a high degree of average nucleotide and core protein identity, indicating vertical transmission of seed endophytes across generations. In silico prediction indicated that the seed endophytes Pantoea and Xanthomonas possessed streamlined genomes with short lengths, low-complexity metabolism, and various plant growth-promoting traits. We also found that all strains of Pantoea and Xanthomonas exhibited cellulase activity and produced indole-3-acetic acid. However, most strains exhibited insignificant antagonism to the major pathogens of rice, such as Magnaporthe oryzae and X. oryzae pv. oryzae.<br><br>CONCLUSION: Overall, our study revealed that microhabitats, rather than site-specific environmental factors or host varieties, shape the rice microbiome. We discovered the vertically transmitted profiles and keystone taxa of the rice microbiome, which led to the isolation of culturable seed endophytes and investigation of their potential roles in plant-microbiome interactions. Our results provide insights on vertically transmitted microbiota and suggest new avenues for improving plant fitness via the manipulation of seed-associated microbiomes.&#xa0; Video Abstract.}, }
@article {pmid36476670, year = {2022}, author = {Jochum, M and Lee, MD and Curry, K and Zaksas, V and Vitalis, E and Treangen, T and Aagaard, K and Ternus, KL}, title = {Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21125}, pmid = {36476670}, issn = {2045-2322}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; T32 HD098068/HD/NICHD NIH HHS/United States ; T32 HL098069/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *COVID-19 ; Gene Ontology ; }, abstract = {To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We then performed a stratified analysis based on mortality amongst the COVID-19 cohort with known outcomes of deceased (n = 10) versus survived (n = 15). Our overarching hypothesis was that there are detectable and functionally significant relationships between BALF microbial metatranscriptomes and the severity of COVID-19 disease onset and progression. We observed 34 functionally discriminant gene ontology (GO) terms in COVID-19 disease compared to the CAP and uninfected cohorts, and 21 GO terms functionally discriminant to COVID-19 mortality (q < 0.05). GO terms enriched in the COVID-19 disease cohort included hydrolase activity, and significant GO terms under the parental terms of biological regulation, viral process, and interspecies interaction between organisms. Notable GO terms associated with COVID-19 mortality included nucleobase-containing compound biosynthetic process, organonitrogen compound catabolic process, pyrimidine-containing compound biosynthetic process, and DNA recombination, RNA binding, magnesium and zinc ion binding, oxidoreductase activity, and endopeptidase activity. A Dirichlet multinomial mixtures clustering analysis resulted in a best model fit using three distinct clusters that were significantly associated with COVID-19 disease and mortality. We additionally observed discriminant taxonomic differences associated with COVID-19 disease and mortality in the genus Sphingomonas, belonging to the Sphingomonadacae family, Variovorax, belonging to the Comamonadaceae family, and in the class Bacteroidia, belonging to the order Bacteroidales. To our knowledge, this is the first study to evaluate significant differences in taxonomic and functional signatures between BALF metatranscriptomes from COVID-19, CAP, and uninfected cohorts, as well as associating these taxa and microbial gene functions with COVID-19 mortality. Collectively, while this data does not speak to causality nor directionality of the association, it does demonstrate a significant relationship between the human microbiome and COVID-19. The results from this study have rendered testable hypotheses that warrant further investigation to better understand the causality and directionality of host-microbiome-pathogen interactions.}, }
@article {pmid36471953, year = {2022}, author = {Wang, HY and Kang, CZ and Wang, YF and Wang, S and Wang, TL and Zhang, Y and Zhou, L and Liu, DH and Guo, LP}, title = {[Medicinal plant microbiome: advances and prospects].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {47}, number = {20}, pages = {5397-5405}, doi = {10.19540/j.cnki.cjcmm.20220615.102}, pmid = {36471953}, issn = {1001-5302}, mesh = {*Plants, Medicinal ; Plant Breeding ; Medicine, Chinese Traditional ; Agriculture ; *Microbiota ; }, abstract = {Medicinal plants are the main source of clinical medication in traditional Chinese medicine(TCM). China has achieved large-scale cultivation and production of medicinal plants. As an important resource for the sustainable development of agriculture in the future, microorganisms can also promote the green, ecological and high-quality development of Chinese medicine agriculture. However, research on the medicinal plant microbiome is still limited. Therefore, based on the development timeline of microbiome research, the present study reviewed the origin, technology, and hotspots of microbiome research and proposed some suggestions for future research according to the advances in medicinal plant microbiome.(1)Systematic investigation of medicinal plant microbiome on the species, genus, and family levels should be carried out on the medicinal plants of different chemotypes in order to reveal the coevolution of the microorganisms and their host plants.(2)Spatial and temporal research on medicinal plant microbiome should be performed to reveal the effects of microorganisms on the growth, development, and secondary metabolite accumulation of medicinal plants, as well as the underlying mechanisms.(3)Model medicinal plant species should be selected and microorganism-plant interaction research models should be established.(4)Core microbiome of medicinal plants should be explored for the future application of crucial microbes in the sustaina-ble agriculture of Chinese medicine.(5)Breeding of medicinal plant-associated microbes should be carried out to lay the foundation for novel medicinal plant breeding strategies.(6)High-throughput sequencing, traditional incubation, and isolation of microbes should be combined to study medicinal plant microbiome, thereby promoting the exploitation and application of uncultured microbial strains.(7)Platforms for the preservation of medicinal plant-associated microbe strains and data of their metabolites should be established and the exchange of information and cooperation between these platforms should be subsequently enhanced. With these suggestions, the efficient and rapid development of medicinal plant microbiome research is expected to be promoted.}, }
@article {pmid36464145, year = {2023}, author = {Kalra, R and Conlan, XA and Goel, M}, title = {Recent advances in research for potential utilization of unexplored lichen metabolites.}, journal = {Biotechnology advances}, volume = {62}, number = {}, pages = {108072}, doi = {10.1016/j.biotechadv.2022.108072}, pmid = {36464145}, issn = {1873-1899}, mesh = {*Lichens/genetics/metabolism/microbiology ; Ecosystem ; Phylogeny ; Symbiosis ; Biomass ; }, abstract = {Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.}, }
@article {pmid36445161, year = {2022}, author = {Sylvain, F&#xc9; and Leroux, N and Normandeau, &#xc9; and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0206422}, pmid = {36445161}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gills/chemistry/microbiology ; Fishes/genetics/microbiology ; *Microbiota/physiology ; Water ; Genomics ; Bacteria/genetics ; }, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, }
@article {pmid36435249, year = {2023}, author = {Travesso, M and Missionário, M and Cruz, S and Calado, R and Madeira, D}, title = {Combined effect of marine heatwaves and light intensity on the cellular stress response and photophysiology of the leather coral Sarcophyton cf. glaucum.}, journal = {The Science of the total environment}, volume = {861}, number = {}, pages = {160460}, doi = {10.1016/j.scitotenv.2022.160460}, pmid = {36435249}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll A ; Ecosystem ; Coral Reefs ; Light ; Symbiosis/physiology ; Antioxidants ; }, abstract = {Marine heatwaves (MHW) are threatening tropical coral reef ecosystems, leading to mass bleaching events worldwide. The combination of heat stress with high irradiance is known to shape the health and redox status of corals, but research is biased toward scleractinian corals, while much less is known on tropical symbiotic soft corals. Here, we evaluated the cellular stress response and the photophysiological performance of the soft coral Sarcophyton cf. glaucum, popularly termed as leather coral, under different global change scenarios. Corals were exposed to different light intensities (high light, low light, ∼662 and 253 μmol photons m[-2] s[-1]) for 30 days (time-point 1) and a subsequent MHW simulation was carried out for 10 days (control 26 vs 32 °C) (time-point 2). Subsequently, corals were returned to control temperature and allowed to recover for 30 days (time-point 3). Photophysiological performance (maximum quantum yield of photosystem II (Fv/Fm), a measure of photosynthetic activity; dark-level fluorescence (F0), as a proxy of chlorophyll a content (Chl a); and zooxanthellae density) and stress biomarkers (total protein, antioxidants, lipid peroxidation, ubiquitin, and heat shock protein 70) were assessed in corals at these three time-points. Corals were especially sensitive to the combination of heat and high light stress, experiencing a decrease in their photosynthetic efficiency under these conditions. Heat stress resulted in bleaching via zooxanthellae loss while high light stress led to pigment (Chl a) loss. This species' antioxidant defenses, and protein degradation were particularly enhanced under heat stress. A recovery was clear for molecular parameters after 30 days of recovery, whereby photophysiological performance required more time to return to basal levels. We conclude that soft corals distributed along intertidal areas, where the light intensity is high, could be especially vulnerable to marine heatwave events, highlighting the need to direct conservation efforts toward these organisms.}, }
@article {pmid36430266, year = {2022}, author = {Schaack, B and Hindré, T and Quansah, N and Hannani, D and Mercier, C and Laurin, D}, title = {Microbiota-Derived Extracellular Vesicles Detected in Human Blood from Healthy Donors.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430266}, issn = {1422-0067}, support = {ANR-15-IDEX-02//Agence Nationale de la Recherche/ ; 2020-2021//&#xc9;tablissement Fran&#xe7;ais du Sang/ ; TIMC Emergence program "LTEE-vesi"//Grenoble Alpes University/ ; }, mesh = {Humans ; *Extracellular Vesicles ; *Microbiota ; Health Status ; Erythrocytes ; Monocytes ; Escherichia coli ; }, abstract = {The microbiota constitutes an important part of the holobiont in which extracellular vesicles (EVs) are key players in health, especially regarding inter- and intra-kingdom communications. Analysis of EVs from the red blood cell concentrates of healthy donors revealed variable amounts of OmpA and LPS in 12 of the 14 analyzed samples, providing indirect experimental evidence of the presence of microbiota EVs in human circulating blood in the absence of barrier disruption. To investigate the role of these microbiota EVs, we tracked the fusion of fluorescent Escherichia coli EVs with blood mononuclear cells and showed that, in the circulating blood, these EVs interacted almost exclusively with monocytes. This study demonstrates that bacterial EVs constitute critical elements of the host-microbiota cellular communication. The analysis of bacterial EVs should thus be systematically included in any characterization of human EVs.}, }
@article {pmid36427961, year = {2022}, author = {Sampson, TR}, title = {Introduction: Unraveling the complex contributions of indigenous microbes to neurological health and disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {xi-xvi}, doi = {10.1016/S0074-7742(22)00138-6}, pmid = {36427961}, issn = {2162-5514}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Nervous System Diseases/drug therapy ; *Microbiota ; *Parkinson Disease ; *Alzheimer Disease ; }, abstract = {The complex interactions between the human body and its indigenous microbes have come into focus as key mediators of neurological health. With both established and emerging association studies, alterations to the gut microbiome are observed to co-occur with many neurological diseases. Whether these associations are due to microbiome-mediated contributions to human health or an effect of the neurological disease itself is largely unknown across conditions. Here, we have collected contributions from a broad group of experts that highlight gut microbiome impacts across numerous neurological conditions. Ranging from neurodevelopmental disorders, to Parkinson's disease, Alzheimer's disease, epilepsy, traumatic injury, and amyotrophic lateral sclerosis, among others, we hope to provide a clearer picture of how our indigenous microbes impact neurological health. The study of these indigenous microbes will continue to reveal critical mechanisms that may 1 day be exploited for therapeutic benefits against these recalcitrant diseases.}, }
@article {pmid36427959, year = {2022}, author = {Payami, H}, title = {The many genomes of Parkinson's disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {59-80}, doi = {10.1016/bs.irn.2022.07.007}, pmid = {36427959}, issn = {2162-5514}, mesh = {Humans ; *Parkinson Disease/genetics ; *Microbiota ; }, abstract = {Genetic component of Parkinson's disease, once firmly believed non-existent, involves the human genome, mitochondrial genome, and the microbiome. Understanding the genomics of PD requires identification of PD-relevant genes and learning how they interact within the hologenome and with their environment. This chapter is an evidence-based perspective of a geneticist on how far we have come in this endeavor. The contemporary scientific society started with a naive and simplistic view of PD, evolved to accept that Parkinson's disease is probably the most complex disease there is, the progress we have made in discovering the genes and elucidating their functions, and now assembling the parts to create the whole.}, }
@article {pmid36426357, year = {2022}, author = {Thuesen, NH and Klausen, MS and Gopalakrishnan, S and Trolle, T and Renaud, G}, title = {Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {987655}, pmid = {36426357}, issn = {1664-3224}, mesh = {Humans ; Sequence Analysis, DNA/methods ; Histocompatibility Testing/methods ; *High-Throughput Nucleotide Sequencing/methods ; *HLA-A Antigens/genetics ; Algorithms ; }, abstract = {Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.}, }
@article {pmid36425038, year = {2022}, author = {Zhu, W and Zhu, M and Liu, X and Xia, J and Wang, H and Chen, R and Li, X}, title = {Adaptive changes of coral Galaxea fascicularis holobiont in response to nearshore stress.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1052776}, pmid = {36425038}, issn = {1664-302X}, abstract = {Global change and local stressors are simultaneously affecting the nearshore corals, and microbiome flexibility may assist corals in thriving under such multiple stressors. Here, we investigated the effects of various environmental variables on Galaxea fascicularis holobiont from nearshore and offshore reefs. These nearshore reefs were more turbid, eutrophic, and warm than offshore reefs. However, coral physiological parameters did not differ significantly. Corals under stressful nearshore environments had low symbiont diversity and selected more tolerant Symbiodiniaceae. The bacterial diversity of offshore corals was significantly higher, and their community composition varied obviously. Diffusion limitations and environmental heterogeneity were essential in structuring microbial communities. Functional annotation analysis demonstrated significant differences between nearshore and offshore corals in bacterial functional groups. Environmental stress significantly reduced the complexity and connectivity of bacterial networks, and the abundances of keystone taxa altered considerably. These results indicated that corals could thrive nearshore through holobiont plasticity to cope with multiple environmental stresses.}, }
@article {pmid36422350, year = {2022}, author = {Duval, C and Marie, B and Foucault, P and Duperron, S}, title = {Establishment of the Bacterial Microbiota in a Lab-Reared Model Teleost Fish, the Medaka Oryzias latipes.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422350}, issn = {2076-2607}, abstract = {Oryzias latipes is an important model organism for physiology, genetics, and developmental studies, and has also emerged as a relevant vertebrate model for aquatic ecotoxicology. Knowledge regarding its associated microbiota on the other hand is still scarce and limited to adults, despite the relevance of the associated microbiome to the host's biology. This study provides the first insights into the establishment of bacterial microbiota during early developmental stages of laboratory-reared medaka using a 16S-rRNA-sequencing-based approach. Major shifts in community compositions are observed, from a Proteobacteria-dominated community in larvae and juveniles to a more phylum-diverse community towards adulthood, with no obvious difference between female and male specimens. Major bacterial taxa found in adults, including genera Cetobacterium and ZOR0006, establish progressively and are rare during early stages. Dominance shifts are comparable to those documented in another major model teleost, the zebrafish. Results from this study provide a basis for future work investigating the influence of medaka-associated bacteria during host development.}, }
@article {pmid36416843, year = {2022}, author = {Fujiwara, F and Miyazawa, K and Nihei, N and Ichihashi, Y}, title = {Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {87}, number = {1}, pages = {21-27}, doi = {10.1093/bbb/zbac191}, pmid = {36416843}, issn = {1347-6947}, support = {//Cabinet Office, Government of Japan/ ; JPJ009237//Moonshot Research and Development Program for Agriculture, Forestry and Fisheries/ ; //Bio-oriented Technology Research Advancement Institution/ ; //RIKEN Junior Research Associate Program/ ; }, mesh = {*Multiomics ; *Agriculture ; Soil ; Soil Microbiology ; Crops, Agricultural/genetics ; }, abstract = {In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.}, }
@article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, }
@article {pmid36372339, year = {2023}, author = {Pei, Y and Chen, S and Diao, X and Wang, X and Zhou, H and Li, Y and Li, Z}, title = {Deciphering the disturbance mechanism of BaP on the symbiosis of Montipora digitata via 4D-Proteomics approach.}, journal = {Chemosphere}, volume = {312}, number = {Pt 1}, pages = {137223}, doi = {10.1016/j.chemosphere.2022.137223}, pmid = {36372339}, issn = {1879-1298}, mesh = {Animals ; *Symbiosis ; Ecosystem ; Antioxidants/metabolism ; Proteomics ; RNA, Ribosomal, 16S/metabolism ; *Anthozoa/metabolism ; Coral Reefs ; }, abstract = {The coral holobiont is mainly composed of coral polyps, zooxanthellae, and coral symbiotic microorganisms, which form the basis of coral reef ecosystems. In recent years, the severe degradation of coral reefs caused by climate warming and environmental pollution has aroused widespread concern. Benzo(a)pyrene (BaP) is a widely distributed pollutant in the environment. However, the underlying mechanisms of coral symbiosis destruction due to the stress of BaP are not well understood. In this study, diaPASEF proteomics and 16S rRNA amplicon pyrosequencing technology were used to reveal the effects of 50 μg/L BaP on Montipora digitate. Data analysis was performed from the perspective of the main symbionts of M. digitata (coral polyps, zooxanthellae, and coral symbiotic microorganisms). The results showed that BaP impaired cellular antioxidant capacity by disrupting the GSH/GSSG cycle, and sustained stress causes severe impairment of energy metabolism and protein degradation in coral polyps. In zooxanthellae, BaP downregulated the protein expression of SOD2 and mtHSP70, which then resulted in oxidative free radical accumulation and apoptosis. For coral symbiotic microorganisms, BaP altered the community structure of microorganisms and decreased immunity. Coral symbiotic microorganisms adapted to the stress of BaP by adjusting energy metabolism and enhancing extracellular electron transfer. BaP adversely affected the three main symbionts of M. digitata via different mechanisms. Decreased antioxidant capacity is a common cause of damages to coral polyps and zooxanthellae, whereas coral symbiotic microorganisms are able to appropriately adapt to oxidative stress. This study assessed the effects of BaP on corals from a symbiotic perspective, which is more comprehensive and reliable. At the same time, data from the study supports new directions for coral research and coral reef protection.}, }
@article {pmid36369436, year = {2023}, author = {Paulino, GVB and Félix, CR and da Silva Oliveira, FA and Gomez-Silvan, C and Melo, VMM and Andersen, GL and Landell, MF}, title = {Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {10}, pages = {26496-26509}, pmid = {36369436}, issn = {1614-7499}, support = {408718/2013-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 441657/2016-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 311553/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 312889/2021-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 60030.1564/2016//Funda&#xe7;&#xe3;o&#xa0;de&#xa0;Amparo&#xa0;&#xe0;&#xa0;Pesquisa&#xa0;do&#xa0;Estado&#xa0;de&#xa0;Alagoas/ ; 23038.000452/2017-16//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Brazil ; Rivers ; Coral Reefs ; *Microbiota ; }, abstract = {Although coral bleaching is increasing worldwide due to warming oceans exacerbated by climate change, there has been a growing recognition that local stressors may play an additional role. Important stressors include the physicochemical and microbiological influences that are related to river runoff. Here, we investigated the microbiota associated to mucus and tissue of endemic coral Siderastrea stellata, collected from Brazilian northeast coral reefs of Barra de Santo Antônio (subject to river runoff) and Maragogi (minimal river runoff) during both the rainy and dry seasons. We sequenced the V4 region of 16S rDNA and used multiple R packages to process raw data and performed statistical analysis to reveal the microbial community structure composition and functional predictions. Major dissimilarities between microbial communities were related to seasonality, while healthy and bleached specimens were mainly associated with the enrichment of several less abundant taxa involved in specific metabolic functions, mainly related to the nitrogen cycle. We were not able to observe the dominance of groups that has been previously associated with bleachings, such as Vibrionaceae or Burkholderiaceae. The influx of freshwater appears to increase the homogeneity between individuals in Barra de Santo Antonio, especially during the rainy season. By contrast, we observed an increased homogeneity between samples in Maragogi during the dry season. Understanding the dynamics of the coral microbiota and how bleaching appears in response to specific environmental variables, in addition to determining the conditions that lead to a more robust coral microbiota, is essential for choosing the most appropriate area and conservation methods, for example.}, }
@article {pmid36365369, year = {2022}, author = {Bunyoo, C and Roongsattham, P and Khumwan, S and Phonmakham, J and Wonnapinij, P and Thamchaipenet, A}, title = {Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365369}, issn = {2223-7747}, support = {2002//Kasetsart University Reinventing University Program/ ; FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; 2021-2026//The Science and Technology Research Partnership for Sustainable Development (SATREPS), JICA, Japan/ ; }, abstract = {Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.}, }
@article {pmid36363690, year = {2022}, author = {Wang, R and Zhang, Q and Ju, M and Yan, S and Zhang, Q and Gu, P}, title = {The Endophytic Fungi Diversity, Community Structure, and Ecological Function Prediction of Sophora alopecuroides in Ningxia, China.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363690}, issn = {2076-2607}, support = {31260452//National Natural Science Foundation of China/ ; 2019YFD1002502//National Key Research and Development project/ ; }, abstract = {Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic fungi in the holobiont of S. alopecuroides is relatively lacking. In this article, the fungal community profiling of roots, stems, leaves, and seeds of S. alopecuroides (at the fruit maturity stage) from Huamachi and Baofeng in Ningxia, China were investigated based on the ITS1 region, using high-throughput sequencing technology. As a result, a total of 751 operational taxonomic units (OTUs) were obtained and further classified into 9 phyla, 27 classes, 66 orders, 141 families, 245 genera, and 340 species. The roots had the highest fungal richness and diversity, while the stems had the highest evenness and pedigree diversity. There also was a significant difference in the richness of the endophytic fungal community between root and seed (p < 0.05). The organ was the main factor affecting the community structure of endophytic fungi in S. alopecuroides. The genera of unclassified Ascomycota, Tricholoma, Apiotrichum, Alternaria, and Aspergillus made up the vast majority of relative abundance, which were common in all four organs as well. The dominant and endemic genera and biomarkers of endophytic fungi in four organs of S. alopecuroides were different and exhibited organ specificity or tissue preference. The endophytic fungi of S. alopecuroides were mainly divided into 15 ecological function groups, among which saprotroph was absolutely dominant, followed by mixotrophic and pathotroph, and the symbiotroph was the least. With this study, we revealed the diversity and community structure and predicted the ecological function of the endophytic fungi of S. alopecuroides, which provided a theoretical reference for the further development and utilization of the endophytic fungi resources of S. alopecuroides.}, }
@article {pmid36361844, year = {2022}, author = {Kiruba N, JM and Saeid, A}, title = {An Insight into Microbial Inoculants for Bioconversion of Waste Biomass into Sustainable "Bio-Organic" Fertilizers: A Bibliometric Analysis and Systematic Literature Review.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361844}, issn = {1422-0067}, mesh = {Fertilizers/analysis ; Biomass ; *Agricultural Inoculants ; Food ; *Refuse Disposal ; Sewage/microbiology ; Bibliometrics ; Soil ; }, abstract = {The plant-microbe holobiont has garnered considerable attention in recent years, highlighting its importance as an ecological unit. Similarly, manipulation of the microbial entities involved in the rhizospheric microbiome for sustainable agriculture has also been in the limelight, generating several commercial bioformulations to enhance crop yield and pest resistance. These bioformulations were termed biofertilizers, with the consistent existence and evolution of different types. However, an emerging area of interest has recently focused on the application of these microorganisms for waste valorization and the production of "bio-organic" fertilizers as a result. In this study, we performed a bibliometric analysis and systematic review of the literature retrieved from Scopus and Web of Science to determine the type of microbial inoculants used for the bioconversion of waste into "bio-organic" fertilizers. The Bacillus, Acidothiobacillus species, cyanobacterial biomass species, Aspergillus sp. and Trichoderma sp. were identified to be consistently used for the recovery of nutrients and bioconversion of wastes used for the promotion of plant growth. Cyanobacterial strains were used predominantly for wastewater treatment, while Bacillus, Acidothiobacillus, and Aspergillus were used on a wide variety of wastes such as sawdust, agricultural waste, poultry bone meal, crustacean shell waste, food waste, and wastewater treatment plant (WWTP) sewage sludge ash. Several bioconversion strategies were observed such as submerged fermentation, solid-state fermentation, aerobic composting, granulation with microbiological activation, and biodegradation. Diverse groups of microorganisms (bacteria and fungi) with different enzymatic functionalities such as chitinolysis, lignocellulolytic, and proteolysis, in addition to their plant growth promoting properties being explored as a consortium for application as an inoculum waste bioconversion to fertilizers. Combining the efficiency of such functional and compatible microbial species for efficient bioconversion as well as higher plant growth and crop yield is an enticing opportunity for "bio-organic" fertilizer research.}, }
@article {pmid36361736, year = {2022}, author = {Graindorge, S and Villette, C and Koechler, S and Groh, C and Comtet-Marre, S and Mercier, P and Magerand, R and Peyret, P and Heintz, D and Schaller, H and Arsène-Ploetze, F}, title = {The Arabidopsis thaliana-Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361736}, issn = {1422-0067}, support = {Projet International de Cooperation Scientifique//French National Centre for Scientific Research/ ; }, mesh = {*Arabidopsis/metabolism ; *Streptomyces/metabolism ; Plant Diseases/genetics/microbiology ; Pseudomonas syringae/metabolism ; *Arabidopsis Proteins/metabolism ; }, abstract = {How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria-Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.}, }
@article {pmid36357618, year = {2022}, author = {Friedman, Y}, title = {Who is the biological patient? A new gradational and dynamic model for one health medicine.}, journal = {History and philosophy of the life sciences}, volume = {44}, number = {4}, pages = {61}, pmid = {36357618}, issn = {1742-6316}, mesh = {Animals ; Humans ; *One Health ; Interdisciplinary Research ; *Medicine ; }, abstract = {One Health medicine aims to improve health by focusing on the relations between the health of humans, animals, and the environment. However, One Health does not provide a clear idea of these relations, which are still represented as conceptually separated and not as one health, as the name implies. Inspired by holobiont research, I suggest a new model and conceptual framework for One Health that expands the notion of the biological patient by providing a gradational and dynamic understanding of environments, patients, and their relations. This new model conceptualizes humans and non-humans, individual organisms, and collectives, as belonging to one system that allows for more or less inclusive understandings of patients. As such, it resolves the conceptual tensions of different One Health approaches and supports the implementation of One Health as an interdisciplinary research field.}, }
@article {pmid36354996, year = {2022}, author = {Castaldi, A and Teta, R and Esposito, G and Beniddir, MA and De Voogd, NJ and Duperron, S and Costantino, V and Bourguet-Kondracki, ML}, title = {Computational Metabolomics Tools Reveal Subarmigerides, Unprecedented Linear Peptides from the Marine Sponge Holobiont Callyspongia subarmigera.}, journal = {Marine drugs}, volume = {20}, number = {11}, pages = {}, pmid = {36354996}, issn = {1660-3397}, mesh = {Animals ; *Callyspongia/microbiology ; Tandem Mass Spectrometry ; *Porifera/chemistry ; Peptides ; Metabolomics ; Molecular Structure ; }, abstract = {A detailed examination of a unique molecular family, restricted to the Callyspongia genus, in a molecular network obtained from an in-house Haplosclerida marine sponge collection (including Haliclona, Callyspongia, Xestospongia, and Petrosia species) led to the discovery of subarmigerides, a series of rare linear peptides from Callyspongia subarmigera, a genus mainly known for polyacetylenes and lipids. The structure of the sole isolated peptide, subarmigeride A (1) was elucidated through extensive 1D and 2D NMR spectroscopy, HRMS/MS, and Marfey's method to assign its absolute configuration. The putative structures of seven additional linear peptides were proposed by an analysis of their respective MS/MS spectra and a comparison of their fragmentation patterns with the heptapeptide 1. Surprisingly, several structurally related analogues of subarmigeride A (1) occurred in one distinct cluster from the molecular network of the cyanobacteria strains of the Guadeloupe mangroves, suggesting that the true producer of this peptide family might be the microbial sponge-associated community, i.e., the sponge-associated cyanobacteria.}, }
@article {pmid36348188, year = {2022}, author = {Rasmussen, N}, title = {René Dubos, the Autochthonous Flora, and the Discovery of the Microbiome.}, journal = {Journal of the history of biology}, volume = {55}, number = {3}, pages = {537-558}, pmid = {36348188}, issn = {1573-0387}, mesh = {Animals ; Humans ; *Microbiota ; *Anthozoa ; Symbiosis ; }, abstract = {Now characterised by high-throughput sequencing methods that enable the study of microbes without lab culture, the human "microbiome" (the microbial flora of the body) is said to have revolutionary implications for biology and medicine. According to many experts, we must now understand ourselves as "holobionts" like lichen or coral, multispecies superorganisms that consist of animal and symbiotic microbes in combination, because normal physiological function depends on them. Here I explore the 1960s research of biologist René Dubos, a forerunner figure mentioned in some historical accounts of the microbiome, and argue that he arrived at the superorganism concept 40 years before the Human Microbiome Project. This raises the question of why his contribution was not hailed as revolutionary at the time and why Dubos is not remembered for it.}, }
@article {pmid36342159, year = {2022}, author = {Cegarra, L and Aguirre, P and Nuñez, MT and Gerdtzen, ZP and Salgado, JC}, title = {Calcium is a noncompetitive inhibitor of DMT1 on the intestinal iron absorption process: empirical evidence and mathematical modeling analysis.}, journal = {American journal of physiology. Cell physiology}, volume = {323}, number = {6}, pages = {C1791-C1806}, doi = {10.1152/ajpcell.00411.2022}, pmid = {36342159}, issn = {1522-1563}, support = {21170027//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; IT21I0027//ANID | Fondo de Fomento al Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (FONDEF)/ ; FB0001//Associative Research Program/ ; FB210024//Scientific and Technological Center of Excellence/ ; }, mesh = {Humans ; *Iron/metabolism ; Caco-2 Cells ; Calcium ; Calcium, Dietary ; *Cation Transport Proteins/metabolism ; Kinetics ; Intestinal Absorption ; Models, Theoretical ; }, abstract = {Iron absorption is a complex and highly controlled process where DMT1 transports nonheme iron through the brush-border membrane of enterocytes to the cytoplasm but does not transport alkaline-earth metals such as calcium. However, it has been proposed that high concentrations of calcium in the diet could reduce iron bioavailability. In this work, we investigate the effect of intracellular and extracellular calcium on iron uptake by Caco-2 cells, as determined by calcein fluorescence quenching. We found that extracellular calcium inhibits iron uptake by Caco-2 cells in a concentration-dependent manner. Chelation of intracellular calcium with BAPTA did not affect iron uptake, which indicates that the inhibitory effect of calcium is not exerted through intracellular calcium signaling. Kinetic studies performed, provided evidence that calcium acts as a reversible noncompetitive inhibitor of the iron transport activity of DMT1. Based on these experimental results, a mathematical model was developed that considers the dynamics of noncompetitive inhibition using a four-state mechanism to describe the inhibitory effect of calcium on the DMT1 iron transport process in intestinal cells. The model accurately predicts the calcein fluorescence quenching dynamics observed experimentally after an iron challenge. Therefore, the proposed model structure is capable of representing the inhibitory effect of extracellular calcium on DMT1-mediated iron entry into the cLIP of Caco-2 cells. Considering the range of calcium concentrations that can inhibit iron uptake, the possible inhibition of dietary calcium on intestinal iron uptake is discussed.}, }
@article {pmid36333777, year = {2022}, author = {Aubé, J and Cambon-Bonavita, MA and Velo-Suárez, L and Cueff-Gauchard, V and Lesongeur, F and Guéganton, M and Durand, L and Reveillaud, J}, title = {A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {189}, pmid = {36333777}, issn = {2049-2618}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Symbiosis ; *Decapoda/genetics ; *Hydrothermal Vents ; Gills ; Immune System ; }, abstract = {BACKGROUND: In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.<br><br>RESULTS: We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.<br><br>CONCLUSION: Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.}, }
@article {pmid36329318, year = {2022}, author = {Shao, Q and Dong, C and Hu, H and Huang, J and Zou, X and Liang, Z and Han, Y}, title = {Effects of Medicinal Plants on Fungal Community Structure and Function in Hospital Grassplot Soil.}, journal = {Current microbiology}, volume = {79}, number = {12}, pages = {377}, pmid = {36329318}, issn = {1432-0991}, support = {[Qian Ke He [2020]6005]//"Hundred" Talent Projects of Guizhou Province/ ; [No. 2018B020205003]//the Key Areas of Research and Development Program of Guangdong Province/ ; [No. 32060011]//the Natural Science Foundation of China/ ; [GNYL[2017]009]//Construction Program of Biology First-class Discipline in Guizhou/ ; }, mesh = {Animals ; Humans ; *Mycobiome ; Soil ; Soil Microbiology ; *Plants, Medicinal ; *Mirabilis ; Fungi/genetics ; Hospitals ; }, abstract = {Hospital grassplot soil is an important repository of pathogenic fungi exposed to the hospital environment, and the diffusion of these fungi-containing soil particles in the air increases the risk of nosocomial fungal infections. In this study, from the perspective of soil microbes-plant holobiont, four medicinal plants Mirabilis jalapa, Artemisia argyi, Viola philippica, and Plantago depressa were used as materials, based on ITS high-throughput amplicon sequencing and simulated pot experiments to explore the effect of medicinal plants on the fungal community in hospital grassplot soil, in order to provide a new exploration for hospital grassplot soil remediation. The results showed that the fungal community ecological guilds in primary test soil was mainly pathogen, and the abundance of animal pathogen with potential threats to human reached 61.36%. After planting medicinal plants, the composition and function of soil fungal community changed significantly. Although this change varied with plant species and growth stages, all samples collected in the pot experiment showed that the pathogen abundance decreased and the saprotroph abundance increased. In addition, 45 of the 46 core fungal genera defined in all potted samples were present in primary test soil, and many of them were human potential pathogens. These findings imply that the idea of enhancing soil quality in hospital grassplot soil by planting specific plants is feasible. However, the initial fungal community of the hospital grassplot soil has a certain stability, and it is difficult to completely eliminate the threat of pathogenic fungi by planting medicinal plants.}, }
@article {pmid36326449, year = {2023}, author = {KleinJan, H and Frioux, C and Califano, G and Aite, M and Fremy, E and Karimi, E and Corre, E and Wichard, T and Siegel, A and Boyen, C and Dittami, SM}, title = {Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation.}, journal = {Molecular ecology}, volume = {32}, number = {3}, pages = {703-723}, pmid = {36326449}, issn = {1365-294X}, mesh = {*Host Microbial Interactions ; Acclimatization/physiology ; Symbiosis ; Fresh Water ; *Phaeophyceae/genetics/microbiology ; }, abstract = {Microbes can modify their hosts' stress tolerance, thus potentially enhancing their ecological range. An example of such interactions is Ectocarpus subulatus, one of the few freshwater-tolerant brown algae. This tolerance is partially due to its (un)cultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. Low salinity acclimation of these algal-bacterial associations was then compared. Salinity significantly impacted bacterial and viral gene expression, albeit in different ways across algal-bacterial communities. In contrast, gene expression of the host and metabolite profiles were affected almost exclusively in the freshwater-intolerant algal-bacterial communities. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, vitamin K synthesis is one possible bacterial service missing specifically in freshwater-intolerant cultures in low salinity. In this condition, we also observed a relative increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a quorum-sensing regulator. This could have resulted in dysbiosis by causing a shift in bacterial behaviour in the intolerant algal-bacterial community. Together, these results provide two promising hypotheses to be examined by future targeted experiments. Although they apply only to the specific study system, they offer an example of how bacteria may impact their host's stress response.}, }
@article {pmid36322483, year = {2022}, author = {Hempel, E and Bibi, F and Faith, JT and Koepfli, KP and Klittich, AM and Duchêne, DA and Brink, JS and Kalthoff, DC and Dalén, L and Hofreiter, M and Westbury, MV}, title = {Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36322483}, issn = {1537-1719}, mesh = {Animals ; Humans ; *Antelopes/genetics ; Biological Evolution ; Phylogeny ; Genome ; *Mustelidae/genetics ; }, abstract = {The blue antelope (Hippotragus leucophaeus) is the only large African mammal species to have become extinct in historical times, yet no nuclear genomic information is available for this species. A recent study showed that many alleged blue antelope museum specimens are either roan (Hippotragus equinus) or sable (Hippotragus niger) antelopes, further reducing the possibilities for obtaining genomic information for this extinct species. While the blue antelope has a rich fossil record from South Africa, climatic conditions in the region are generally unfavorable to the preservation of ancient DNA. Nevertheless, we recovered two blue antelope draft genomes, one at 3.4× mean coverage from a historical specimen (∼200 years old) and one at 2.1× mean coverage from a fossil specimen dating to 9,800-9,300 cal years BP, making it currently the oldest paleogenome from Africa. Phylogenomic analyses show that blue and sable antelope are sister species, confirming previous mitogenomic results, and demonstrate ancient gene flow from roan into blue antelope. We show that blue antelope genomic diversity was much lower than in roan and sable antelope, indicative of a low population size since at least the early Holocene. This supports observations from the fossil record documenting major decreases in the abundance of blue antelope after the Pleistocene-Holocene transition. Finally, the persistence of this species throughout the Holocene despite low population size suggests that colonial-era human impact was likely the decisive factor in the blue antelope's extinction.}, }
@article {pmid36319835, year = {2022}, author = {Moffat, JJ and Coffroth, MA and Wallingford, PD and terHorst, CP}, title = {Symbiont genotype influences holobiont response to increased temperature.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18394}, pmid = {36319835}, issn = {2045-2322}, support = {OCE-1559286//National Science Foundation/ ; OCE-1559105//National Science Foundation/ ; }, mesh = {Animals ; Temperature ; Coral Reefs ; *Anthozoa/physiology ; *Dinoflagellida/physiology ; Symbiosis ; Genotype ; }, abstract = {As coral reefs face warming oceans and increased coral bleaching, a whitening of the coral due to loss of microalgal endosymbionts, the possibility of evolutionary rescue offers some hope for reef persistence. In tightly linked mutualisms, evolutionary rescue may occur through evolution of the host and/or endosymbionts. Many obligate mutualisms are composed of relatively small, fast-growing symbionts with greater potential to evolve on ecologically relevant time scales than their relatively large, slower growing hosts. Numerous jellyfish species harbor closely related endosymbiont taxa to other cnidarian species such as coral, and are commonly used as a model system for investigating cnidarian mutualisms. We examined the potential for adaptation of the upside-down jellyfish Cassiopea xamachana to increased temperature via evolution of its microalgal endosymbiont, Symbiodinium microadriaticum. We quantified trait variation among five algal genotypes in response to three temperatures (26 °C, 30 °C, and 32 °C) and fitness of hosts infected with each genotype. All genotypes showed positive growth rates at each temperature, but rates of respiration and photosynthesis decreased with increased temperature. Responses varied among genotypes but were unrelated to genetic similarity. The effect of temperature on asexual reproduction and the timing of development in the host also depended on the genotype of the symbiont. Natural selection could favor different algal genotypes at different temperatures, affecting host fitness. This eco-evolutionary interaction may be a critical component of understanding species resilience in increasingly stressful environments.}, }
@article {pmid36315059, year = {2023}, author = {Shantz, AA and Ladd, MC and Ezzat, L and Schmitt, RJ and Holbrook, SJ and Schmeltzer, E and Vega Thurber, R and Burkepile, DE}, title = {Positive interactions between corals and damselfish increase coral resistance to temperature stress.}, journal = {Global change biology}, volume = {29}, number = {2}, pages = {417-431}, doi = {10.1111/gcb.16480}, pmid = {36315059}, issn = {1365-2486}, support = {1547952//Division of Ocean Sciences/ ; 1637396//Division of Ocean Sciences/ ; //Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Symbiosis ; Temperature ; Climate Change ; Fishes ; *Perciformes ; }, abstract = {By the century's end, many tropical seas will reach temperatures exceeding most coral species' thermal tolerance on an annual basis. The persistence of corals in these regions will, therefore, depend on their abilities to tolerate recurrent thermal stress. Although ecologists have long recognized that positive interspecific interactions can ameliorate environmental stress to expand the realized niche of plants and animals, coral bleaching studies have largely overlooked how interactions with community members outside of the coral holobiont shape the bleaching response. Here, we subjected a common coral, Pocillopora grandis, to 10 days of thermal stress in aquaria with and without the damselfish Dascyllus flavicaudus (yellowtail dascyllus), which commonly shelter within these corals, to examine how interactions with damselfish impacted coral thermal tolerance. Corals often benefit from nutrients excreted by animals they interact with and prior to thermal stress, corals grown with damselfish showed improved photophysiology (Fv /Fm) and developed larger endosymbiont populations. When exposed to thermal stress, corals with fish performed as well as control corals maintained at ambient temperatures without fish. In contrast, corals exposed to thermal stress without fish experienced photophysiological impairment, a more than 50% decline in endosymbiont density, and a 36% decrease in tissue protein content. At the end of the experiment, thermal stress caused average calcification rates to decrease by over 80% when damselfish were absent but increase nearly 25% when damselfish were present. Our study indicates that damselfish-derived nutrients can increase coral thermal tolerance and are consistent with the Stress Gradient Hypothesis, which predicts that positive interactions become increasingly important for structuring communities as environmental stress increases. Because warming of just a few degrees can exceed corals' temperature tolerance to trigger bleaching and mortality, positive interactions could play a critical role in maintaining some coral species in warming regions until climate change is aggressively addressed.}, }
@article {pmid36314753, year = {2022}, author = {Koziol, A and Odriozola, I and Nyholm, L and Leonard, A and San José, C and Pauperio, J and Ferreira, C and Hansen, AJ and Aizpurua, O and Gilbert, MTP and Alberdi, A}, title = {Enriching captivity conditions with natural elements does not prevent the loss of wild-like gut microbiota but shapes its compositional variation in two small mammals.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1318}, pmid = {36314753}, issn = {2045-8827}, mesh = {Animals ; *Gastrointestinal Microbiome ; Bacteria/genetics ; *Microbiota ; Feces ; Mammals/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {As continued growth in gut microbiota studies in captive and model animals elucidates the importance of their role in host biology, further pursuit of how to retain a wild-like microbial community is becoming increasingly important to obtain representative results from captive animals. In this study, we assessed how the gut microbiota of two wild-caught small mammals, namely Crocidura russula (Eulipotyphla, insectivore) and Apodemus sylvaticus (Rodentia, omnivore), changed when bringing them into captivity. We analyzed fecal samples of 15 A. sylvaticus and 21 C. russula, immediately after bringing them into captivity and 5 weeks later, spread over two housing treatments: a "natural" setup enriched with elements freshly collected from nature and a "laboratory" setup with sterile artificial elements. Through sequencing of the V3-V4 region of the 16S recombinant RNA gene, we found that the initial microbial diversity dropped during captivity in both species, regardless of treatment. Community composition underwent a change of similar magnitude in both species and under both treatments. However, we did observe that the temporal development of the gut microbiome took different trajectories (i.e., changed in different directions) under different treatments, particularly in C. russula, suggesting that C. russula may be more susceptible to environmental change. The results of this experiment do not support the use of microbially enriched environments to retain wild-like microbial diversities and compositions, yet show that specific housing conditions can significantly affect the drift of microbial communities under captivity.}, }
@article {pmid36300791, year = {2023}, author = {Snelders, NC and Boshoven, JC and Song, Y and Schmitz, N and Fiorin, GL and Rovenich, H and van den Berg, GCM and Torres, DE and Petti, GC and Prockl, Z and Faino, L and Seidl, MF and Thomma, BPHJ}, title = {A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria.}, journal = {The New phytologist}, volume = {237}, number = {3}, pages = {944-958}, doi = {10.1111/nph.18576}, pmid = {36300791}, issn = {1469-8137}, mesh = {Plant Proteins/metabolism ; Virulence ; *Actinobacteria/genetics/metabolism ; Receptors, Cell Surface/metabolism ; Receptors, Immunologic/genetics ; Plant Diseases/microbiology ; *Verticillium ; Fungal Proteins/genetics/metabolism ; }, abstract = {Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens.}, }
@article {pmid36298701, year = {2022}, author = {Olesen, AS and Kodama, M and Skovgaard, K and Møbjerg, A and Lohse, L and Limborg, MT and Bøtner, A and Belsham, GJ}, title = {Influence of African Swine Fever Virus on Host Gene Transcription within Peripheral Blood Mononuclear Cells from Infected Pigs.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298701}, issn = {1999-4915}, mesh = {Swine ; Animals ; *African Swine Fever Virus/physiology ; *African Swine Fever ; Leukocytes, Mononuclear/metabolism ; Real-Time Polymerase Chain Reaction ; RNA, Messenger/metabolism ; Transcription, Genetic ; }, abstract = {African swine fever virus (ASFV) has become a global threat to the pig production industry and has caused enormous economic losses in many countries in recent years. Peripheral blood mononuclear cells (PBMCs) from pigs infected with ASFV not only express ASFV genes (almost 200 in number) but have altered patterns of host gene expression as well. Both up- and down-regulation of host cell gene expression can be followed using RNAseq on poly(A)+ mRNAs harvested from the PBMCs of pigs collected at different times post-infection. Consistent with the time course of changes in viral gene expression, only few and limited changes in host gene expression were detected at 3 days post-infection (dpi), but by 6 dpi, marked changes in the expression of over 1300 host genes were apparent. This was co-incident with the major increase in viral gene expression. The majority of the changes in host gene expression were up-regulation, but many down-regulated genes were also identified. The patterns of changes in gene expression within the PBMCs detected by RNAseq were similar in each of the four infected pigs. Furthermore, changes in the expression of about twenty selected host genes, known to be important in host defence and inflammatory responses, were confirmed using high-throughput microfluidic qPCR assays.}, }
@article {pmid36296289, year = {2022}, author = {Carper, DL and Appidi, MR and Mudbhari, S and Shrestha, HK and Hettich, RL and Abraham, PE}, title = {The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296289}, issn = {2076-2607}, support = {Secure Biosystems Design Science Focus Area//United States Department of Energy/ ; Plant-Microbe Interfaces Science Focus Area//United States Department of Energy/ ; Center for Bioenergy Innovation//United States Department of Energy/ ; }, abstract = {Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant-microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant-microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.}, }
@article {pmid36293657, year = {2022}, author = {Lim, DW and Wang, JH}, title = {Gut Microbiome: The Interplay of an "Invisible Organ" with Herbal Medicine and Its Derived Compounds in Chronic Metabolic Disorders.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {20}, pages = {}, pmid = {36293657}, issn = {1660-4601}, support = {2020R1F1A1074155//National Research Foundation of Korea/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Herbal Medicine ; *Plants, Medicinal ; Phytotherapy ; Chronic Disease ; *Metabolic Diseases/drug therapy ; }, abstract = {Resembling a concealed "organ" in a holobiont, trillions of gut microbes play complex roles in the maintenance of homeostasis, including participating in drug metabolism. The conventional opinion is that most of any drug is metabolized by the host and that individual differences are principally due to host genetic factors. However, current evidence indicates that only about 60% of the individual differences in drug metabolism are attributable to host genetics. Although most common chemical drugs regulate the gut microbiota, the gut microbiota is also known to be involved in drug metabolism, like the host. Interestingly, many traditional herbal medicines and derived compounds are biotransformed by gut microbiota, manipulating the compounds' effects. Accordingly, the gut microbiota and its specified metabolic pathways can be deemed a promising target for promoting drug efficacy and safety. However, the evidence regarding causality and the corresponding mechanisms concerning gut microbiota and drug metabolism remains insufficient, especially regarding drugs used to treat metabolic disorders. Therefore, the present review aims to comprehensively summarize the bidirectional roles of gut microbiota in the effects of herbal medicine in metabolic diseases to provide vital clues for guiding the clinical application of precision medicine and personalized drug development.}, }
@article {pmid36287022, year = {2022}, author = {Puntin, G and Sweet, M and Fraune, S and Medina, M and Sharp, K and Weis, VM and Ziegler, M}, title = {Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {86}, number = {4}, pages = {e0005322}, pmid = {36287022}, issn = {1098-5557}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Ecosystem ; Coral Reefs ; Bacteria ; Archaea ; }, abstract = {Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.}, }
@article {pmid36274502, year = {2022}, author = {Foucault, P and Gallet, A and Duval, C and Marie, B and Duperron, S}, title = {Gut microbiota and holobiont metabolome composition of the medaka fish (Oryzias latipes) are affected by a short exposure to the cyanobacterium Microcystis aeruginosa.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {253}, number = {}, pages = {106329}, doi = {10.1016/j.aquatox.2022.106329}, pmid = {36274502}, issn = {1879-1514}, mesh = {Animals ; *Microcystis ; *Oryzias/physiology ; *Gastrointestinal Microbiome ; *Water Pollutants, Chemical/toxicity ; *Cyanobacteria ; Metabolome ; }, abstract = {Blooms of toxic cyanobacteria are a common stress encountered by aquatic fauna. Evidence indicates that long-lasting blooms affect fauna-associated microbiota. Because of their multiple roles, host-associated microbes are nowadays considered relevant to ecotoxicology, yet the respective timing of microbiota versus functional changes in holobionts response needs to be clarified. The response of gut microbiota and holobiont's metabolome to exposure to a dense culture of Microcystis aeruginosa was investigated as a microcosm-simulated bloom in the model fish species Oryzias latipes (medaka). Both gut microbiota and gut metabolome displayed significant composition changes after only 2 days of exposure. A dominant symbiont, member of the Firmicutes, plummeted whereas various genera of Proteobacteria and Actinobacteriota increased in relative abundance. Changes in microbiota composition occurred earlier and faster compared to metabolome composition. Liver and muscle metabolome were much less affected than guts, supporting that the gut and associated microbiota are in the front row upon exposure. This study highlights that even short cyanobacterial blooms, that are increasingly frequent, trigger changes in microbiota composition and holobiont metabolome. It emphasizes the relevance of multi-omics approaches to explore organism's response to an ecotoxicological stress.}, }
@article {pmid36261416, year = {2022}, author = {Siddique, S and Radakovic, ZS and Hiltl, C and Pellegrin, C and Baum, TJ and Beasley, H and Bent, AF and Chitambo, O and Chopra, D and Danchin, EGJ and Grenier, E and Habash, SS and Hasan, MS and Helder, J and Hewezi, T and Holbein, J and Holterman, M and Janakowski, S and Koutsovoulos, GD and Kranse, OP and Lozano-Torres, JL and Maier, TR and Masonbrink, RE and Mendy, B and Riemer, E and Sobczak, M and Sonawala, U and Sterken, MG and Thorpe, P and van Steenbrugge, JJM and Zahid, N and Grundler, F and Eves-van den Akker, S}, title = {The genome and lifestage-specific transcriptomes of a plant-parasitic nematode and its host reveal susceptibility genes involved in trans-kingdom synthesis of vitamin B5.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6190}, pmid = {36261416}, issn = {2041-1723}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/N021908/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S006397/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Animals ; *Parasites ; Pantothenic Acid ; Transcriptome ; *Tylenchida ; *Cysts ; }, abstract = {Plant-parasitic nematodes are a major threat to crop production in all agricultural systems. The scarcity of classical resistance genes highlights a pressing need to find new ways to develop nematode-resistant germplasm. Here, we sequence and assemble a high-quality phased genome of the model cyst nematode Heterodera schachtii to provide a platform for the first system-wide dual analysis of host and parasite gene expression over time, covering all major parasitism stages. Analysis of the hologenome of the plant-nematode infection site identified metabolic pathways that were incomplete in the parasite but complemented by the host. Using a combination of bioinformatic, genetic, and biochemical approaches, we show that a highly atypical completion of vitamin B5 biosynthesis by the parasitic animal, putatively enabled by a horizontal gene transfer from a bacterium, is required for full pathogenicity. Knockout of either plant-encoded or now nematode-encoded steps in the pathway significantly reduces parasitic success. Our experiments establish a reference for cyst nematodes, further our understanding of the evolution of plant-parasitism by nematodes, and show that congruent differential expression of metabolic pathways in the infection hologenome represents a new way to find nematode susceptibility genes. The approach identifies genome-editing-amenable targets for future development of nematode-resistant crops.}, }
@article {pmid36254722, year = {2022}, author = {Jonas, L and Hill, R}, title = {Uptake of inorganic and organic phosphorus compounds by two marine sponges and their associated bacterial communities in aquaria.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6128-6143}, doi = {10.1111/1462-2920.16250}, pmid = {36254722}, issn = {1462-2920}, mesh = {Animals ; Symbiosis ; *Porifera/microbiology ; *Microbiota ; Phosphorus ; Nitrogen ; *Cyanobacteria ; Carbon ; Organophosphorus Compounds ; Phosphates ; }, abstract = {Marine sponges are abundant filter-feeders in benthic ecosystems and many host copious microorganisms. Sponges and their symbionts have emerged as major players within marine biogeochemical cycles, facilitating uptake and release of carbon, nitrogen, and sulfur. Sponge holobionts' role in transforming dissolved carbon and nitrogen is well established; however, the same depth of understanding has not yet been extended to phosphorus. In this aquaria-based study, [32] P-labelled orthophosphate and ATP were used to determine that two sponges, Lendenfeldia chondrodes and Hymeniacidon heliophila, both take up ambient dissolved inorganic phosphate (DIP) and dissolved organic phosphorus (DOP). Subsequent genetic analyses and chemical extraction showed that sponge symbionts have the potential to synthesise polyphosphate (poly-P) and that this energy-rich form of stored phosphorus is present in both sponges. L. chondrodes, an oligotrophic sponge with a microbiome dominated by cyanobacteria, stores more phosphorus as poly-P (6%-8% of total phosphorus) than H. heliophila (0.55%), a eutrophic sponge with low cyanobacterial abundance. DIP/DOP uptake, as well as poly-P storage, may be driven by two factors: cyanobacterial abundance and nutrient availability. Considering their prevalence in phosphorus-limited ecosystems and their ability to pump large amounts of seawater, sponge holobionts are likely to be key players within benthic phosphorus cycles.}, }
@article {pmid36250983, year = {2022}, author = {Schmittmann, L and Rahn, T and Busch, K and Fraune, S and Pita, L and Hentschel, U}, title = {Stability of a dominant sponge-symbiont in spite of antibiotic-induced microbiome disturbance.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6392-6410}, doi = {10.1111/1462-2920.16249}, pmid = {36250983}, issn = {1462-2920}, mesh = {Animals ; *Porifera/microbiology ; Dysbiosis ; Anti-Bacterial Agents ; *Microbiota/genetics ; Symbiosis ; *Rhodobacteraceae/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Marine sponges are known for their complex and stable microbiomes. However, the lack of a gnotobiotic sponge-model and experimental methods to manipulate both the host and the microbial symbionts currently limit our mechanistic understanding of sponge-microbial symbioses. We have used the North Atlantic sponge species Halichondria panicea to evaluate the use of antibiotics to generate gnotobiotic sponges. We further asked whether the microbiome can be reestablished via recolonization with the natural microbiome. Experiments were performed in marine gnotobiotic facilities equipped with a custom-made, sterile, flow-through aquarium system. Bacterial abundance dynamics were monitored qualitatively and quantitatively by 16 S rRNA gene amplicon sequencing and qPCR, respectively. Antibiotics induced dysbiosis by favouring an increase of opportunistic, antibiotic-resistant bacteria, resulting in more complex, but less specific bacteria-bacteria interactions than in untreated sponges. The abundance of the dominant symbiont, Candidatus Halichondribacter symbioticus, remained overall unchanged, reflecting its obligately symbiotic nature. Recolonization with the natural microbiome could not reverse antibiotic-induced dysbiosis. However, single bacterial taxa that were transferred, successfully recolonized the sponge and affected bacteria-bacteria interactions. By experimentally manipulating microbiome composition, we could show the stability of a sponge-symbiont clade despite microbiome dysbiosis. This study contributes to understanding both host-bacteria and bacteria-bacteria interactions in the sponge holobiont.}, }
@article {pmid36246452, year = {2022}, author = {Iglesias-Carrasco, M and Tobias, JA and Duchêne, DA}, title = {Bird lineages colonizing urban habitats have diversified at high rates across deep time.}, journal = {Global ecology and biogeography : a journal of macroecology}, volume = {31}, number = {9}, pages = {1784-1793}, pmid = {36246452}, issn = {1466-822X}, abstract = {AIM: Urbanization exposes species to novel ecological conditions. Some species thrive in urban areas, whereas many others are excluded from these human-made environments. Previous analyses suggest that the ability to cope with rapid environmental change is associated with long-term patterns of diversification, but whether the suite of traits associated with the ability to colonize urban environments is linked to this process remains poorly understood.<br><br>LOCATION: World.<br><br>TIME PERIOD: Current.<br><br>MAJOR TAXA STUDIED: Passerine birds.<br><br>METHODS: We applied macroevolutionary models to a large dataset of passerine birds to compare the evolutionary history of urban-tolerant species with that of urban-avoidant species. Specifically, we examined models of state-dependent speciation and extinction to assess the macroevolution of urban tolerance as a binary trait, in addition to models of quantitative trait-dependent diversification based on relative urban abundance. We also ran simulation-based model assessments to explore potential sources of bias.<br><br>RESULTS: We provide evidence that historically, species with traits promoting urban colonization have undergone faster diversification than urban-avoidant species, indicating that urbanization favours clades with a historical tendency towards rapid speciation or reduced extinction. In addition, we find that past transitions towards states that currently impede urban colonization by passerines have been more frequent than in the opposite direction. Furthermore, we find a portion of urban-avoidant passerines to be recent and to undergo fast diversification. All highly supported models give this result consistently.<br><br>MAIN CONCLUSIONS: Urbanization is mainly associated with the loss of lineages that are inherently more vulnerable to extinction over deep time, whereas cities tend to be colonized by less vulnerable lineages, for which urbanization might be neutral or positive in terms of longer-term diversification. Urban avoidance is associated with high rates of recent diversification for some clades occurring in regions with relatively intact natural ecosystems and low current levels of urbanization.}, }
@article {pmid36232445, year = {2022}, author = {Han, T and Liao, X and Zhu, Y and Liu, Y and Lu, N and Li, Y and Guo, Z and Chen, JY and He, C and Lu, Z}, title = {Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circadian Genes.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232445}, issn = {1422-0067}, mesh = {ARNTL Transcription Factors/genetics ; Animals ; *Anthozoa/genetics ; *Dinoflagellida/genetics ; Phylogeny ; Symbiosis/genetics ; Transcriptome ; }, abstract = {Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.}, }
@article {pmid36230966, year = {2022}, author = {Ali, H and Pei, M and Li, H and Fang, W and Mao, H and Khan, HA and Nadeem, T and Lu, G and Olsson, S}, title = {The Wheat Head Blight Pathogen Fusarium graminearum Can Recruit Collaborating Bacteria from Soil.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36230966}, issn = {2073-4409}, mesh = {Bacteria/genetics ; Fusarium ; Gentamicins ; Plant Diseases/microbiology ; *Soil ; *Triticum/microbiology ; }, abstract = {In nature, fungal endophytes often have facultative endohyphal bacteria (FEB). Can a model plant pathogenic fungus have them, and does it affect their phenotype? We constructed a growth system/microcosm to allow an F. graminearum isolate to grow through natural soil and then re-isolated it on a gentamicin-containing medium, allowing endohyphal growth of bacteria while killing other bacteria. F. graminearum PH-1 labelled with a His1mCherry gene staining the fungal nuclei fluorescent red was used to confirm the re-isolation of the fungus. Most new re-isolates contained about 10 16SrRNA genes per fungal mCherry gene determined by qPCR. The F. graminearum + FEB holobiont isolates containing the bacteria were sub-cultured several times, and their bacterial contents were stable. Sequencing the bacterial 16SrRNA gene from several Fg-FEB holobiont isolates revealed endophytic bacteria known to be capable of nitrogen fixation. We tested the pathogenicity of one common Fg-FEB holobiont association, F. graminearum + Stenatrophomonas maltophilia, and found increased pathogenicity. The 16SrRNA gene load per fungal His1mCherry gene inside the wheat stayed the same as previously found in vitro. Finally, strong evidence was found for Fg-S. maltophilia symbiotic nitrogen fixation benefitting the fungus.}, }
@article {pmid36209500, year = {2023}, author = {Armengaud, J}, title = {Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {115-125}, pmid = {36209500}, issn = {1462-2920}, mesh = {*Proteomics/methods ; *Microbiota ; Biotechnology ; Proteome ; }, abstract = {In the medical, environmental, and biotechnological fields, microbial communities have attracted much attention due to their roles and numerous possible applications. The study of these communities is challenging due to their diversity and complexity. Innovative methods are needed to identify the taxonomic components of individual microbiota, their changes over time, and to determine how microoorganisms interact and function. Metaproteomics is based on the identification and quantification of proteins, and can potentially provide this full picture. Due to the wide molecular panorama and functional insights it provides, metaproteomics is gaining momentum in microbiome and holobiont research. Its full potential should be unleashed in the coming years with progress in speed and cost of analyses. In this exploratory crystal ball exercise, I discuss the technical and conceptual advances in metaproteomics that I expect to drive innovative research over the next few years in microbiology. I also debate the concepts of 'microbial dark matter' and 'Metaproteomics-Assembled Proteomes (MAPs)' and present some long-term prospects for metaproteomics in clinical diagnostics and personalized medicine, environmental monitoring, agriculture, and biotechnology.}, }
@article {pmid36209397, year = {2023}, author = {van Oppen, MJH and Raina, JB}, title = {Coral holobiont research needs spatial analyses at the microbial scale.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {179-183}, pmid = {36209397}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Bacteria/genetics ; Spatial Analysis ; Symbiosis ; }, }
@article {pmid36204199, year = {2022}, author = {Marco, S and Loredana, M and Riccardo, V and Raffaella, B and Walter, C and Luca, N}, title = {Microbe-assisted crop improvement: a sustainable weapon to restore holobiont functionality and resilience.}, journal = {Horticulture research}, volume = {9}, number = {}, pages = {uhac160}, pmid = {36204199}, issn = {2662-6810}, abstract = {In the past years, breeding programs have been mainly addressed on pushing the commercial features, forgetting important traits, such as those related to environmental stress resilience, that are instead present in wild relatives. Among the traits neglected by breeding processes, the ability to recruit beneficial microorganisms that recently is receiving a growing attention due to its potentiality. In this context, this review will provide a spotlight on critical issues of the anthropocentric point of view that, until now, has characterized the selection of elite plant genotypes. Its effects on the plant-microbiome interactions, and the possibility to develop novel strategies mediated by the exploitation of beneficial root-microbe interactions, will be discussed. More sustainable microbial-assisted strategies might in fact foster the green revolution and the achievement of a more sustainable agriculture in a climatic change scenario.}, }
@article {pmid36195213, year = {2023}, author = {Connor, KL and Bloise, E and DeSantis, TZ and Lye, SJ}, title = {Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity.}, journal = {The Journal of nutritional biochemistry}, volume = {111}, number = {}, pages = {109172}, doi = {10.1016/j.jnutbio.2022.109172}, pmid = {36195213}, issn = {1873-4847}, support = {MOP-81238//CIHR/Canada ; FDN-143262//CIHR/Canada ; }, mesh = {Animals ; Female ; Mice ; Pregnancy ; ATP Binding Cassette Transporter, Subfamily G, Member 2 ; Biomarkers ; *Malnutrition/metabolism ; Maternal Nutritional Physiological Phenomena ; *Neoplasm Proteins/metabolism ; RNA, Messenger ; }, abstract = {Malnutrition can influence maternal physiology and programme offspring development. Yet, in pregnancy, little is known about how dietary challenges that influence maternal phenotype affect gut structure and function. Emerging evidence suggests that interactions between the environment, multidrug resistance (MDR) transporters and microbes may influence maternal adaptation to pregnancy and regulate fetoplacental development. We hypothesized that the gut holobiont (host and microbes) during pregnancy adapts differently to suboptimal maternal diets, evidenced by changes in the gut microenvironment, morphology, and expression of key protective MDR transporters during pregnancy. Mice were fed a control diet (CON) during pregnancy, or undernourished (UN) by 30% of control intake from gestational day (GD) 5.5-18.5, or fed 60% high fat diet (HF) for 8 weeks before and during pregnancy. At GD18.5, maternal small intestinal (SI) architecture (H&amp;E), proliferation (Ki67), P-glycoprotein (P-gp - encoded by Abcb1a/b) and breast cancer resistance protein (BCRP/Abcg2) MDR transporter expression and levels of pro-inflammatory biomarkers were assessed. Circulating inflammatory biomarkers and maternal caecal microbiome composition (G3 PhyloChip[TM]) were measured. MDR transporter expression was also assessed in fetal gut. HF diet increased maternal SI crypt depth and proinflammatory load, and decreased SI expression of Abcb1a mRNA, whilst UN increased SI villi proliferation and Abcb1a, but decreased Abcg2, mRNA expression. There were significant associations between Abcb1a and Abcg2 mRNA levels with relative abundance of specific microbial taxa. Using a systems physiology approach we report that common nutritional adversities provoke adaptations in the pregnancy holobiont in mice, and reveal new mechanisms that could influence reproductive outcomes and fetal development.}, }
@article {pmid36183766, year = {2023}, author = {Nalley, EM and Tuttle, LJ and Conklin, EE and Barkman, AL and Wulstein, DM and Schmidbauer, MC and Donahue, MJ}, title = {A systematic review and meta-analysis of the direct effects of nutrients on corals.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159093}, doi = {10.1016/j.scitotenv.2022.159093}, pmid = {36183766}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll A ; Coral Reefs ; Nitrogen/pharmacology ; Nutrients ; }, abstract = {Chronic exposure of coral reefs to elevated nutrient conditions can modify the performance of the coral holobiont and shift the competitive interactions of reef organisms. Many studies have now quantified the links between nutrients and coral performance, but few have translated these studies to directly address coastal water quality standards. To address this management need, we conducted a systematic review of peer-reviewed studies, public reports, and gray literature that examined the impacts of dissolved inorganic nitrogen (DIN: nitrate, nitrite, and ammonium) and dissolved inorganic phosphorus (DIP: phosphate) on scleractinian corals. The systematic review resulted in 47 studies with comparable data on coral holobiont responses to nutrients: symbiont density, chlorophyll a (chl-a) concentration, photosynthesis, photosynthetic efficiency, growth, calcification, adult survival, juvenile survival, and fertilization. Mixed-effects meta-regression meta-analyses were used to determine the magnitude of the positive or negative effects of DIN and DIP on coral responses. Zooxanthellae density (DIN &amp; DIP), chl-a concentration (DIN), photosynthetic rate (DIN), and growth (DIP) all exhibited positive responses to nutrient addition; maximum quantum yield (DIP), growth (DIN), larval survival (DIN), and fertilization (DIN) exhibited negative responses. In lieu of developing specific thresholds for the management of nutrients as a stressor on coral reefs, we highlight important inflection points in the magnitude and direction of the effects of inorganic nutrients and identify trends among coral responses. The responses of corals to nutrients are complex, warranting conservative guidelines for elevated nutrient concentrations on coral reefs.}, }
@article {pmid36175840, year = {2022}, author = {Campana, S and Riesgo, A and Jongepier, E and Fuss, J and Muyzer, G and de Goeij, JM}, title = {Meta-transcriptomic comparison of two sponge holobionts feeding on coral- and macroalgal-dissolved organic matter.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {674}, pmid = {36175840}, issn = {1471-2164}, mesh = {Amino Acids ; Animals ; *Anthozoa/genetics ; Coral Reefs ; Dissolved Organic Matter ; Lipids ; *Microbiota ; *Porifera/genetics ; Transcriptome ; }, abstract = {BACKGROUND: Sponge holobionts (i.e., the host and its associated microbiota) play a key role in the cycling of dissolved organic matter (DOM) in marine ecosystems. On coral reefs, an ecological shift from coral-dominated to algal-dominated ecosystems is currently occurring. Given that benthic corals and macroalgae release different types of DOM, in different abundances and with different bioavailability to sponge holobionts, it is important to understand how the metabolic activity of the host and associated microbiota change in response to the exposure to both DOM sources. Here, we look at the differential gene expression of two sponge holobionts 6 hours after feeding on naturally sourced coral- and macroalgal-DOM using RNA sequencing and meta-transcriptomic analysis.<br><br>RESULTS: We found a slight, but significant differential gene expression in the comparison between the coral- and macroalgal-DOM treatments in both the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Haliclona vansoesti. In the hosts, processes that regulate immune response, signal transduction, and metabolic pathways related to cell proliferation were elicited. In the associated microbiota carbohydrate metabolism was upregulated in both treatments, but coral-DOM induced further lipid and amino acids biosynthesis, while macroalgal-DOM caused a stress response. These differences could be driven by the presence of distinct organic macronutrients in the two DOM sources and of small pathogens or bacterial virulence factors in the macroalgal-DOM.<br><br>CONCLUSIONS: This work provides two new sponge meta-transcriptomes and a database of putative genes and genetic pathways that are involved in the differential processing of coral- versus macroalgal-DOM as food source to sponges with high and low abundances of associated microbes. These pathways include carbohydrate metabolism, signaling pathways, and immune responses. However, the differences in the meta-transcriptomic responses of the sponge holobionts after 6&#x2009;hours of feeding on the two DOM sources were small. Longer-term responses to both DOM sources should be assessed to evaluate how the metabolism and the ecological function of sponges will be affected when reefs shift from coral towards algal dominance.}, }
@article {pmid36172550, year = {2022}, author = {Wu, D and Yang, L and Gu, J and Tarkowska, D and Deng, X and Gan, Q and Zhou, W and Strnad, M and Lu, Y}, title = {A Functional Genomics View of Gibberellin Metabolism in the Cnidarian Symbiont Breviolum minutum.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {927200}, pmid = {36172550}, issn = {1664-462X}, abstract = {Dinoflagellate inhabitants of the reef-building corals exchange nutrients and signals with host cells, which often benefit the growth of both partners. Phytohormones serve as central hubs for signal integration between symbiotic microbes and their hosts, allowing appropriate modulation of plant growth and defense in response to various stresses. However, the presence and function of phytohormones in photosynthetic dinoflagellates and their function in the holobionts remain elusive. We hypothesized that endosymbiotic dinoflagellates may produce and employ phytohormones for stress responses. Using the endosymbiont of reef corals Breviolum minutum as model, this study aims to exam whether the alga employ analogous signaling systems by an integrated multiomics approach. We show that key gibberellin (GA) biosynthetic genes are widely present in the genomes of the selected dinoflagellate algae. The non-13-hydroxylation pathway is the predominant route for GA biosynthesis and the multifunctional GA dioxygenase in B. minutum has distinct substrate preference from high plants. GA biosynthesis is modulated by the investigated bleaching-stimulating stresses at both transcriptional and metabolic levels and the exogenously applied GAs improve the thermal tolerance of the dinoflagellate. Our results demonstrate the innate ability of a selected Symbiodiniaceae to produce the important phytohormone and the active involvement of GAs in the coordination and the integration of the stress response.}, }
@article {pmid36171216, year = {2022}, author = {Sardar, P and Šustr, V and Chroňáková, A and Lorenc, F and Faktorová, L}, title = {De novo metatranscriptomic exploration of gene function in the millipede holobiont.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16173}, pmid = {36171216}, issn = {2045-2322}, mesh = {Amino Acids, Essential ; Animals ; *Arthropods/genetics ; Bacteroidetes ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.}, }
@article {pmid36161195, year = {2022}, author = {Verma, NK and Tan, SJ and Chen, J and Chen, H and Ismail, MH and Rice, SA and Bifani, P and Hariharan, S and Paul, VD and Sriram, B and Dam, LC and Chan, CC and Ho, P and Goh, BC and Chung, SJ and Goh, KCM and Thong, SH and Kwa, AL and Ostrowski, A and Aung, TT and Razali, H and Low, SWY and Bhattacharyya, MS and Gautam, HK and Lakshminarayanan, R and Sicheritz-Pontén, T and Clokie, MRJ and Moreira, W and van Steensel, MAM}, title = {inPhocus: Current State and Challenges of Phage Research in Singapore.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {1}, pages = {6-11}, pmid = {36161195}, issn = {2641-6549}, abstract = {Bacteriophages and phage-derived proteins are a promising class of antibacterial agents that experience a growing worldwide interest. To map ongoing phage research in Singapore and neighboring countries, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore (NTU) and Yong Loo Lin School of Medicine, National University of Singapore (NUS) recently co-organized a virtual symposium on Bacteriophage and Bacteriophage-Derived Technologies, which was attended by more than 80 participants. Topics were discussed relating to phage life cycles, diversity, the roles of phages in biofilms and the human gut microbiome, engineered phage lysins to combat polymicrobial infections in wounds, and the challenges and prospects of clinical phage therapy. This perspective summarizes major points discussed during the symposium and new perceptions that emerged after the panel discussion.}, }
@article {pmid36160957, year = {2022}, author = {Nie, Y and Lau, SYL and Tan, X and Lu, X and Liu, S and Tahvanainen, T and Isoda, R and Ye, Q and Hashidoko, Y}, title = {Sphagnum capillifolium holobiont from a subarctic palsa bog aggravates the potential of nitrous oxide emissions.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {974251}, pmid = {36160957}, issn = {1664-462X}, abstract = {Melting permafrost mounds in subarctic palsa mires are thawing under climate warming and have become a substantial source of N2O emissions. However, mechanistic insights into the permafrost thaw-induced N2O emissions in these unique habitats remain elusive. We demonstrated that N2O emission potential in palsa bogs was driven by the bacterial residents of two dominant Sphagnum mosses especially of Sphagnum capillifolium (SC) in the subarctic palsa bog, which responded to endogenous and exogenous Sphagnum factors such as secondary metabolites, nitrogen and carbon sources, temperature, and pH. SC's high N2O emission activity was linked with two classes of distinctive hyperactive N2O emitters, including Pseudomonas sp. and Enterobacteriaceae bacteria, whose hyperactive N2O emitting capability was characterized to be dominantly pH-responsive. As the nosZ gene-harboring emitter, Pseudomonas sp. SC-H2 reached a high level of N2O emissions that increased significantly with increasing pH. For emitters lacking the nosZ gene, an Enterobacteriaceae bacterium SC-L1 was more adaptive to natural acidic conditions, and N2O emissions also increased with pH. Our study revealed previously unknown hyperactive N2O emitters in Sphagnum capillifolium found in melting palsa mound environments, and provided novel insights into SC-associated N2O emissions.}, }
@article {pmid36159890, year = {2021}, author = {Shen, A and Millard, A}, title = {Phage Genome Annotation: Where to Begin and End.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {2}, number = {4}, pages = {183-193}, pmid = {36159890}, issn = {2641-6549}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {With the renewed interest in phage research, coupled with the rising accessibility to affordable sequencing, ever increasing numbers of phage genomes are being sequenced. Therefore, there is an increased need to assemble and annotate phage genomes. There is a plethora of tools and platforms that allow phage genomes to be assembled and annotated. The choice of tools can often be bewildering for those new to phage genome assembly. Here we provide an overview of the assembly and annotation process from obtaining raw reads to genome submission, with worked examples, providing those new to genome assembly and annotation with a guided pathway to genome submission. We focus on the use of open access tools that can be incorporated into workflows to allow easy repetition of steps, highlighting multiple tools that can be used and common pitfalls that may occur.}, }
@article {pmid36157287, year = {2022}, author = {Clokie, MRJ and Sicheritz-Pontén, TE}, title = {Phage Therapy: Insights from the Past, the Great Need of the Present, and Glimpses into the Future.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {2}, pages = {65-66}, doi = {10.1089/phage.2022.29031.mcl}, pmid = {36157287}, issn = {2641-6549}, }
@article {pmid36148301, year = {2022}, author = {Tous, N and Marcos, S and Goodarzi Boroojeni, F and Pérez de Rozas, A and Zentek, J and Estonba, A and Sandvang, D and Gilbert, MTP and Esteve-Garcia, E and Finn, R and Alberdi, A and Tarradas, J}, title = {Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {884925}, pmid = {36148301}, issn = {1664-042X}, abstract = {Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.}, }
@article {pmid36147515, year = {2021}, author = {Rangel-Pineros, G and Millard, A and Michniewski, S and Scanlan, D and Sirén, K and Reyes, A and Petersen, B and Clokie, MRJ and Sicheritz-Pontén, T}, title = {From Trees to Clouds: PhageClouds for Fast Comparison of ∼640,000 Phage Genomic Sequences and Host-Centric Visualization Using Genomic Network Graphs.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {2}, number = {4}, pages = {194-203}, pmid = {36147515}, issn = {2641-6549}, abstract = {Background: Fast and computationally efficient strategies are required to explore genomic relationships within an increasingly large and diverse phage sequence space. Here, we present PhageClouds, a novel approach using a graph database of phage genomic sequences and their intergenomic distances to explore the phage genomic sequence space. Methods: A total of 640,000 phage genomic sequences were retrieved from a variety of databases and public virome assemblies. Intergenomic distances were calculated with dashing, an alignment-free method suitable for handling massive data sets. These data were used to build a Neo4j[®] graph database. Results: PhageClouds supported the search of related phages among all complete phage genomes from GenBank for a single query phage in just 10 s. Moreover, PhageClouds expanded the number of closely related phage sequences detected for both finished and draft phage genomes, in comparison with searches exclusively targeting phage entries from GenBank. Conclusions: PhageClouds is a novel resource that will facilitate the analysis of phage genomic sequences and the characterization of assembled phage genomes.}, }
@article {pmid36144461, year = {2022}, author = {Miral, A and Kautsky, A and Alves-Carvalho, S and Cottret, L and Guillerm-Erckelboudt, AY and Buguet, M and Rouaud, I and Tranchimand, S and Tomasi, S and Bartoli, C}, title = {Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144461}, issn = {2076-2607}, support = {ECOSYMB//National Research Institute for Agriculture, Food and Environment/ ; D&#xe9;fi Scientifique 2022//University of Rennes 1/ ; }, abstract = {As rock inhabitants, lichens are exposed to extreme and fluctuating abiotic conditions associated with poor sources of nutriments. These extreme conditions confer to lichens the unique ability to develop protective mechanisms. Consequently, lichen-associated microbes disclose highly versatile lifestyles and ecological plasticity, enabling them to withstand extreme environments. Because of their ability to grow in poor and extreme habitats, bacteria associated with lichens can tolerate a wide range of pollutants, and they are known to produce antimicrobial compounds. In addition, lichen-associated bacteria have been described to harbor ecological functions crucial for the evolution of the lichen holobiont. Nevertheless, the ecological features of lichen-associated microbes are still underestimated. To explore the untapped ecological diversity of lichen-associated bacteria, we adopted a novel culturomic approach on the crustose lichen Rhizocarpon geographicum. We sampled R. geographicum in French habitats exposed to oil spills, and we combined nine culturing methods with 16S rRNA sequencing to capture the greatest bacterial diversity. A deep functional analysis of the lichen-associated bacterial collection showed the presence of a set of bacterial strains resistant to a wide range of antibiotics and displaying tolerance to Persistent Organic Pollutants (POPs). Our study is a starting point to explore the ecological features of the lichen microbiota.}, }
@article {pmid36138466, year = {2022}, author = {Keller-Costa, T and Kozma, L and Silva, SG and Toscan, R and Gonçalves, J and Lago-Lestón, A and Kyrpides, NC and Nunes da Rocha, U and Costa, R}, title = {Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {151}, pmid = {36138466}, issn = {2049-2618}, mesh = {Animals ; Ankyrins ; *Anthozoa/microbiology ; Chitin ; *Chitinases ; *Gammaproteobacteria ; Metagenomics/methods ; *Microbiota/genetics ; Oxygen ; Phylogeny ; Protein Serine-Threonine Kinases ; *Rhodobacteraceae ; Symbiosis ; }, abstract = {BACKGROUND: The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater.<br><br>RESULTS: Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity.<br><br>CONCLUSION: This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.}, }
@article {pmid36136562, year = {2022}, author = {Favero, C and Giordano, L and Mihaila, SM and Masereeuw, R and Ortiz, A and Sanchez-Niño, MD}, title = {Postbiotics and Kidney Disease.}, journal = {Toxins}, volume = {14}, number = {9}, pages = {}, pmid = {36136562}, issn = {2072-6651}, support = {860329 Marie-Curie ITN "STRATEGY-CKD"/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Humans ; *Kidney Diseases/etiology/therapy ; Prebiotics ; *Probiotics/therapeutic use ; *Synbiotics ; gamma-Aminobutyric Acid ; }, abstract = {Chronic kidney disease (CKD) is projected to become the fifth global cause of death by 2040 as a result of key shortcomings in the current methods available to diagnose and treat kidney diseases. In this regard, the novel holobiont concept, used to describe an individual host and its microbial community, may pave the way towards a better understanding of kidney disease pathogenesis and progression. Microbiota-modulating or -derived interventions include probiotics, prebiotics, synbiotics and postbiotics. As of 2019, the concept of postbiotics was updated by the International Scientific Association of Probiotics and Prebiotics (ISAPP) to refer to preparations of inanimate microorganisms and/or their components that confer a health benefit to the host. By explicitly excluding purified metabolites without a cellular biomass, any literature making use of such term is potentially rendered obsolete. We now review the revised concept of postbiotics concerning their potential clinical applications and research in kidney disease, by discussing in detail several formulations that are undergoing preclinical development such as GABA-salt for diet-induced hypertension and kidney injury, sonicated Lactobacillus paracasei in high fat diet-induced kidney injury, GABA-salt, lacto-GABA-salt and postbiotic-GABA-salt in acute kidney injury, and O. formigenes lysates for hyperoxaluria. Furthermore, we provide a roadmap for postbiotics research in kidney disease to expedite clinical translation.}, }
@article {pmid36135762, year = {2022}, author = {Ghotbi, M and Kelting, O and Blümel, M and Tasdemir, D}, title = {Gut and Gill-Associated Microbiota of the Flatfish European Plaice (Pleuronectes platessa): Diversity, Metabolome and Bioactivity against Human and Aquaculture Pathogens.}, journal = {Marine drugs}, volume = {20}, number = {9}, pages = {}, pmid = {36135762}, issn = {1660-3397}, mesh = {Animals ; Aquaculture ; Fishes ; *Flounder ; Gills ; Humans ; Metabolome ; *Methicillin-Resistant Staphylococcus aureus ; *Microbiota ; }, abstract = {Similar to other marine holobionts, fish are colonized by complex microbial communities that promote their health and growth. Fish-associated microbiota is emerging as a promising source of bioactive metabolites. Pleuronectes platessa (European plaice, plaice), a flatfish with commercial importance, is common in the Baltic Sea. Here we used a culture-dependent survey followed by molecular identification to identify microbiota associated with the gills and the gastrointestinal tract (GIT) of P. platessa, then profiled their antimicrobial activity and metabolome. Altogether, 66 strains (59 bacteria and 7 fungi) were isolated, with Proteobacteria being the most abundant phylum. Gill-associated microbiota accounted for higher number of isolates and was dominated by the Proteobacteria (family Moraxellaceae) and Actinobacteria (family Nocardiaceae), whereas Gram-negative bacterial families Vibrionaceae and Shewanellaceae represented the largest group associated with the GIT. The EtOAc extracts of the solid and liquid media cultures of 21 bacteria and 2 fungi representing the diversity of cultivable plaice-associated microbiota was profiled for their antimicrobial activity against three fish pathogens, human bacterial pathogen panel (ESKAPE) and two human fungal pathogens. More than half of all tested microorganisms, particularly those originating from the GIT epithelium, exhibited antagonistic effect against fish pathogens (Lactococcus garvieae, Vibrio ichthyoenteri) and/or human pathogens (Enterococcus faecium, methicillin-resistant Staphylococcus aureus). Proteobacteria represented the most active isolates. Notably, the solid media extracts displayed higher activity against fish pathogens, while liquid culture extracts were more active against human pathogens. Untargeted metabolomics approach using feature-based molecular networking showed the high chemical diversity of the liquid extracts that contained undescribed clusters. This study highlights plaice-associated microbiota as a potential source of antimicrobials for the control of human and the aquaculture-associated infections. This is the first study reporting diversity, bioactivity and chemical profile of culture-dependent microbiota of plaice.}, }
@article {pmid36133177, year = {2022}, author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H}, title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.}, journal = {Access microbiology}, volume = {4}, number = {8}, pages = {acmi000405}, pmid = {36133177}, issn = {2516-8290}, abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.}, }
@article {pmid36128640, year = {2022}, author = {Perera, IU and Fujiyoshi, S and Nishiuchi, Y and Nakai, T and Maruyama, F}, title = {Zooplankton act as cruise ships promoting the survival and pathogenicity of pathogenic bacteria.}, journal = {Microbiology and immunology}, volume = {66}, number = {12}, pages = {564-578}, pmid = {36128640}, issn = {1348-0421}, support = {18K19674//Japan Society for the Promotion of Science/ ; 18KK0436//Japan Society for the Promotion of Science/ ; 20H00562//Japan Society for the Promotion of Science/ ; 20K18903//Japan Society for the Promotion of Science/ ; //Career Advancement Project (CAP) Researcher program at Hiroshima University/ ; JPMJSA1705//Science and Technology Research Partnership for Sustainable Development/ ; 20wm0225012h0001//Japan Agency for Medical Research and Development/ ; 21fk0108129h0502//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; Humans ; *Zooplankton ; *Ecosystem ; Bacteria ; }, abstract = {Bacteria in general interact with zooplankton in aquatic ecosystems. These zooplankton-bacterial interactions help to shape the bacterial community by regulating bacterial abundances. Such interactions are even more significant and crucially in need of investigation in the case of pathogenic bacteria, which cause severe diseases in humans and animals. Among the many associations between a host metazoan and pathogenic bacteria, zooplankton provide nutrition and protection from stressful conditions, promote the horizontal transfer of virulence genes, and act as a mode of pathogen transport. These interactions allow the pathogen to survive and proliferate in aquatic environments and to endure water treatment processes, thereby creating a potential risk to human health. This review highlights current knowledge on the contributions of zooplankton to the survival and pathogenicity of pathogenic bacteria. We also discuss the need to consider these interactions as a risk factor in water treatment processes.}, }
@article {pmid36127636, year = {2022}, author = {Sun, X and Ciucani, MM and Rasmussen, JA and Gilbert, MTP and Sinding, MS}, title = {Genomic evidence refutes the hypothesis that the Bornean banteng is a distinct species.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {110}, pmid = {36127636}, issn = {2730-7182}, mesh = {Animals ; Asia, Southeastern ; Borneo ; Cattle ; *Genome, Mitochondrial/genetics ; *Genomics ; }, abstract = {The banteng (Bos javanicus) is an endangered species within the wild Asian Bos complex, that has traditionally been subdivided into three geographically isolated subspecies based on (i) mainland Southeast Asia (B. j. birmanicus), (ii) Java (B. j. javanicus), and (iii) Borneo (B. j. lowi). However, analysis of a single Bornean banteng mitochondrial genome generated through a genome skimming approach was used to suggest that it may actually represent a distinct species (Ishige et al. in Mitochondrial DNA A DNA Mapp Seq Anal 27(4):2453-4. http://doi.org/10.3109/19401736.2015.1033694 , 2016). To explore this hypothesis further, we leveraged on the GenBank (NCBI) raw read sequencing data originally used to construct the mitochondrial genome and reconstructed its nuclear genome at low (0.2×) coverage. When analysed in the context of nuclear genomic data representing a broad reference panel of Asian Bos species, we find the Bornean banteng affiliates strongly with the Javan banteng, in contradiction to the expectation if the separate species hypothesis was correct. Thus, despite the Bornean banteng's unusual mitochondrial lineage, we argue there is no genomic evidence that the Bornean banteng is a distinct species.}, }
@article {pmid36127241, year = {2023}, author = {Arnault, G and Mony, C and Vandenkoornhuyse, P}, title = {Plant microbiota dysbiosis and the Anna Karenina Principle.}, journal = {Trends in plant science}, volume = {28}, number = {1}, pages = {18-30}, doi = {10.1016/j.tplants.2022.08.012}, pmid = {36127241}, issn = {1878-4372}, mesh = {*Dysbiosis ; *Microbiota ; Plants ; }, abstract = {Microorganisms are associated with all plants, recently leading to the hologenome concept. We reviewed the assembly processes of plant microbiota and analyzed its structure during the emergence of dysbioses. In particular, we discussed the Anna Karenina Principle (AKP) based on Leo Tolstoy's assertion applied to plant microbiota: 'All healthy microbiota are alike; each disease-associated microbiota is sick in its own way.' We propose the AKP to explain how stochastic processes in plant microbiota assembly due to several external stressors could lead to plant diseases. Finally, we propose the AKP to conceptualize plant dysbioses as a transitory loss of host capacity to regulate its microbiota, implying a loss of function that leads to a reduction of the host's fitness.}, }
@article {pmid36125280, year = {2022}, author = {Martinez, S and Grover, R and Baker, DM and Ferrier-Pagès, C}, title = {Symbiodiniaceae Are the First Site of Heterotrophic Nitrogen Assimilation in Reef-Building Corals.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0160122}, pmid = {36125280}, issn = {2150-7511}, mesh = {Animals ; *Anthozoa/metabolism ; Heterotrophic Processes ; Nitrogen/metabolism ; *Dinoflagellida ; Symbiosis ; *Ammonium Compounds/metabolism ; Amino Acids/metabolism ; }, abstract = {Coral reefs depend on the highly optimized mutualistic relationship between corals and Symbiodiniaceae dinoflagellates. Both partners exchange nutrients obtained through heterotrophy of the host and autotrophy of the symbionts. While heterotrophy helps corals withstand the harmful effects of seawater warming, the exchange of heterotrophic nutrients between the two partners is poorly understood. Here, we used compound-specific δ[15]N and δ[13]C of amino acids (δ[15]NAA and δ[13]CAA) and a [15]N pulse-chase experiment with Artemia salina nauplii in two coral-dinoflagellate associations to trace the assimilation and allocation of heterotrophic nutrients within the partners. We observed that changes in the trophic position (TPGlx-Phe), δ[15]NAA, and δ[13]CAA with heterotrophy were holobiont-dependent. Furthermore, while TPGlx-Phe and δ[15]N of all AAs significantly increased with heterotrophy in the symbionts and host of Stylophora pistillata, only the δ[15]NAA of the symbionts changed in Turbinaria reniformis. Together with the pulse-chase experiment, the results suggested a direct transfer of heterotrophically acquired AAs to the symbionts of S. pistillata and a transfer of ammonium to the symbionts of T. reniformis. Overall, we demonstrated that heterotrophy underpinned the nutrition of Symbiodinaceae and possibly influenced their stress tolerance under changing environmental conditions. IMPORTANCE Coral reefs rely upon the highly optimized nutritional symbiosis between corals and Symbiodiniaceae dinoflagellates. Heterotrophic feeding on plankton is key to the resistance of corals to environmental stress. Yet, a detailed understanding of heterotrophic nutrient assimilation and utilization within the symbiosis is lacking. Here, we used the advanced tools of compound-specific isotope analysis of amino acids and [15]N-labeling of plankton to show that heterotrophy underpinned the nutrition of Symbiodinaceae. Symbionts received either heterotrophically acquired amino acids or recycled ammonium due to their association with the coral host. This study brought new insight into the nutrient exchanges in coral-Symbiodiniaceae associations and allowed a better understanding of the mechanisms involved in coral resistance to environmental stress.}, }
@article {pmid36124627, year = {2022}, author = {Drummond, JS and Rosado, BHP}, title = {On the role of the phyllosphere community in leaf wettability and water shedding.}, journal = {Journal of experimental botany}, volume = {73}, number = {22}, pages = {7204-7207}, doi = {10.1093/jxb/erac350}, pmid = {36124627}, issn = {1460-2431}, mesh = {*Water ; *Plant Leaves ; }, }
@article {pmid36115215, year = {2022}, author = {Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Neves, RC and Jørgensen, A and Schiøtt, M and Gilbert, MTP and Møbjerg, N}, title = {Corrigendum to "Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription" [Comparative Biochemistry and Physiology Part A: Molecular &amp; Integrative Physiology 271 (2022), 111245].}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {274}, number = {}, pages = {111317}, doi = {10.1016/j.cbpa.2022.111317}, pmid = {36115215}, issn = {1531-4332}, }
@article {pmid36115214, year = {2022}, author = {Neves, RC and Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Gilbert, MTP and Møbjerg, N}, title = {Corrigendum to "Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome" [Comparative Biochemistry and Physiology Part A: Molecular &amp; Integrative Physiology 267 (2022), 111169].}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {274}, number = {}, pages = {111316}, doi = {10.1016/j.cbpa.2022.111316}, pmid = {36115214}, issn = {1531-4332}, }
@article {pmid36112690, year = {2022}, author = {Rinsky, M and Weizman, E and Ben-Asher, HW and Eyal, G and Zhu, B and Levy, O}, title = {Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis.}, journal = {Science advances}, volume = {8}, number = {37}, pages = {eabo6467}, pmid = {36112690}, issn = {2375-2548}, support = {DP2 GM140924/GM/NIGMS NIH HHS/United States ; }, abstract = {Studying chronobiology in reef-building corals is challenging due to the tightly coupled symbiosis with their photosynthetic algae, Symbiodiniaceae. Although symbiosis requires metabolic synchronization and coordination of cellular processes in the holobiont, the cross-talk between the host and symbiont's clocks is still puzzling. Here, we use the mesophotic coral Euphyllia paradivisa to examine temporal gene expression patterns in symbiotic and aposymbiotic morphs exposed to natural light/dark cycles and constant darkness. Our comparative transcriptomic analyses revealed circadian and circatidal cycles of gene expression with a predominant diel pattern in both coral morphs. We found a substantial number of transcripts consistently rhythmic under both light conditions, including genes likely involved in the cnidarians' circadian clock, thus indicating that an endogenous clock, which can oscillate independently from the Symbiodiniaceae clock, exists in E. paradivisa. The analysis further manifests the remarkable impacts of symbiosis on transcriptional rhythms and implies that the algae's presence influences the host's biorhythm.}, }
@article {pmid36110388, year = {2022}, author = {Pinacho-Guendulain, B and Montiel-Castro, AJ and Ramos-Fernández, G and Pacheco-López, G}, title = {Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates.}, journal = {Frontiers in integrative neuroscience}, volume = {16}, number = {}, pages = {876849}, pmid = {36110388}, issn = {1662-5145}, abstract = {The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.}, }
@article {pmid36100860, year = {2022}, author = {Næsborg-Nielsen, C and Eisenhofer, R and Fraser, TA and Wilkinson, V and Burridge, CP and Carver, S}, title = {Sarcoptic mange changes bacterial and fungal microbiota of bare-nosed wombats (Vombatus ursinus).}, journal = {Parasites &amp; vectors}, volume = {15}, number = {1}, pages = {323}, pmid = {36100860}, issn = {1756-3305}, support = {LP180101251//Australian Research Council Linkage Programme/ ; }, mesh = {Animals ; Goats/parasitology ; Humans ; *Marsupialia/parasitology ; *Mycobiome ; RNA, Ribosomal, 16S/genetics ; Sarcoptes scabiei/genetics ; *Scabies/parasitology ; Swine ; }, abstract = {BACKGROUND: Sarcoptes scabiei is globally distributed and one of the most impactful mammalian ectoparasites. Sarcoptic mange, caused by infection with S. scabiei, causes disruption of the epidermis and its bacterial microbiota, but its effects on host fungal microbiota and on the microbiota of marsupials in general have not been studied. Here, we (i) examine bacterial and fungal microbiota changes associated with mange in wild bare-nosed wombats (BNWs) and (ii) evaluate whether opportunistic pathogens are potentiated by S. scabiei infection in this species.<br><br>METHODS: Using Amplicon Sequencing of the 16S rRNA and ITS2 rDNA genes, we detected skin microbiota changes of the bare-nosed wombat (Vombatus ursinus). We compared the alpha and beta diversity among healthy, moderate, and severe disease states using ANOVA and PERMANOVA with nesting. Lastly, we identified taxa that differed between disease states using analysis of composition of microbes (ANCOM) testing.<br><br>RESULTS: We detected significant changes in the microbial communities and diversity with mange in BNWs. Severely affected BNWs had lower amplicon sequence variant (ASV) richness compared to that of healthy individuals, and the microbial communities were significantly different between disease states with higher relative abundance of potentially pathogenic microbial taxa in mange-affected BNWs including Staphylococcus sciuri, Corynebacterium spp., Brevibacterium spp., Brachybacterium spp., and Pseudogymnascus spp. and Debaryomyces spp.<br><br>CONCLUSION: This study represents the first investigation of microbial changes in association with sarcoptic mange in a marsupial host, as well as the first investigation of fungal microbial changes on the skin of any host suffering from sarcoptic mange. Our results are broadly consistent with bacterial microbiota changes observed in humans, pigs, canids, and Iberian ibex, suggesting the epidermal microbial impacts of mange may be generalisable across host species. We recommend that future studies investigating skin microbiota changes include both bacterial and fungal data to gain a more complete picture of the effects of sarcoptic mange.}, }
@article {pmid36100319, year = {2022}, author = {Bettenfeld, P and Cadena I Canals, J and Jacquens, L and Fernandez, O and Fontaine, F and van Schaik, E and Courty, PE and Trouvelot, S}, title = {The microbiota of the grapevine holobiont: A key component of plant health.}, journal = {Journal of advanced research}, volume = {40}, number = {}, pages = {1-15}, pmid = {36100319}, issn = {2090-1224}, mesh = {Bacteria ; Fungi ; *Microbiota ; Plant Diseases ; Plants ; }, abstract = {BACKGROUND: Grapevine is a woody, perennial plant of high economic importance worldwide. Like other plants, it lives in close association with large numbers of microorganisms. Bacteria, fungi and viruses are structured in communities, and each individual can be beneficial, neutral or harmful to the plant. In this sense, microorganisms can interact with each other and regulate plant functions (including immunity) and even provide new ones. Thus, the grapevine associated with its microbial communities constitutes a supra-organism, also called a holobiont, whose functioning is linked to established plant-microorganism interactions.<br><br>AIM OF REVIEW: The overall health of the plant may be conditioned by the diversity and structure of microbial communities. Consequently, an optimal microbial composition will consist of a microbial balance allowing the plant to be healthy. Conversely, an imbalance of microbial populations could lead to (or be generated by) a decline of the plant. The microbiome is an active component of the host also responsive to biotic and abiotic changes; in that respect, a better understanding of the most important drivers of the composition of plant microbiomes is needed.<br><br>This article presents the current state of the art about the grapevine microbiota and its composition according to the plant compartments and the influencing factors. We also focus on situations of imbalance, in particular during plant disease or decline. Finally, we discuss the possible interest of microbial engineering in an agrosystem such as viticulture.}, }
@article {pmid36099871, year = {2022}, author = {Bove, CB and Ingersoll, MV and Davies, SW}, title = {Help Me, Symbionts, You're My Only Hope: Approaches to Accelerate our Understanding of Coral Holobiont Interactions.}, journal = {Integrative and comparative biology}, volume = {62}, number = {6}, pages = {1756-1769}, doi = {10.1093/icb/icac141}, pmid = {36099871}, issn = {1557-7023}, mesh = {Animals ; *Anthozoa/genetics ; Symbiosis ; *Microbiota ; *Dinoflagellida/physiology ; Coral Reefs ; }, abstract = {Tropical corals construct the three-dimensional framework for one of the most diverse ecosystems on the planet, providing habitat to a plethora of species across taxa. However, these ecosystem engineers are facing unprecedented challenges, such as increasing disease prevalence and marine heatwaves associated with anthropogenic global change. As a result, major declines in coral cover and health are being observed across the world's oceans, often due to the breakdown of coral-associated symbioses. Here, we review the interactions between the major symbiotic partners of the coral holobiont-the cnidarian host, algae in the family Symbiodiniaceae, and the microbiome-that influence trait variation, including the molecular mechanisms that underlie symbiosis and the resulting physiological benefits of different microbial partnerships. In doing so, we highlight the current framework for the formation and maintenance of cnidarian-Symbiodiniaceae symbiosis, and the role that immunity pathways play in this relationship. We emphasize that understanding these complex interactions is challenging when you consider the vast genetic variation of the cnidarian host and algal symbiont, as well as their highly diverse microbiome, which is also an important player in coral holobiont health. Given the complex interactions between and among symbiotic partners, we propose several research directions and approaches focused on symbiosis model systems and emerging technologies that will broaden our understanding of how these partner interactions may facilitate the prediction of coral holobiont phenotype, especially under rapid environmental change.}, }
@article {pmid36059041, year = {2022}, author = {Pei, JY and Yu, WF and Zhang, JJ and Kuo, TH and Chung, HH and Hu, JJ and Hsu, CC and Yu, KF}, title = {Mass spectrometry-based metabolomic signatures of coral bleaching under thermal stress.}, journal = {Analytical and bioanalytical chemistry}, volume = {414}, number = {26}, pages = {7635-7646}, pmid = {36059041}, issn = {1618-2650}, support = {42090041//National Natural Science Foundation of China/ ; 21665003//National Natural Science Foundation of China/ ; 42030502//National Natural Science Foundation of China/ ; 2018GXNSFAA281354//Guangxi Natural Science Fund Project/ ; AD17129063//Guangxi Natural Science Fund Project/ ; AA17204074//Guangxi Natural Science Fund Project/ ; }, mesh = {Animals ; Coral Bleaching ; Betaine/metabolism ; *Anthozoa ; Mass Spectrometry ; Biomarkers/metabolism ; Amino Acids/metabolism ; *Biological Products ; Tricarboxylic Acids ; Lipids ; }, abstract = {Coral bleaching caused by climate change has resulted in large-scale coral reef decline worldwide. However, the knowledge of physiological response mechanisms of scleractinian corals under high-temperature stress is still challenging. Here, untargeted mass spectrometry-based metabolomics combining with Global Natural Product Social Molecular Networking (GNPS) was utilized to investigate the physiological response of the coral species Pavona decussata under thermal stress. A wide variety of metabolites (including lipids, fatty acids, amino acids, peptides, osmolytes) were identified as the potential biomarkers and subjected to metabolic pathway enrichment analysis. We discovered that, in the thermal-stressed P. decussata coral holobiont, (1) numerous metabolites in classes of lipids and amino acids significantly decreased, indicating an enhanced lipid hydrolysis and aminolysis that contributed to up-regulation in gluconeogenesis to meet energy demand for basic survival; (2) pantothenate and panthenol, two essential intermediates in tricarboxylic acid (TCA) cycle, were up-regulated, implying enhanced efficiency in energy production; (3) small peptides (e.g., Glu-Leu and Glu-Glu-Glu-Glu) and lyso-platelet-activating factor (lysoPAF) possibly implicated a strengthened coral immune response; (4) the down-regulation of betaine and trimethylamine N-oxide (TMAO), known as osmolyte compounds for maintaining holobiont homeostasis, might be the result of disruption of coral holobiont.}, }
@article {pmid38818306, year = {2022}, author = {Gerna, D and Clara, D and Antonielli, L and Mitter, B and Roach, T}, title = {Seed Imbibition and Metabolism Contribute Differentially to Initial Assembly of the Soybean Holobiont.}, journal = {Phytobiomes journal}, volume = {8}, number = {1}, pages = {21-33}, pmid = {38818306}, issn = {2471-2906}, abstract = {Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont's life cycle, seeds are hubs for microbial communities' assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean (Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes' richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds.}, }
@article {pmid36005488, year = {2022}, author = {Sikorskaya, TV and Ermolenko, EV and Efimova, KV and Dang, LTP}, title = {Coral Holobionts Possess Distinct Lipid Profiles That May Be Shaped by Symbiodiniaceae Taxonomy.}, journal = {Marine drugs}, volume = {20}, number = {8}, pages = {}, pmid = {36005488}, issn = {1660-3397}, support = {21-54-54002//Russian Foundation for Basic Research/ ; QTRU01.10/21-22//Vietnam Academy of Science and Technology/ ; }, mesh = {Acclimatization ; Animals ; *Anthozoa ; Complex Mixtures ; Coral Reefs ; *Dinoflagellida ; Symbiosis ; }, abstract = {Symbiotic relationships are very important for corals. Abiotic stressors cause the acclimatization of cell membranes in symbionts, which possess different membrane acclimatization strategies. Membrane stability is determined by a unique lipid composition and, thus, the profile of thylakoid lipids can depend on coral symbiont species. We have analyzed and compared thylakoid lipidomes (mono- and digalactosyldiacylglycerols (MGDG and DGDG), sulfoquinovosyldiacylglycerols (SQDG), and phosphatidylglycerols (PG)) of crude extracts from symbiotic reef-building coral Acropora sp., the hydrocoral Millepora platyphylla, and the octocoral Sinularia flexibilis. S. flexibilis crude extracts were characterized by a very high SQDG/PG ratio, a DGDG/MGDG ratio < 1, a lower degree of galactolipid unsaturation, a higher content of SQDG with polyunsaturated fatty acids, and a thinner thylakoid membrane which may be explained by the presence of thermosensitive dinoflagellates Cladocopium C3. In contrast, crude extracts of M. platyphylla and Acropora sp. exhibited the lipidome features of thermotolerant Symbiodiniaceae. M. platyphylla and Acropora sp. colonies contained Cladocopium C3u and Cladocopium C71/C71a symbionts, respectively, and their lipidome profiles showed features that indicate thermotolerance. We suggest that an association with symbionts that exhibit the thermotolerant thylakoid lipidome features, combined with a high Symbiodiniaceae diversity, may facilitate further acclimatization/adaptation of M. platyphylla and Acropora sp. holobionts in the South China Sea.}, }
@article {pmid36001672, year = {2022}, author = {Bieker, VC and Battlay, P and Petersen, B and Sun, X and Wilson, J and Brealey, JC and Bretagnolle, F and Nurkowski, K and Lee, C and Barreiro, FS and Owens, GL and Lee, JY and Kellner, FL and van Boheeman, L and Gopalakrishnan, S and Gaudeul, M and Mueller-Schaerer, H and Lommen, S and Karrer, G and Chauvel, B and Sun, Y and Kostantinovic, B and Dalén, L and Poczai, P and Rieseberg, LH and Gilbert, MTP and Hodgins, KA and Martin, MD}, title = {Uncovering the genomic basis of an extraordinary plant invasion.}, journal = {Science advances}, volume = {8}, number = {34}, pages = {eabo5115}, pmid = {36001672}, issn = {2375-2548}, mesh = {*Ambrosia/genetics ; Europe ; Genomics ; *Introduced Species ; Sequence Analysis, DNA ; }, abstract = {Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.}, }
@article {pmid35998007, year = {2022}, author = {Indraningrat, AAG and Steinert, G and Becking, LE and Mueller, B and de Goeij, JM and Smidt, H and Sipkema, D}, title = {Sponge holobionts shift their prokaryotic communities and antimicrobial activity from shallow to lower mesophotic depths.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {10}, pages = {1265-1283}, pmid = {35998007}, issn = {1572-9699}, support = {20140812021557//Indonesia Endowment Fund for Education (LPDP)/ ; 17660-1//Rufford Foundation/ ; 607786 (BluePharmTrain)//FP7 People: Marie-Curie Actions/ ; }, mesh = {*Anti-Bacterial Agents ; *Chloroflexi/genetics ; Complex Mixtures ; Gram-Negative Bacteria ; Gram-Positive Bacteria/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In this study, we used 16S rRNA gene amplicon sequencing to investigate prokaryotic community composition of the Caribbean sponges Xestospongia muta and Agelas sventres from three depth ranges: < 30 m (shallow), 30-60 m (upper mesophotic), and 60-90 m (lower mesophotic). The prokaryotic community in shallow samples of X. muta was enriched in Cyanobacteria, Chloroflexota, and Crenarchaeota compared to samples from mesophotic depths, while mesophotic samples of X. muta were enriched in Acidobacteriota. For A. sventres, relative abundance of Acidobacteriota, Chloroflexota, and Gammaproteobacteria was higher in shallow samples, while Proteobacteria and Crenarchaeota were enriched in mesophotic A. sventres samples. Antimicrobial activity was evaluated by screening crude extracts of sponges against a set of Gram-positive and Gram-negative bacteria, a yeast, and an oomycete. Antibacterial activities from crude extracts of shallow sponge individuals were generally higher than observed from mesophotic individuals, that showed limited or no antibacterial activities. Conversely, the highest anti-oomycete activity was found from crude extracts of X. muta individuals from lower mesophotic depth, but without a clear pattern across the depth gradient. These results indicate that sponge-associated prokaryotic communities and the antimicrobial activity of sponges change within species across a depth gradient from shallow to mesophotic depth.}, }
@article {pmid35997836, year = {2022}, author = {Ide, K and Nakano, Y and Ito, M and Nishikawa, Y and Fujimura, H and Takeyama, H}, title = {The Effect of Co-Culture of Two Coral Species on Their Bacterial Composition Under Captive Environments.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {24}, number = {5}, pages = {871-881}, pmid = {35997836}, issn = {1436-2236}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biological Factors ; Coculture Techniques ; Coral Reefs ; RNA, Ribosomal, 16S/genetics ; Water ; }, abstract = {Coral symbionts are important members of the coral holobiont, and coral bacterial flora are essential in host health maintenance and coral conservation. Coral symbionts are affected by various environmental factors, such as seawater temperature, pH, and salinity. Although physicochemical and chemical factors have been highlighted as possible causes of these effects, the effects of water flow and the co-culture of different species corals have not been elucidated. In this study, we designed an artificial rearing environment to examine the impact of environmental and biological factors on Acropora tenuis, one of the major coral species in Okinawa, and Montipora digitata, during their co-culture. We intervened with the water flow to reveal that the movement of the rearing environment alters the bacterial flora of A. tenuis. During the rearing under captive environment, the alpha diversity of the coral microbiota increased, suggesting the establishment of rare bacteria from the ocean. No differences in the bacterial composition between the control and water flow groups were observed under the rearing conditions. However, the structure of the bacterial flora was significantly different in the co-culture group. Comparison of bacterial community succession strongly suggested that the differences observed were due to the suppressed transmission of bacteria from the ocean in the co-culture group. These results enhance our understanding of interactions between corals and shed light on the importance of regional differences and bacterial composition of coral flora.}, }
@article {pmid35992720, year = {2022}, author = {Scheuring, I and Rasmussen, JA and Bozzi, D and Limborg, MT}, title = {A strategic model of a host-microbe-microbe system reveals the importance of a joint host-microbe immune response to combat stress-induced gut dysbiosis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912806}, pmid = {35992720}, issn = {1664-302X}, abstract = {Microbiomes provide key ecological functions to their host; however, most host-associated microbiomes are too complicated to allow a model of essential host-microbe-microbe interactions. The intestinal microbiota of salmonids may offer a solution since few dominating species often characterize it. Healthy fish coexist with a mutualistic Mycoplasma sp. species, while stress allows the spread of pathogenic strains, such as Aliivibrio sp. Even after a skin infection, the Mycoplasma does not recover; Aliivibrio sp. often remains the dominant species, or Mycoplasma-Aliivibrio coexistence was occasionally observed. We devised a model involving interactions among the host immune system, Mycoplasma sp. plus a toxin-producing pathogen. Our model embraces a complete microbiota community and is in harmony with experimental results that host-Mycoplasma mutualism prevents the spread of pathogens. Contrary, stress suppresses the host immune system allowing dominance of pathogens, and Mycoplasma does not recover after stress disappears.}, }
@article {pmid35992708, year = {2022}, author = {Stencel, A and Wloch-Salamon, D}, title = {A pluralistic view of holobionts in the context of process ontology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {911577}, pmid = {35992708}, issn = {1664-302X}, abstract = {Developing precise definitions and fine categories is an important part of the scientific endeavour, enabling fidelity of transfers of knowledge and the progress of science. Currently, as a result of research on symbiotic microorganisms, science has been flooded with discoveries which appear to undermine many commonly accepted concepts and to introduce new ones that often require updated conceptualisations. One question currently being debated concerns whether or not a holobiont can be considered an organism. Based on which concept, physiology or evolutionary, of the organism is chosen, the verdict differs. We attempt here to show how a change in perspective, from that of substance ontology into that of process ontology, is capable of reconciling opposing positions within the existing discussion and enabling the implementation of conceptual pluralism.}, }
@article {pmid35976256, year = {2022}, author = {Huang, W and Yang, E and Yu, K and Meng, L and Wang, Y and Liang, J and Huang, X and Wang, G}, title = {Lower cold tolerance of tropical Porites lutea is possibly detrimental to its migration to relatively high latitude refuges in the South China Sea.}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5339-5355}, doi = {10.1111/mec.16662}, pmid = {35976256}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll ; Cold Temperature ; Coral Reefs ; *Dinoflagellida ; }, abstract = {As high temperature stress due to climate change threatens tropical corals, cooler areas at relatively high latitudes may be potential refuges. Tolerance to low temperatures is critical in determining whether corals can successfully migrate to higher latitudes. However, the physiological and molecular adaptations that protect corals from low temperature stress are unclear. In this study, scleractinian Porites lutea samples from the tropical Xisha Islands (XS) and subtropical Daya Bay (DY) in the South China Sea were subjected to a reduction in ambient temperature from 26 to 12°C. Differences in physiological changes and gene expression were analysed. P. lutea from both XS and DY exhibited physiological bleaching under low temperature stress, and the Symbiodiniaceae density, Fv/Fm, and chlorophyll-α content were significantly reduced. Symbiosome antioxidative stress and metabolic enzyme activity first increased and then decreased. RNA-seq analysis showed that the host responded to low temperature stress by activating immune, apoptotic, and autophagic pathways and reducing metabolic levels. Nevertheless, Symbiodiniaceae lacked the physiological regulatory capacity to adapt to low temperatures. The lower cold tolerance of XS tropical P. lutea may attribute to lower oxidative stress resistance, lower photosynthetic capacity, worse energy supply, and higher susceptibility to bacterial and viral infections and diseases in XS corals. The difference in cold tolerance may result from genetic differences between the geographic populations and is possibly detrimental to the migration of tropical coral to relatively high latitude refuges. This study provides a theoretical basis for anthropogenically assisted coral migration as a response to global change.}, }
@article {pmid35965269, year = {2023}, author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {392-407}, pmid = {35965269}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; }, abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.}, }
@article {pmid35963227, year = {2022}, author = {Ip, JC and Zhang, Y and Xie, JY and Yeung, YH and Qiu, JW}, title = {Comparative transcriptomics of two coral holobionts collected during the 2017 El Niño heat wave reveal differential stress response mechanisms.}, journal = {Marine pollution bulletin}, volume = {182}, number = {}, pages = {114017}, doi = {10.1016/j.marpolbul.2022.114017}, pmid = {35963227}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa/physiology ; Chlorophyll A ; Coral Reefs ; El Nino-Southern Oscillation ; Symbiosis ; Transcriptome ; }, abstract = {Although coral species exhibit differential susceptibility to stressors, little is known about the underlying molecular mechanisms. Here we compared scleractinian corals Montipora peltiformis and Platygyra carnosa collected during the 2017 El Niño heat wave. Zooxanthellae density and chlorophyll a content declined and increased substantially during and after heat stress event, respective. However, the magnitude of change was larger in M. peltiformis. Transcriptome analysis showed that heat-stressed corals corresponded to metabolic depression and catabolism of amino acids in both hosts which might promote their survival. However, only M. peltiformis has developed the bleached coral phenotype with corresponding strong stress- and immune-related responses in the host and symbiont, and strong suppression of photosynthesis-related genes in the symbiont. Overall, our study reveals differences among species in the homeostatic capacity to prevent the development of the bleached phenotype under environmental stressors, eventually determining their likelihood of survival in the warming ocean.}, }
@article {pmid35960256, year = {2022}, author = {Johnston, EC and Cunning, R and Burgess, SC}, title = {Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae).}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5368-5385}, pmid = {35960256}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {The congruence between phylogenies of tightly associated groups of organisms (cophylogeny) reflects evolutionary links between ecologically important interactions. However, despite being a classic example of an obligate symbiosis, tests of cophylogeny between scleractinian corals and their photosynthetic algal symbionts have been hampered in the past because both corals and algae contain genetically unresolved and morphologically cryptic species. Here, we studied co-occurring, cryptic Pocillopora species from Mo'orea, French Polynesia, that differ in their relative abundance across depth. We constructed new phylogenies of the host Pocillopora (using complete mitochondrial genomes, genomic loci, and thousands of single nucleotide polymorphisms) and their Symbiodiniaceae symbionts (using ITS2 and psbA[ncr] markers) and tested for cophylogeny. The analysis supported the presence of five Pocillopora species on the fore reef at Mo'orea that mostly hosted either Cladocopium latusorum or C. pacificum. Only Pocillopora species hosting C. latusorum also hosted taxa from Symbiodinium and Durusdinium. In general, the Cladocopium phylogeny mirrored the Pocillopora phylogeny. Within Cladocopium species, lineages also differed in their associations with Pocillopora haplotypes, except those showing evidence of nuclear introgression, and with depth in the two most common Pocillopora species. We also found evidence for a new Pocillopora species (haplotype 10), that has so far only been sampled from French Polynesia, that warrants formal identification. The linked phylogenies of these Pocillopora and Cladocopium species and lineages suggest that symbiont speciation is driven by niche diversification in the host, but there is still evidence for symbiont flexibility in some cases.}, }
@article {pmid35958152, year = {2022}, author = {Somera, TS and Mazzola, M}, title = {Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {949404}, pmid = {35958152}, issn = {1664-302X}, abstract = {Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to "reshape" the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.}, }
@article {pmid35943423, year = {2022}, author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV}, title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.}, journal = {Molecular ecology}, volume = {31}, number = {19}, pages = {4979-4990}, pmid = {35943423}, issn = {1365-294X}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; DNA, Ancient ; *Dinoflagellida/genetics ; Ecosystem ; Genome ; }, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we utilized aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE to 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence aDNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.}, }
@article {pmid37938252, year = {2022}, author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E}, title = {Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {65}, pmid = {37938252}, issn = {2730-6151}, abstract = {Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.}, }
@article {pmid35918644, year = {2022}, author = {Montoya, P and Cadena, CD and Claramunt, S and Duchêne, DA}, title = {Environmental niche and flight intensity are associated with molecular evolutionary rates in a large avian radiation.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {95}, pmid = {35918644}, issn = {2730-7182}, mesh = {Animals ; Biological Evolution ; Birds/genetics ; Evolution, Molecular ; *Flight, Animal/physiology ; Phylogeny ; *Wings, Animal/anatomy &amp; histology ; }, abstract = {BACKGROUND: Metabolic activity and environmental energy are two of the most studied putative drivers of molecular evolutionary rates. Their extensive study, however, has resulted in mixed results and has rarely included the exploration of interactions among various factors impacting molecular evolutionary rates across large clades. Taking the diverse avian family Furnariidae as a case study, we examined the association between several estimates of molecular evolutionary rates with proxies of metabolic demands imposed by flight (wing loading and wing shape) and proxies of environmental energy across the geographic ranges of species (temperature and UV radiation).<br><br>RESULTS: We found weak evidence of a positive effect of environmental and morphological variables on mitochondrial substitution rates. Additionally, we found that temperature and UV radiation interact to explain molecular rates at nucleotide sites affected by selection and population size (non-synonymous substitutions), contrary to the expectation of their impact on sites associated with mutation rates (synonymous substitutions). We also found a negative interaction between wing shape (as described by the hand-wing index) and body mass explaining mitochondrial molecular rates, suggesting molecular signatures of positive selection or reduced population sizes in small-bodied species with greater flight activity.<br><br>CONCLUSIONS: Our results suggest that the demands of flight and environmental energy pose multiple evolutionary pressures on the genome either by driving mutation rates or via their association with natural selection or population size. Data from whole genomes and detailed physiology across taxa will bring a more complete picture of the impact of metabolism, population size, and the environment on avian genome evolution.}, }
@article {pmid37746232, year = {2022}, author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Consolo, VF and Berón, CM}, title = {Culex quinquefasciatus Holobiont: A Fungal Metagenomic Approach.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {918052}, pmid = {37746232}, issn = {2673-6128}, abstract = {Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.}, }
@article {pmid35910618, year = {2022}, author = {Vad, J and Duran Suja, L and Summers, S and Henry, TB and Roberts, JM}, title = {Marine Sponges in a Snowstorm - Extreme Sensitivity of a Sponge Holobiont to Marine Oil Snow and Chemically Dispersed Oil Pollution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909853}, pmid = {35910618}, issn = {1664-302X}, abstract = {Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and "marine oil snow" contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.}, }
@article {pmid35902906, year = {2022}, author = {Morrow, KM and Pankey, MS and Lesser, MP}, title = {Community structure of coral microbiomes is dependent on host morphology.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {113}, pmid = {35902906}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; *Microbiota/genetics ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities.<br><br>RESULTS: The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community.<br><br>CONCLUSIONS: The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.}, }
@article {pmid35902758, year = {2022}, author = {Cziesielski, MJ and Liew, YJ and Cui, G and Aranda, M}, title = {Increased incompatibility of heterologous algal symbionts under thermal stress in the cnidarian-dinoflagellate model Aiptasia.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {760}, pmid = {35902758}, issn = {2399-3642}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics/metabolism ; Ecosystem ; *Sea Anemones/genetics/metabolism ; Symbiosis/genetics ; }, abstract = {Rising ocean temperatures are increasing the rate and intensity of coral mass bleaching events, leading to the collapse of coral reef ecosystems. To better understand the dynamics of coral-algae symbioses, it is critical to decipher the role each partner plays in the holobiont's thermotolerance. Here, we investigated the role of the symbiont by comparing transcriptional heat stress responses of anemones from two thermally distinct locations, Florida (CC7) and Hawaii (H2) as well as a heterologous host-symbiont combination composed of CC7 host anemones inoculated with the symbiont Breviolum minutum (SSB01) from H2 anemones (CC7-B01). We find that oxidative stress and apoptosis responses are strongly influenced by symbiont type, as further confirmed by caspase-3 activation assays, but that the overall response to heat stress is dictated by the compatibility of both partners. Expression of genes essential to symbiosis revealed a shift from a nitrogen- to a carbon-limited state only in the heterologous combination CC7-B01, suggesting a bioenergetic disruption of symbiosis during stress. Our results indicate that symbiosis is highly fine-tuned towards particular partner combinations and that heterologous host-symbiont combinations are metabolically less compatible under stress. These results are essential for future strategies aiming at increasing coral resilience using heterologous thermotolerant symbionts.}, }
@article {pmid35895230, year = {2022}, author = {Xiang, X and Poli, D and Degnan, BM and Degnan, SM}, title = {Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {24}, number = {4}, pages = {722-732}, pmid = {35895230}, issn = {1436-2236}, support = {DP170102353//Australian Research Council/ ; }, mesh = {Animals ; Bacteria/genetics ; Gene Expression Profiling/methods ; *Porifera/genetics/microbiology ; RNA, Messenger/genetics ; *RNA, Ribosomal ; RNA-Seq ; }, abstract = {Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.}, }
@article {pmid35895126, year = {2022}, author = {Barbato, M and Vacchini, V and Engelen, AH and Patania, G and Mapelli, F and Borin, S and Crotti, E}, title = {What lies on macroalgal surface: diversity of polysaccharide degraders in culturable epiphytic bacteria.}, journal = {AMB Express}, volume = {12}, number = {1}, pages = {98}, pmid = {35895126}, issn = {2191-0855}, support = {634486//Horizon 2020/ ; UIDB/04326/2020//Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa/ ; CEECINST/00114/2018//Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa/ ; }, abstract = {Macroalgal surface constitutes a peculiar ecological niche and an advantageous substratum for microorganisms able to degrade the wide diversity of algal glycans. The degrading enzymatic activities of macroalgal epiphytes are of paramount interest for the industrial by-product sector and biomass resource applications. We characterized the polysaccharide hydrolytic profile of bacterial isolates obtained from three macroalgal species: the red macroalgae Asparagopsis taxiformis and Sphaerococcus coronopifolius (Rhodophyceae) and the brown Halopteris scoparia (Phaeophyceae), sampled in South Portugal. Bacterial enrichment cultures supplemented with chlorinated aliphatic compounds, typically released by marine algae, were established using as inoculum the decaying biomass of the three macroalgae, obtaining a collection of 634 bacterial strains. Although collected from the same site and exposed to the same seawater seeding microbiota, macroalgal cultivable bacterial communities in terms of functional and phylogenetic diversity showed host specificity. Isolates were tested for the hydrolysis of starch, pectin, alginate and agar, exhibiting a different hydrolytic potential according to their host: A. taxiformis showed the highest percentage of active isolates (91%), followed by S. coronopifolius (54%) and H. scoparia (46%). Only 30% of the isolates were able to degrade starch, while the other polymers were degraded by 55-58% of the isolates. Interestingly, several isolates showed promiscuous capacities to hydrolyze more than one polysaccharide. The isolate functional fingerprint was statistically correlated to bacterial phylogeny, host species and enrichment medium. In conclusion, this work depicts macroalgae as holobionts with an associated microbiota of interest for blue biotechnologies, suggesting isolation strategies and bacterial targets for polysaccharidases' discovery.}, }
@article {pmid35894614, year = {2022}, author = {Tanabe, N and Takasu, R and Hirose, Y and Kamei, Y and Kondo, M and Nakabachi, A}, title = {Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0175722}, pmid = {35894614}, issn = {2165-0497}, mesh = {Animals ; Bacillus subtilis/metabolism ; Cell Division ; *Citrus/metabolism/microbiology ; Escherichia coli/metabolism ; *Gammaproteobacteria/metabolism ; *Hemiptera/metabolism/microbiology ; *Polyketides/metabolism/pharmacology ; Symbiosis ; }, abstract = {Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri. IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.}, }
@article {pmid35889095, year = {2022}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Junca, H and Sidjabat, HE and Cano-Lozano, JA and Villamil Díaz, LM}, title = {Competitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889095}, issn = {2076-2607}, support = {ING181-2016//Universidad de La Sabana/ ; INGPHD-6-2017//Universidad de La Sabana/ ; INGPHD-9-2019//Universidad de La Sabana/ ; 808-2018-contract CT 329-2019//MINCIENCIAS- Patrimonio Aut&#xf3;nomo Fondo Nacional de Financiamiento para la Ciencia, la Tecnolog&#xed;a y la Innovaci&#xf3;n Francisco Jos&#xe9; de Caldas/ ; 727-2015, contract CT 122-2017//MINCIENCIAS/ ; }, abstract = {This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.}, }
@article {pmid35884910, year = {2022}, author = {Amedei, A}, title = {Editorial of Special Issue "Pharmacomicrobiomics in Non-Communicable Disease".}, journal = {Biomedicines}, volume = {10}, number = {7}, pages = {}, pmid = {35884910}, issn = {2227-9059}, abstract = {The human superorganism, also known as the human holobiont, is a complex organism made up of host body as well as the bacteria, archaea, viruses, and fungi that live inside it along with their genes [...].}, }
@article {pmid35881247, year = {2023}, author = {King, NG and Smale, DA and Thorpe, JM and McKeown, NJ and Andrews, AJ and Browne, R and Malham, SK}, title = {Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {154-162}, pmid = {35881247}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Crassostrea/microbiology ; Temperature ; Bacteria/genetics ; Seasons ; Seawater/microbiology ; }, abstract = {A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35875588, year = {2022}, author = {Chun, SJ and Cui, Y and Yoo, SH and Lee, JR}, title = {Organic Connection of Holobiont Components and the Essential Roles of Core Microbes in the Holobiont Formation of Feral Brassica napus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {920759}, pmid = {35875588}, issn = {1664-302X}, abstract = {Brassica napus (Rapeseed) is an econfomically important oil-producing crop. The microbial interactions in the plant holobiont are fundamental to the understanding of plant growth and health. To investigate the microbial dynamics in the holobiont of feral B. napus, a total of 215 holobiont samples, comprised of bulk soil, primary root, lateral root, dead leaf, caulosphere, basal leaf, apical leaf, carposphere, and anthosphere, were collected from five different grassland sites in South Korea. The soil properties differed in different sampling sites, but prokaryotic communities were segregated according to plant holobiont components. The structures of the site-specific SparCC networks were similar across the regions. Recurrent patterns were found in the plant holobionts in the recurrent network. Ralstonia sp., Massilia sp., and Rhizobium clusters were observed consistently and were identified as core taxa in the phyllosphere, dead leaf microbiome, and rhizosphere, respectively. Arthropod-related microbes, such as Wolbachia sp., Gilliamella sp., and Corynebacteriales amplicon sequence variants, were found in the anthosphere. PICRUSt2 analysis revealed that microbes also possessed specific functions related to holobiont components, such as functions related to degradation pathways in the dead leaf microbiome. Structural equation modeling analysis showed the organic connections among holobiont components and the essential roles of the core microbes in the holobiont formations in natural ecosystem. Microbes coexisting in a specific plant showed relatively stable community structures, even though the regions and soil characteristics were different. Microbes in each plant component were organically connected to form their own plant holobiont. In addition, plant-related microbes, especially core microbes in each holobiont, showed recurrent interaction patterns that are essential to an understanding of the survival and coexistence of plant microbes in natural ecosystems.}, }
@article {pmid35868367, year = {2022}, author = {de Menezes, TA and de Freitas, MAM and Lima, MS and Soares, AC and Leal, C and Busch, MS and Tschoeke, DA and de O Vidal, L and Atella, GC and Kruger, RH and Setubal, J and Vasconcelos, AA and de Mahiques, MM and Siegle, E and Asp, NE and Cosenza, C and Hajdu, E and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Fluxes of the Amazon River plume nutrients and microbes into marine sponges.}, journal = {The Science of the total environment}, volume = {847}, number = {}, pages = {157474}, doi = {10.1016/j.scitotenv.2022.157474}, pmid = {35868367}, issn = {1879-1026}, mesh = {Animals ; Nutrients ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S ; *Rivers ; }, abstract = {Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km[2] off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ[13]C and δ[15]N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.}, }
@article {pmid35867396, year = {2022}, author = {Gerna, D and Clara, D and Allwardt, D and Mitter, B and Roach, T}, title = {Tailored Media Are Key to Unlocking the Diversity of Endophytic Bacteria in Distinct Compartments of Germinating Seeds.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0017222}, pmid = {35867396}, issn = {2165-0497}, mesh = {*Bacteria ; Endophytes ; Germination ; *Microbiota ; Plants ; Seeds/microbiology ; }, abstract = {Seeds offer an internal microbial niche, termed the endosphere, colonized by communities of endophytic bacteria. To elucidate the functions of seed endophytes during germination and early plant growth, studies with culturable isolates are essential. Conventional growth media favor few fast-growing taxa, while micro organisms with restricted nutrient requirements are usually outcompeted prior to isolation. Consequently, current knowledge of the interaction between seeds and their endophytes remains limited to only few bacterial taxa, despite a "black box" of unculturable isolates colonizing the endosphere. Here, we designed various solid media to mimic the endosphere of germinating soybean (Glycine max L.) seeds and assessed their effect on the diversity of culturable endophytic bacteria. The embryonic axis (i.e., the future plant) possessed higher richness and harbored more unique genera (i.e., Brevundimonas, Methylobacterium, Microbacterium, Pseudoclavibacter, and Rathayibacter) than cotyledons (i.e., seed storage organs). Overall, media containing germinating and ground seeds enabled culturing and isolation of the broadest diversity of endophytic bacteria, viewed through the molecular identification of 246 isolates. The use of multiple tailored media helped uncover trophic adaptation of the core taxa. Furthermore, comparison of seeds from four lots of distinct cultivars and origin revealed few overlapping taxa, indicating that the parental environment, including soil and fertilization regime, influenced seed endophytic diversity. Extended diversity of native seed endophytic bacteria revealed the functional relevance of unique Arthrobacter, Bacillus, and Curtobacterium strains to seed germination under salt stress, exemplifying the importance of enhanced culturing approaches to elucidate the role of microbiota in seed germination. IMPORTANCE Plant growth-promoting endophytic isolates that appear to advance seed germination are often obtained from plant niches other than the seed endosphere. Isolating pure cultures of native endophytes from seeds during germination is crucial to investigate their function during early plant growth. Here, the diversity of endophytic bacteria isolated from seeds during soybean germination was enhanced by combining media tailored to the nutritional composition of the seed endosphere, including pregerminated seeds themselves. Our results show that isolation from distinct soybean seed compartments affected such diversity, with the embryonic axis harboring more unique taxa while displaying higher endophytic richness. Furthermore, using pools of seeds from separate lots, each corresponding to a certain cultivar and field site, supported isolation of further unique strains that often unveiled substantial effects on germination performance. Such findings are relevant to assist studies on the interactions between seeds and their native endophytic bacteria.}, }
@article {pmid35864739, year = {2022}, author = {Martínez-Arias, C and Witzell, J and Solla, A and Martin, JA and Rodríguez-Calcerrada, J}, title = {Beneficial and pathogenic plant-microbe interactions during flooding stress.}, journal = {Plant, cell &amp; environment}, volume = {45}, number = {10}, pages = {2875-2897}, pmid = {35864739}, issn = {1365-3040}, mesh = {*Floods ; *Microbiota/physiology ; Oxygen/metabolism ; Plant Roots/metabolism ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.}, }
@article {pmid35862823, year = {2022}, author = {Loureiro, C and Galani, A and Gavriilidou, A and Chaib de Mares, M and van der Oost, J and Medema, MH and Sipkema, D}, title = {Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0035722}, pmid = {35862823}, issn = {2379-5077}, mesh = {Animals ; *Porifera/genetics ; Metagenome ; *Microbiota/genetics ; Bacteria/genetics ; *Biological Products/metabolism ; }, abstract = {Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.}, }
@article {pmid35862808, year = {2022}, author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA}, title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0012022}, pmid = {35862808}, issn = {2379-5077}, mesh = {*Populus/genetics ; *Ascomycota/genetics ; *Microbiota/genetics ; Trees/microbiology ; Metabolome ; }, abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.}, }
@article {pmid35862435, year = {2022}, author = {Howe, J and Rink, JC and Wang, B and Griffin, AS}, title = {Multicellularity in animals: The potential for within-organism conflict.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {32}, pages = {e2120457119}, pmid = {35862435}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; *Cell Lineage ; Clone Cells ; Developmental Biology ; *Insecta/growth &amp; development ; Reproduction ; }, abstract = {Metazoans function as individual organisms but also as "colonies" of cells whose single-celled ancestors lived and reproduced independently. Insights from evolutionary biology about multicellular group formation help us understand the behavior of cells: why they cooperate, and why cooperation sometimes breaks down. Current explanations for multicellularity focus on two aspects of development which promote cooperation and limit conflict among cells: a single-cell bottleneck, which creates organisms composed of clones, and a separation of somatic and germ cell lineages, which reduces the selective advantage of cheating. However, many obligately multicellular organisms thrive with neither, creating the potential for within-organism conflict. Here, we argue that the prevalence of such organisms throughout the Metazoa requires us to refine our preconceptions of conflict-free multicellularity. Evolutionary theory must incorporate developmental mechanisms across a broad range of organisms-such as unusual reproductive strategies, totipotency, and cell competition-while developmental biology must incorporate evolutionary principles. To facilitate this cross-disciplinary approach, we provide a conceptual overview from evolutionary biology for developmental biologists, using analogous examples in the well-studied social insects.}, }
@article {pmid35860838, year = {2022}, author = {Miral, A and Jargeat, P and Mambu, L and Rouaud, I and Tranchimand, S and Tomasi, S}, title = {Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods.}, journal = {Environmental microbiology reports}, volume = {14}, number = {6}, pages = {856-872}, pmid = {35860838}, issn = {1758-2229}, mesh = {*Lichens/microbiology ; Phylogeny ; *Ascomycota ; *Microbiota ; Symbiosis ; }, abstract = {Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture-dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non-studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture-dependent techniques.}, }
@article {pmid35857470, year = {2022}, author = {Wada, N and Hsu, MT and Tandon, K and Hsiao, SS and Chen, HJ and Chen, YH and Chiang, PW and Yu, SP and Lu, CY and Chiou, YJ and Tu, YC and Tian, X and Chen, BC and Lee, DC and Yamashiro, H and Bourne, DG and Tang, SL}, title = {High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata.}, journal = {Science advances}, volume = {8}, number = {27}, pages = {eabo2431}, pmid = {35857470}, issn = {2375-2548}, abstract = {Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.}, }
@article {pmid35847106, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Xu, K and Liu, J and Zhu, W and Zhu, J and He, C and Han, C and Qin, C and Luo, H and Chen, K and Zheng, Y and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916280}, pmid = {35847106}, issn = {1664-302X}, abstract = {The host and its symbiotic bacteria form a biological entity, holobiont, in which they share a dynamic connection characterized by symbiosis, co-metabolism, and coevolution. However, how these collaborative relationships were maintained over evolutionary time remains unclear. In this research, the small non-coding RNA (sncRNA) profiles of cecum and their bacteria contents were measured from lines of chickens that have undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. The results from these lines that originated from a common founder population and maintained under the same husbandry showed an association between host intestinal sncRNA expression profile (miRNA, lncRNA fragment, mRNA fragment, snoRNA, and snRNA) and intestinal microbiota. Correlation analyses suggested that some central miRNAs and mRNA fragments had interactions with the abundance of intestinal microbial species and microbiota functions. miR-6622-3p, a significantly differentially expressed (DE) miRNA was correlated with a body weight gain related bacterium, Alistipes putredinis. Our results showed that host sncRNAs may be mediators of interaction between the host and its intestinal microbiome. This provides additional clue for holobiont concepts.}, }
@article {pmid35832387, year = {2022}, author = {Hernández, M and Mayer, MPA and Santi-Rocca, J}, title = {Editorial: The Human Microbiota in Periodontitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {952205}, pmid = {35832387}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *Periodontitis ; }, }
@article {pmid35818766, year = {2022}, author = {Sánchez-Suárez, J and Díaz, L and Junca, H and Garcia-Bonilla, E and Villamil, L}, title = {Microbiome composition of the marine sponge Cliona varians at the neotropical southern Caribbean Sea displays a predominant core of Rhizobiales and Nitrosopumilaceae.}, journal = {Journal of applied microbiology}, volume = {133}, number = {3}, pages = {2027-2038}, doi = {10.1111/jam.15714}, pmid = {35818766}, issn = {1365-2672}, support = {80740-168-2019//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n (Minciencias)/ ; ING-175-2016//Universidad de La Sabana/ ; }, mesh = {Animals ; Archaea ; Caribbean Region ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Porifera/microbiology ; Seawater/microbiology ; }, abstract = {AIMS: This work aims to characterize the microbial diversity of the encrusting sponge Cliona varians, a pore-forming and coral reef bioeroding marine sponge of emerging spread related to ocean acidification.<br><br>METHODS AND RESULTS: We analysed the microbiome composition by 16S V4 amplicon next-generation sequencing in a community of the bioeroding coral reef encrusting/excavating marine sponge Cliona varians thriving at the Southern Caribbean Sea. About 87.21% and 6.76% of the sequences retrieved were assigned to the domain Bacteria and Archaea. The most predominant operational taxonomic units were classified as members of the order Rhizobiales and family Nitrosopumilaceae, representing members of not yet characterized genera. Features found strictly conserved in the strain/genomic representatives reported in those microbial taxa are nitrogen fixation and transformation.<br><br>CONCLUSION: Our results suggest, in accordance with recent results, that these microbiome members and associated functions could be contributing to the biological fitness of the sponge to be able to colonize and bioerode in environments with low access and scarce availability of nitrogen sources.<br><br>Coral reefs bioresources such as sponge holobionts are intriguing and complex ecosystem units. This study contributes to the knowledge of how C. varians microbiota is composed or shaped, which is crucial to understand its ecological functions.}, }
@article {pmid35816968, year = {2022}, author = {Griffin, ME and Hang, HC}, title = {Microbial mechanisms to improve immune checkpoint blockade responsiveness.}, journal = {Neoplasia (New York, N.Y.)}, volume = {31}, number = {}, pages = {100818}, pmid = {35816968}, issn = {1476-5586}, support = {R01 CA245292/CA/NCI NIH HHS/United States ; R21 AI156674/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Immunotherapy ; *Microbiota ; *Neoplasms/drug therapy/genetics ; }, abstract = {The human microbiota acts as a diverse source of molecular cues that influence the development and homeostasis of the immune system. Beyond endogenous roles in the human holobiont, host-microbial interactions also alter outcomes for immune-related diseases and treatment regimens. Over the past decade, sequencing analyses of cancer patients have revealed correlations between microbiota composition and the efficacy of cancer immunotherapies such as checkpoint inhibitors. However, very little is known about the exact mechanisms that link specific microbiota with patient responses, limiting our ability to exploit these microbial agents for improved oncology care. Here, we summarize current progress towards a molecular understanding of host-microbial interactions in the context of checkpoint inhibitor immunotherapies. By highlighting the successes of a limited number of studies focused on identifying specific, causal molecules, we underscore how the exploration of specific microbial features such as proteins, enzymes, and metabolites may translate into precise and actionable therapies for personalized patient care in the clinic.}, }
@article {pmid35783967, year = {2022}, author = {Plaszkó, T and Szűcs, Z and Cziáky, Z and Ács-Szabó, L and Csoma, H and Géczi, L and Vasas, G and Gonda, S}, title = {Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish (Armoracia rusticana, Brassicaceae) Roots.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {921008}, pmid = {35783967}, issn = {1664-462X}, abstract = {The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.}, }
@article {pmid35779528, year = {2022}, author = {de Ferran, V and Figueiró, HV and de Jesus Trindade, F and Smith, O and Sinding, MS and Trinca, CS and Lazzari, GZ and Veron, G and Vianna, JA and Barbanera, F and Kliver, S and Serdyukova, N and Bulyonkova, T and Ryder, OA and Gilbert, MTP and Koepfli, KP and Eizirik, E}, title = {Phylogenomics of the world's otters.}, journal = {Current biology : CB}, volume = {32}, number = {16}, pages = {3650-3658.e4}, doi = {10.1016/j.cub.2022.06.036}, pmid = {35779528}, issn = {1879-0445}, mesh = {Animals ; Base Sequence ; *Otters/genetics ; Phylogeny ; }, abstract = {Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,[1-5] a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.}, }
@article {pmid35777916, year = {2022}, author = {Xu, P and Fan, X and Mao, Y and Cheng, H and Xu, A and Lai, W and Lv, T and Hu, Y and Nie, Y and Zheng, X and Meng, Q and Wang, Y and Cernava, T and Wang, M}, title = {Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens.}, journal = {Journal of advanced research}, volume = {39}, number = {}, pages = {49-60}, pmid = {35777916}, issn = {2090-1224}, mesh = {Bacteria ; *Camellia sinensis ; *Microbiota ; Plant Leaves/microbiology ; Plants ; Tea ; }, abstract = {INTRODUCTION: A broad spectrum of rhizosphere bacteria and fungi were shown to play a central role for health, fitness and productivity of their host plants. However, implications of host metabolism on microbiota assembly in the phyllosphere and potential consequences for holobiont functioning were sparsely addressed. Previous observations indicated that tea plants might reduce disease occurrence in various forests located in their proximity; the underlying mechanisms and potential implications of the phyllosphere microbiota remained elusive.<br><br>OBJECTIVES: This study aimed atdeciphering microbiome assembly in the tea plant phyllosphere throughout shoot development as well as elucidating potential implications of host metabolites in this process. The main focus was to explore hidden interconnections between the homeostasis of the phyllosphere microbiome and resistance to fungal pathogens.<br><br>METHODS: Profiling of host metabolites and microbiome analyses based on high-throughput sequencing were integrated to identify drivers of microbiome assembly throughout shoot development in the phyllosphere of tea plants. This was complemented by tracking of beneficial microorganisms in all compartments of the plant. Synthetic assemblages (SynAss), bioassays and field surveys were implemented to verify functioning of the phyllosphere microbiota.<br><br>RESULTS: Theophylline and epigallocatechin gallate, two prevalent metabolites at the early and late shoot development stage respectively, were identified as the main drivers of microbial community assembly. Flavobacterium and Myriangium were distinct microbial responders at the early stage, while Parabacteroides and Mortierella were more enriched at the late stage. Reconstructed, stage-specific SynAss suppressed various tree phytopathogens by 13.0%-69.3% in vitro and reduced disease incidence by 8.24%-41.3% in vivo.<br><br>CONCLUSION: The findings indicate that a functional phyllosphere microbiota was assembled along with development-specific metabolites in tea plants, which continuously suppressed prevalent fungal pathogens. The insights gained into the temporally resolved metabolite response of the tea plant microbiota could provide novel solutions for disease management.}, }
@article {pmid35775576, year = {2022}, author = {Gilbert, SF and Hadfield, MG}, title = {Symbiosis of disciplines: how can developmental biologists join conservationists in sustaining and restoring earth's biodiversity?.}, journal = {Development (Cambridge, England)}, volume = {149}, number = {13}, pages = {}, doi = {10.1242/dev.199960}, pmid = {35775576}, issn = {1477-9129}, mesh = {*Biodiversity ; Ecosystem ; Genomics ; *Symbiosis ; }, abstract = {What can developmental biology contribute toward mitigating the consequences of anthropogenic assaults on the environment and climate change? In this Spotlight article, we advocate a developmental biology that takes seriously Lynn Margulis' claim that 'the environment is part of the body'. We believe this to be a pre-condition for developmental biology playing important roles in conservation and environmental restoration. We need to forge a developmental biology of the holobiont - the multi-genomic physiologically integrated organism that is also a functional biome. To this end, we highlight how developmental biology needs to explore more deeply the interactions between developing organisms, and their chemical, physical and biotic environments.}, }
@article {pmid35773344, year = {2022}, author = {Wang, W and Tang, K and Wang, P and Zeng, Z and Xu, T and Zhan, W and Liu, T and Wang, Y and Wang, X}, title = {The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {8}, pages = {1132-1144}, pmid = {35773344}, issn = {2397-334X}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Vibrio ; Virus Activation ; }, abstract = {The coral reef microbiome is central to reef health and resilience. Competitive interactions between opportunistic coral pathogens and other commensal microbes affect the health of coral. Despite great advances over the years in sequencing-based microbial profiling of healthy and diseased coral, the molecular mechanism underlying colonization competition has been much less explored. In this study, by examining the culturable bacteria inhabiting the gastric cavity of healthy Galaxea fascicularis, a scleractinian coral, we found that temperate phages played a major role in mediating colonization competition in the coral microbiota. Specifically, the non-toxigenic Vibrio sp. inhabiting the healthy coral had a much higher colonization capacity than the coral pathogen Vibrio coralliilyticus, yet this advantage was diminished by the latter killing the former. Pathogen-encoded LodAB, which produces hydrogen peroxide, triggers the lytic cycle of prophage in the non-toxicogenic Vibrio sp. Importantly, V. coralliilyticus could outcompete other coral symbiotic bacteria (for example, Endozoicomonas sp.) through LodAB-dependent prophage induction. Overall, we reveal that LodAB can be used by pathogens as an important weapon to gain a competitive advantage over lysogenic competitors when colonizing corals.}, }
@article {pmid35767862, year = {2022}, author = {Bendová, B and Mikula, O and Vošlajerová Bímová, B and Čížková, D and Daniszová, K and Ďureje, &#x13d; and Hiadlovská, Z and Macholán, M and Martin, JF and Piálek, J and Schmiedová, L and Kreisinger, J}, title = {Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {8}, pages = {}, doi = {10.1093/femsec/fiac078}, pmid = {35767862}, issn = {1574-6941}, mesh = {Animals ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mice ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are, therefore, an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under seminatural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of codivergence with their hosts. Helicobacters represent promising candidates for studying GM-host coadaptations and the fitness effects of their interactions.}, }
@article {pmid35764640, year = {2022}, author = {Cerca, J and Petersen, B and Lazaro-Guevara, JM and Rivera-Colón, A and Birkeland, S and Vizueta, J and Li, S and Li, Q and Loureiro, J and Kosawang, C and Díaz, PJ and Rivas-Torres, G and Fernández-Mazuecos, M and Vargas, P and McCauley, RA and Petersen, G and Santos-Bay, L and Wales, N and Catchen, JM and Machado, D and Nowak, MD and Suh, A and Sinha, NR and Nielsen, LR and Seberg, O and Gilbert, MTP and Leebens-Mack, JH and Rieseberg, LH and Martin, MD}, title = {The genomic basis of the plant island syndrome in Darwin's giant daisies.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3729}, pmid = {35764640}, issn = {2041-1723}, mesh = {Biological Evolution ; *DNA Transposable Elements/genetics ; *Genomics ; Synteny/genetics ; }, abstract = {The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.}, }
@article {pmid35748637, year = {2023}, author = {Poulin, R and Jorge, F and Salloum, PM}, title = {Inter-individual variation in parasite manipulation of host phenotype: A role for parasite microbiomes?.}, journal = {The Journal of animal ecology}, volume = {92}, number = {4}, pages = {807-812}, doi = {10.1111/1365-2656.13764}, pmid = {35748637}, issn = {1365-2656}, mesh = {Animals ; *Parasites ; Host-Parasite Interactions ; *Microbiota ; Ecology ; Phenotype ; }, abstract = {Alterations in host phenotype induced by metazoan parasites are widespread in nature, yet the underlying mechanisms and the sources of intraspecific variation in the extent of those alterations remain poorly understood. In light of the microbiome revolution sweeping through ecology and evolutionary biology, we hypothesise that the composition of symbiotic microbial communities living within individual parasites influences the nature and extent of their effect on host phenotype. The interests of both the parasite and its symbionts are aligned through the latter's vertical transmission, favouring joint contributions to the manipulation of host phenotype. Our hypothesis can explain the variation in the extent to which parasites alter host phenotype, as microbiome composition varies among individual parasites. We propose two non-exclusive approaches to test the hypothesis, furthering the integration of microbiomes into studies of host-parasite interactions.}, }
@article {pmid35746877, year = {2022}, author = {Roik, A and Reverter, M and Pogoreutz, C}, title = {A roadmap to understanding diversity and function of coral reef-associated fungi.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {6}, pages = {}, pmid = {35746877}, issn = {1574-6976}, mesh = {Animals ; Coral Reefs ; Ecosystem ; *Anthozoa/microbiology/physiology ; Symbiosis ; *Microbiota ; Fungi ; }, abstract = {Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.}, }
@article {pmid35729906, year = {2022}, author = {Williams, SD and Klinges, JG and Zinman, S and Clark, AS and Bartels, E and Villoch Diaz Maurino, M and Muller, EM}, title = {Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13574}, pmid = {35729906}, issn = {2167-8359}, mesh = {Animals ; Coral Reefs ; Florida ; RNA, Ribosomal, 16S/genetics ; Endangered Species ; *Anthozoa/genetics ; Bacteria/genetics ; Rickettsiales/genetics ; *Microbiota/genetics ; }, abstract = {Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.}, }
@article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, }
@article {pmid35720593, year = {2022}, author = {Toghueo, RMK and Zabalgogeazcoa, I and Pereira, EC and Vazquez de Aldana, BR}, title = {A Diaporthe Fungal Endophyte From a Wild Grass Improves Growth and Salinity Tolerance of Tritordeum and Perennial Ryegrass.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {896755}, pmid = {35720593}, issn = {1664-462X}, abstract = {Some microbiome components can provide functions that extend the capabilities of plants, increasing the environmental adaptability and performance of holobionts. Festuca rubra subsp. pruinosa is a perennial grass adapted to rocky sea cliffs, where soil and nutrients are very limited, and exposure to salinity is continuous. This study aimed to investigate if a Diaporthe fungal endophyte belonging to the core microbiome of Festuca rubra roots could improve the performance of two agricultural grasses. In a greenhouse experiment, plants of tritordeum (Triticum durum x Hordeum chilense) and perennial ryegrass (Lolium perenne) were inoculated with Diaporthe strain EB4 and subjected to two salinity conditions (0 and 200 mM NaCl). Biomass production, mineral elements, proline, hormone profiles, antioxidant capacity, and total phenolic compounds were examined in plants, and fungal functions potentially related to the promotion of plant growth were determined. The inoculation with Diaporthe promoted plant growth of both grasses, increasing leaf biomass (84% in tritordeum and 29% in perennial ryegrass), root biomass, nutrient content (N, Ca, Mg, and Fe), and the production of indole 3-acetic acid, regardless of the salinity treatment. Improved growth and nutrient uptake might occur because Diaporthe produces several extracellular enzymes capable of recycling organic nutrient pools. In addition, the fungus produced indole 3-acetic acid in vitro and modulated the production of this phytohormone in the plant. Under salinity, the activity of Diaporthe ameliorated the stress, increasing proline, nutrient uptake in roots, gibberellins, and indole 3-acetic acid, which in turn results into improved growth. Thus, this fungus can transfer to alternative hosts some advantages useful at its original habitat.}, }
@article {pmid35718641, year = {2022}, author = {Ricci, F and Leggat, W and Page, CE and Ainsworth, TD}, title = {Coral growth anomalies, neoplasms, and tumors in the Anthropocene.}, journal = {Trends in microbiology}, volume = {30}, number = {12}, pages = {1160-1173}, doi = {10.1016/j.tim.2022.05.013}, pmid = {35718641}, issn = {1878-4380}, mesh = {Animals ; *Anthozoa ; Gene Expression Profiling ; *Neoplasms ; Coral Reefs ; }, abstract = {One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.}, }
@article {pmid35715703, year = {2022}, author = {Lan, Y and Sun, J and Chen, C and Wang, H and Xiao, Y and Perez, M and Yang, Y and Kwan, YH and Sun, Y and Zhou, Y and Han, X and Miyazaki, J and Watsuji, TO and Bissessur, D and Qiu, JW and Takai, K and Qian, PY}, title = {Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2132-2143}, pmid = {35715703}, issn = {1751-7370}, support = {42176110//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18K06401//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Hydrothermal Vents/microbiology ; Metagenomics ; Phylogeny ; Snails/physiology ; Symbiosis/genetics ; }, abstract = {The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.}, }
@article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, }
@article {pmid35714829, year = {2022}, author = {Zhu, Y and Liao, X and Han, T and Chen, JY and He, C and Lu, Z}, title = {Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration.}, journal = {Genomics}, volume = {114}, number = {4}, pages = {110404}, doi = {10.1016/j.ygeno.2022.110404}, pmid = {35714829}, issn = {1089-8646}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; *MicroRNAs/genetics ; Symbiosis ; Transcriptome ; }, abstract = {Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.}, }
@article {pmid35698170, year = {2022}, author = {Wang, K and Gao, P and Geng, L and Liu, C and Zhang, J and Shu, C}, title = {Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {90}, pmid = {35698170}, issn = {2049-2618}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Fermentation ; Gastrointestinal Tract ; Larva ; *Lignin/metabolism ; }, abstract = {BACKGROUND: The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.<br><br>RESULTS: Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.<br><br>CONCLUSIONS: This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.}, }
@article {pmid35674443, year = {2022}, author = {Low, A and Soh, M and Miyake, S and Seedorf, H}, title = {Host Age Prediction from Fecal Microbiota Composition in Male C57BL/6J Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0073522}, pmid = {35674443}, issn = {2165-0497}, mesh = {Animals ; Bacteroidetes ; Bayes Theorem ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {The lifelong relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Microbiome composition throughout the life span of a host remains largely understudied. Here, the fecal microbiota of conventionally raised C57BL/6J male mice was characterized throughout almost the entire adult life span, from "maturing" (9 weeks) until "very old" (112 weeks) age. Our results suggest that microbiota changes occur throughout life but are more pronounced in maturing to middle-age mice than in mice later in life. Phylum-level analysis indicates a shift of the Bacteroidota-to-Firmicutes ratio in favor of Firmicutes in old and very old mice. More Firmicutes amplicon sequence variants (ASVs) were transient with varying successional patterns than Bacteroidota ASVs, which varied primarily during maturation. Microbiota configurations from five defined life phases were used as training sets in a Bayesian model, which effectively enabled the prediction of host age. These results suggest that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. The sensitivity of the age prediction to dietary perturbations was tested by applying this approach to two age-matched groups of C57BL/6J mice that were fed either a standard or western diet. The predicted age for the western diet-fed animals was on average 27 ± 11 (mean ± standard deviation) weeks older than that of standard diet-fed animals. This indicates that the fecal microbiota-based predicted age may be influenced not only by the host age and physiology but also potentially by other factors such as diet. IMPORTANCE The gut microbiome of a host changes with age. Cross-sectional studies demonstrate that microbiota of different age groups are distinct but do not demonstrate the temporal change that a longitudinal study is able to show. Here, we performed a longitudinal study of adult mice for over 2 years. We identified life stages where compositional changes were more dynamic and showed temporal changes for the more abundant species. Using a Bayesian model, we could reliably predict the life stages of the mice. Application of the same training set to mice fed different dietary regimens revealed that life-stage age predictions were possible for mice fed the same diet but less so for mice fed different diets. This study sheds light on the temporal changes that occur within the gut microbiota of laboratory mice over their life span and may inform researchers on the appropriate mouse age for their research.}, }
@article {pmid35669951, year = {2022}, author = {Jury, CP and Boeing, BM and Trapido-Rosenthal, H and Gates, RD and Toonen, RJ}, title = {Nitric oxide production rather than oxidative stress and cell death is associated with the onset of coral bleaching in Pocillopora acuta.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13321}, pmid = {35669951}, issn = {2167-8359}, mesh = {Animals ; *Coral Reefs ; Nitric Oxide/metabolism ; Coral Bleaching ; *Anthozoa/metabolism ; Oxidative Stress ; Cell Death ; Nitric Oxide Synthase/metabolism ; }, abstract = {Elevated seawater temperatures associated with climate change lead to coral bleaching. While the ultimate causes of bleaching are well understood, the proximate physiological mechanisms underlying the bleaching response are not as well defined. Here we measured nitric oxide synthase activity, oxidative stress, and cell death in algal symbionts (Symbiodinaceae) freshly isolated from the reef-building coral Pocillopora acuta collected in the field under natural non-bleaching conditions and from corals experimentally exposed to elevated temperatures. Nitric oxide synthase activity in the algal symbionts was >3 orders of magnitude higher than that of the host and increased dramatically with increasing temperature and time of exposure (up to 72 h), consistent with the onset of bleaching for these corals. Oxidative stress and cell death among the algal symbionts were highest in coral holobionts exposed to intermediate as opposed to maximal temperatures, suggesting that these mechanisms are not proximal triggers for bleaching in this species. Our results point to nitric oxide production by the algal symbionts, rather than symbiont dysfunction, as a more important driver of coral bleaching under acute thermal stress in this coral.}, }
@article {pmid35654830, year = {2022}, author = {Hudspith, M and de Goeij, JM and Streekstra, M and Kornder, NA and Bougoure, J and Guagliardo, P and Campana, S and van der Wel, NN and Muyzer, G and Rix, L}, title = {Harnessing solar power: photoautotrophy supplements the diet of a low-light dwelling sponge.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2076-2086}, pmid = {35654830}, issn = {1751-7370}, support = {715513//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {Animals ; Carbon ; Diet ; Ecosystem ; *Porifera ; *Solar Energy ; Water ; }, abstract = {The ability of organisms to combine autotrophy and heterotrophy gives rise to one of the most successful nutritional strategies on Earth: mixotrophy. Sponges are integral members of shallow-water ecosystems and many host photosynthetic symbionts, but studies on mixotrophic sponges have focused primarily on species residing in high-light environments. Here, we quantify the contribution of photoautotrophy to the respiratory demand and total carbon diet of the sponge Chondrilla caribensis, which hosts symbiotic cyanobacteria and lives in low-light environments. Although the sponge is net heterotrophic at 20 m water depth, photosynthetically fixed carbon potentially provides up to 52% of the holobiont's respiratory demand. When considering the total mixotrophic diet, photoautotrophy contributed an estimated 7% to total daily carbon uptake. Visualization of inorganic [13]C- and [15]N-incorporation using nanoscale secondary ion mass spectrometry (NanoSIMS) at the single-cell level confirmed that a portion of nutrients assimilated by the prokaryotic community was translocated to host cells. Photoautotrophy can thus provide an important supplemental source of carbon for sponges, even in low-light habitats. This trophic plasticity may represent a widespread strategy for net heterotrophic sponges hosting photosymbionts, enabling the host to buffer against periods of nutritional stress.}, }
@article {pmid35648435, year = {2022}, author = {Høie, MH and Kiehl, EN and Petersen, B and Nielsen, M and Winther, O and Nielsen, H and Hallgren, J and Marcatili, P}, title = {NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W510-W515}, pmid = {35648435}, issn = {1362-4962}, mesh = {Amino Acid Sequence ; *Deep Learning ; *Protein Structure, Secondary ; *Proteins/chemistry/metabolism ; *Natural Language Processing ; Datasets as Topic ; Solvents/chemistry ; Time Factors ; Internet ; Computers ; Software ; }, abstract = {Recent advances in machine learning and natural language processing have made it possible to profoundly advance our ability to accurately predict protein structures and their functions. While such improvements are significantly impacting the fields of biology and biotechnology at large, such methods have the downside of high demands in terms of computing power and runtime, hampering their applicability to large datasets. Here, we present NetSurfP-3.0, a tool for predicting solvent accessibility, secondary structure, structural disorder and backbone dihedral angles for each residue of an amino acid sequence. This NetSurfP update exploits recent advances in pre-trained protein language models to drastically improve the runtime of its predecessor by two orders of magnitude, while displaying similar prediction performance. We assessed the accuracy of NetSurfP-3.0 on several independent test datasets and found it to consistently produce state-of-the-art predictions for each of its output features, with a runtime that is up to to 600 times faster than the most commonly available methods performing the same tasks. The tool is freely available as a web server with a user-friendly interface to navigate the results, as well as a standalone downloadable package.}, }
@article {pmid35640792, year = {2022}, author = {Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Neves, RC and Jørgensen, A and Schiøtt, M and Gilbert, MTP and Møbjerg, N}, title = {Extreme freeze-tolerance in cryophilic tardigrades relies on controlled ice formation but does not involve significant change in transcription.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {271}, number = {}, pages = {111245}, doi = {10.1016/j.cbpa.2022.111245}, pmid = {35640792}, issn = {1531-4332}, mesh = {Animals ; Cold Temperature ; Freezing ; *Ice ; *Tardigrada/genetics ; Temperature ; }, abstract = {Subzero temperatures are among the most significant factors defining the distribution of organisms, yet, certain taxa have evolved to overcome this barrier. The microscopic tardigrades are among the most freeze-tolerant animals, with selected species reported to survive milli-Kelvin temperatures. Here, we estimate survival of fully hydrated eutardigrades of the species Ramazzottius varieornatus following exposures to -20 °C and -80 °C as well as -196 °C with or without initial cooling to -80 °C. The tardigrades easily survive these temperatures, yet with a significant decrease in viability following rapid cooling by direct exposure to -196 °C. Hence, post-freeze recovery of R. varieornatus seems to rely on cooling rate and thus controlled ice formation. Cryophilic organisms are renowned for having cold-active enzymes that secure appropriate reaction rates at low temperatures. Hence, extreme freeze-tolerance in R. varieornatus could potentially involve syntheses of cryoprotectants and de novo transcription. We therefore generated a reference transcriptome for this cryophilic R. varieornatus population and explored for differential gene expression patterns following cooling to -80 °C as compared to active 5 °C controls. Specifically, we tested for fast transcription potentially occurring within 25 min of cooling from room temperature to a supercooling point of ca. -20 °C, at which the tardigrades presumably freeze and enter into the ametabolic state of cryobiosis. Our analyses revealed no evidence for differential gene expression. We, therefore, conclude that extreme freeze-tolerance in R. varieornatus relies on controlled extracellular freezing with any freeze-tolerance related genes being constitutively expressed.}, }
@article {pmid35639297, year = {2022}, author = {Wang, G and Liu, J and Li, Y and Li, J and Luo, J and Chen, B and Liao, Z and Su, H and Liang, J and Yu, K}, title = {Description of Prasinibacter corallicola gen. nov., sp. nov., a zeaxanthin-producing bacterium isolated from stony coral Porites lutea.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {7}, pages = {933-941}, pmid = {35639297}, issn = {1572-9699}, support = {42090041//National Natural Sciences Foundation of China/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Bacterial Typing Techniques ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; Ninhydrin ; Phospholipids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Vitamin K 2/chemistry ; Zeaxanthins ; }, abstract = {Thermal stress is considered one of the main causes of mass scleractinian coral degradation; however, it is still unknown how corals can adapt to future global warming. In this study, 11 strains of coral-associated Flavobacteria were shown to produce zeaxanthin, a carotenoid antioxidant, which may help coral holobionts to alleviate thermal stress. In addition, a novel zeaxanthin-producing Flavobacterium, designated R38[T], was identified using polyphasic taxonomy. Although strain R38[T] shared a maximum 16S rRNA gene sequence similarity of 93% with Mesoflavibacter aestuarii KYW614[T], phylogenetic analyses based on whole genome and 16S rRNA gene sequences revealed that strain R38[T] forms a distinct branch in a robust cluster composed of strain R38[T] and Leptobacterium flavescens KCTC 22160[T] under the family Flavobacteriaceae. Strain R38[T] exhibited average nucleotide identities of 70.2% and 72.5% for M. aestuarii KYW614[T] and L. flavescens KCTC 22160[T], respectively. The only detected respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G + C content was 33.2 mol%. The major polar lipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified ninhydrin phospholipid, three unidentified ninhydrin-positive lipids, and three unidentified lipids. The major cellular fatty acids were iso - C15: 0, iso - C15: 0 ω6c, C16:2 DMA, and C13:1 ω3c. The distinct biochemical, chemotaxonomic, phylogenetic, and phylogenomic differences from validly published taxa suggest that strain R38[T] represents a new species of a new genus, for which Prasinibacter corallicola gen. nov., sp. nov. is proposed. The type strain R38[T] (= MCCC 1K03889[T] = KCTC 72444[T]).}, }
@article {pmid35635927, year = {2022}, author = {Zwart, H}, title = {"Love is a microbe too": Microbiome dialectics.}, journal = {Endeavour}, volume = {46}, number = {1-2}, pages = {100816}, doi = {10.1016/j.endeavour.2022.100816}, pmid = {35635927}, issn = {1873-1929}, mesh = {Human Genome Project ; Humans ; Language ; *Microbiota ; Symbiosis ; }, abstract = {Whereas the Human Genome Project was an anthropocentric research endeavour, microbiome research entails a much more interactive and symbiotic view of human existence, seeing human beings as holobionts, a term coined by Lynn Margulis to emphasise the interconnectedness and multiplicity of organisms. In this paper, building on previous authors, a dialectical perspective on microbiome research will be adopted, striving to supersede the ontological divide between self and other, humans and microbes, and to incorporate the microbiome as a crucial dimension of human existence, not only corporally, but also in terms of mood and cognition. On the practical level, microbiome insights promise to offer opportunities for self-care and self-management, allowing us to consciously interact with our microbiome to foster wellness and health. How to distinguish realistic scenarios from hype? Here again, an interactive (dialectical) approach is adopted, arguing that practices of the self should result from mutual learning between laboratory research and life-world experience.}, }
@article {pmid35630391, year = {2022}, author = {Hernandez, J and Rhimi, S and Kriaa, A and Mariaule, V and Boudaya, H and Drut, A and Jablaoui, A and Mkaouar, H and Saidi, A and Biourge, V and Borgi, MA and Rhimi, M and Maguin, E}, title = {Domestic Environment and Gut Microbiota: Lessons from Pet Dogs.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630391}, issn = {2076-2607}, support = {PS-Com-Pro Project//Royal Canin/ ; 41786NC//Campus France/ ; MICAfrica 952583//European Commission/ ; }, abstract = {Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota-host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.}, }
@article {pmid35620601, year = {2022}, author = {Lin, S and Yu, K and Zhou, Z}, title = {Editorial: Physiological Regulation and Homeostasis Among Coral Holobiont Partners.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {921401}, pmid = {35620601}, issn = {1664-042X}, }
@article {pmid35619157, year = {2022}, author = {Sahu, KP and Kumar, A and Sakthivel, K and Reddy, B and Kumar, M and Patel, A and Sheoran, N and Gopalakrishnan, S and Prakash, G and Rathour, R and Gautam, RK}, title = {Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {28}, pmid = {35619157}, issn = {2524-6372}, support = {File No: 09/083(0367)/2016-EMR-I//Council&#xa0;of&#xa0;Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future.<br><br>RESULTS: The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network&#xa0;analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings.<br><br>CONCLUSIONS: PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.}, }
@article {pmid35609205, year = {2022}, author = {Demarchi, B and Stiller, J and Grealy, A and Mackie, M and Deng, Y and Gilbert, T and Clarke, J and Legendre, LJ and Boano, R and Sicheritz-Pontén, T and Magee, J and Zhang, G and Bunce, M and Collins, MJ and Miller, G}, title = {Ancient proteins resolve controversy over the identity of Genyornis eggshell.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2109326119}, pmid = {35609205}, issn = {1091-6490}, mesh = {Animals ; Humans ; Phylogeny ; *Egg Shell ; *Birds/genetics ; DNA/genetics ; Biological Evolution ; Fossils ; DNA, Ancient ; }, abstract = {The realization that ancient biomolecules are preserved in "fossil" samples has revolutionized archaeological science. Protein sequences survive longer than DNA, but their phylogenetic resolution is inferior; therefore, careful assessment of the research questions is required. Here, we show the potential of ancient proteins preserved in Pleistocene eggshell in addressing a longstanding controversy in human and animal evolution: the identity of the extinct bird that laid large eggs which were exploited by Australia's indigenous people. The eggs had been originally attributed to the iconic extinct flightless bird Genyornis newtoni (†Dromornithidae, Galloanseres) and were subsequently dated to before 50 ± 5 ka by Miller et al. [Nat. Commun. 7, 10496 (2016)]. This was taken to represent the likely extinction date for this endemic megafaunal species and thus implied a role of humans in its demise. A contrasting hypothesis, according to which the eggs were laid by a large mound-builder megapode (Megapodiidae, Galliformes), would therefore acquit humans of their responsibility in the extinction of Genyornis. Ancient protein sequences were reconstructed and used to assess the evolutionary proximity of the undetermined eggshell to extant birds, rejecting the megapode hypothesis. Authentic ancient DNA could not be confirmed from these highly degraded samples, but morphometric data also support the attribution of the eggshell to Genyornis. When used in triangulation to address well-defined hypotheses, paleoproteomics is a powerful tool for reconstructing the evolutionary history in ancient samples. In addition to the clarification of phylogenetic placement, these data provide a more nuanced understanding of the modes of interactions between humans and their environment.}, }
@article {pmid35604942, year = {2022}, author = {Ørsted, M and Yashiro, E and Hoffmann, AA and Kristensen, TN}, title = {Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness.}, journal = {PLoS genetics}, volume = {18}, number = {5}, pages = {e1010206}, pmid = {35604942}, issn = {1553-7404}, mesh = {Animals ; Drosophila melanogaster/genetics ; *Genetic Fitness ; Genetic Variation ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is becoming increasingly clear that microbial symbionts influence key aspects of their host's fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.}, }
@article {pmid35604874, year = {2022}, author = {Snelders, NC and Rovenich, H and Thomma, BPHJ}, title = {Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom.}, journal = {FEMS microbiology reviews}, volume = {46}, number = {5}, pages = {}, pmid = {35604874}, issn = {1574-6976}, mesh = {Animals ; Fungi ; Mammals ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.}, }
@article {pmid35602056, year = {2022}, author = {Ren, CG and Kong, CC and Liu, ZY and Zhong, ZH and Yang, JC and Wang, XL and Qin, S}, title = {A Perspective on Developing a Plant 'Holobiont' for Future Saline Agriculture.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {763014}, pmid = {35602056}, issn = {1664-302X}, abstract = {Soil salinity adversely affects plant growth and has become a major limiting factor for agricultural development worldwide. There is a continuing demand for sustainable technology innovation in saline agriculture. Among various bio-techniques being used to reduce the salinity hazard, symbiotic microorganisms such as rhizobia and arbuscular mycorrhizal (AM) fungi have proved to be efficient. These symbiotic associations each deploy an array of well-tuned mechanisms to provide salinity tolerance for the plant. In this review, we first comprehensively cover major research advances in symbiont-induced salinity tolerance in plants. Second, we describe the common signaling process used by legumes to control symbiosis establishment with rhizobia and AM fungi. Multi-omics technologies have enabled us to identify and characterize more genes involved in symbiosis, and eventually, map out the key signaling pathways. These developments have laid the foundation for technological innovations that use symbiotic microorganisms to improve crop salt tolerance on a larger scale. Thus, with the aim of better utilizing symbiotic microorganisms in saline agriculture, we propose the possibility of developing non-legume 'holobionts' by taking advantage of newly developed genome editing technology. This will open a new avenue for capitalizing on symbiotic microorganisms to enhance plant saline tolerance for increased sustainability and yields in saline agriculture.}, }
@article {pmid35590396, year = {2022}, author = {Unzueta-Martínez, A and Scanes, E and Parker, LM and Ross, PM and O'Connor, W and Bowen, JL}, title = {Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {32}, pmid = {35590396}, issn = {2524-4671}, support = {1938052//National Science Foundation/ ; 1451070//National Science Foundation/ ; }, abstract = {BACKGROUND: The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.<br><br>RESULTS: We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.<br><br>CONCLUSION: Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome.}, }
@article {pmid35589992, year = {2023}, author = {King, NG and Moore, PJ and Thorpe, JM and Smale, DA}, title = {Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1265-1275}, pmid = {35589992}, issn = {1432-184X}, support = {MR/S032827/1/MRC_/Medical Research Council/United Kingdom ; MR/S032827/1//UKRI/ ; NE/S011692/1//Natural Environment Research Council/ ; }, mesh = {Humans ; *Kelp/microbiology ; Ecosystem ; *Laminaria/microbiology ; Forests ; Bacteria/genetics ; *Microbiota ; }, abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35589814, year = {2022}, author = {Drury, C and Bean, NK and Harris, CI and Hancock, JR and Huckeba, J and H, CM and Roach, TNF and Quinn, RA and Gates, RD}, title = {Intrapopulation adaptive variance supports thermal tolerance in a reef-building coral.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {486}, pmid = {35589814}, issn = {2399-3642}, mesh = {Animals ; *Anthozoa/genetics ; Chromatography, Liquid ; Coral Reefs ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Coral holobionts are multi-species assemblages, which adds significant complexity to genotype-phenotype connections underlying ecologically important traits like coral bleaching. Small scale heterogeneity in bleaching is ubiquitous in the absence of strong environmental gradients, which provides adaptive variance needed for the long-term persistence of coral reefs. We used RAD-seq, qPCR and LC-MS/MS metabolomics to characterize host genomic variation, symbiont community and biochemical correlates in two bleaching phenotypes of the vertically transmitting coral Montipora capitata. Phenotype was driven by symbiosis state and host genetic variance. We documented 5 gene ontologies that were significantly associated with both the binary bleaching phenotype and symbiont composition, representing functions that confer a phenotype via host-symbiont interactions. We bred these corals and show that symbiont communities were broadly conserved in bulk-crosses, resulting in significantly higher survivorship under temperature stress in juveniles, but not larvae, from tolerant parents. Using a select and re-sequence approach, we document numerous gene ontologies selected by heat stress, some of which (cell signaling, antioxidant activity, pH regulation) have unique selection dynamics in larvae from thermally tolerant parents. These data show that vertically transmitting corals may have an adaptive advantage under climate change if host and symbiont variance interact to influence bleaching phenotype.}, }
@article {pmid35588270, year = {2022}, author = {Bashir, F and Kovács, S and Ábrahám, &#xc1; and Nagy, K and Ayaydin, F and Valkony-Kelemen, I and Ferenc, G and Galajda, P and Tóth, SZ and Sass, L and Kós, PB and Vass, I and Szabó, M}, title = {Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform.}, journal = {Lab on a chip}, volume = {22}, number = {16}, pages = {2986-2999}, doi = {10.1039/d2lc00130f}, pmid = {35588270}, issn = {1473-0189}, mesh = {Animals ; *Anthozoa/physiology ; *Dinoflagellida/physiology ; Microfluidics ; Protoplasts ; Reactive Oxygen Species ; Singlet Oxygen ; }, abstract = {Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.}, }
@article {pmid35579919, year = {2022}, author = {Soldan, R and Fusi, M and Preston, GM}, title = {Approaching the domesticated plant holobiont from a community evolution perspective.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {5}, pages = {}, doi = {10.1099/mic.0.001188}, pmid = {35579919}, issn = {1465-2080}, support = {BB/M011224/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R009236/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Microbiota/genetics ; Phenotype ; *Plants ; }, abstract = {Plants establish a pivotal relationship with their microbiome and are often conceptualized as holobionts. Nonetheless, holobiont theories have attracted much criticism, especially concerning the fact that the holobiont is rarely a unit of selection. In previous work, we discussed how the plant microbiome can be considered to be an 'ecosystem on a leash', which is subject to the influence of natural selection acting on plant traits. We proposed that in domesticated plants the assembly of the plant microbiome can usefully be conceptualized as being subject to a 'double leash', which encompasses both the effect of artificial selection imposed by the domesticator on plant traits and the leash from the plant to the microbiome. Here we approach the domesticated plant holobiont, simply defined as a community of organisms, from a community evolution point of view, and show how community heritability (a measure of community selection) complements the 'double-leash' framework in providing a community-level view of plant domestication and its impact on plant-microbe interactions. We also propose simple experiments that could be performed to investigate whether plant domestication has altered the potential for community selection at the holobiont level.}, }
@article {pmid35578838, year = {2023}, author = {de Oliveira, BFR and Freitas-Silva, J and Canellas, ALB and Costa, WF and Laport, MS}, title = {Time for a Change! A Spotlight on Many Neglected Facets of Sponge Microbial Biotechnology.}, journal = {Current pharmaceutical biotechnology}, volume = {24}, number = {4}, pages = {471-485}, doi = {10.2174/1389201023666220516103715}, pmid = {35578838}, issn = {1873-4316}, mesh = {Animals ; *Anti-Infective Agents/pharmacology/therapeutic use/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Biotechnology ; *Microbiota ; *Porifera ; }, abstract = {The sponge-microorganism partnership is one of the most successful symbiotic associations exploited from a biotechnological perspective. During the last thirty years, sponge-associated bacteria have been increasingly harnessed for bioactive molecules, notably antimicrobials and cytotoxic compounds. Unfortunately, there are gaps in sponge microbial biotechnology, with a multitude of applications being understudied or ignored. In this context, the current perspective aims to shed light on these underrated facets of sponge microbial biotechnology with a balance of existent reports and proposals for further research in the field. Our overview has showcased that the members of the sponge microbiome produce biomolecules whose usage can be valuable for several economically- relevant and demanding sectors. Outside the exhaustive search for antimicrobial secondary metabolites, sponge-associated microorganisms are gifted producers of antibiofilm, antivirulence and chronic diseases-attenuating substances highly envisaged by the pharmaceutical industry. Despite still at an infant stage of research, anti-ageing enzymes and pigments of special interest for the cosmetic and cosmeceutical sectors have also been reported from the sponge microbial symbionts. In a world urging for sustainability, sponge-associated microorganisms have been proven as fruitful resources for bioremediation, including recovery of heavy-metal contaminated areas, bioleaching processes, and as bioindicators of environmental pollution. In conclusion, we propose alternatives to better assess these neglected biotechnological applications of the sponge microbiome in the hope of sparking the interest of the scientific community toward their deserved exploitation.}, }
@article {pmid35568404, year = {2022}, author = {Chen, Y and Pan, T and Chai, G and Li, Z}, title = {Complete genome of Mycetocola spongiae MSC19[T] isolated from deep-sea sponge Cacospongia mycofijiensis indicates the adaptation to deep-sea environment and sponge-microbe symbioses.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100955}, doi = {10.1016/j.margen.2022.100955}, pmid = {35568404}, issn = {1876-7478}, mesh = {*Actinomycetales ; Animals ; Bacteria ; High-Throughput Nucleotide Sequencing ; Phylogeny ; *Porifera/microbiology ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Genome of Mycetocola spongiae MSC19[T], a novel marine sponge-associated Actinobacteria isolated from the Mariana Trench sponge Cacospongia mycofijiensis, was sequenced. The genome has one circular chromosome of 3,196,754 bp, with an average GC content of 66.43 mol%, and 2887 coding sequences. Gene annotation shows that M. spongiae MSC19[T] possesses series of genes related to adaptation to deep-sea environmental stresses including cold shock, heat shock, osmotic stress and oxidative stress. Genes encoding for heavy metal resistance, multidrug resistance and multiple natural product biosynthesis which are crucial for survival in the extreme environment are also detected in the genome. The potentials to synthesize kinds of vitamins and eukaryotic-like proteins indicates the possible nutrient exchange and mutual recognization between M. spongiae MSC19[T] and its sponge host. The genome provides insights into the stress resistance and ecological fitness of bacterial symbionts in the deep-sea sponge holobionts.}, }
@article {pmid35546350, year = {2022}, author = {Chua, PYS and Rasmussen, JA}, title = {Taking metagenomics under the wings.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {8}, pages = {447}, pmid = {35546350}, issn = {1740-1534}, mesh = {Animals ; *Metagenomics ; *Wings, Animal ; }, }
@article {pmid35538057, year = {2022}, author = {Patrono, LV and Vrancken, B and Budt, M and Düx, A and Lequime, S and Boral, S and Gilbert, MTP and Gogarten, JF and Hoffmann, L and Horst, D and Merkel, K and Morens, D and Prepoint, B and Schlotterbeck, J and Schuenemann, VJ and Suchard, MA and Taubenberger, JK and Tenkhoff, L and Urban, C and Widulin, N and Winter, E and Worobey, M and Schnalke, T and Wolff, T and Lemey, P and Calvignac-Spencer, S}, title = {Archival influenza virus genomes from Europe reveal genomic variability during the 1918 pandemic.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2314}, pmid = {35538057}, issn = {2041-1723}, support = {R01 HG006139/HG/NHGRI NIH HHS/United States ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genome, Viral/genetics ; Genomics ; Humans ; *Influenza A Virus, H1N1 Subtype/genetics ; *Influenza A virus/genetics ; *Influenza, Human/epidemiology/genetics ; }, abstract = {The 1918 influenza pandemic was the deadliest respiratory pandemic of the 20th century and determined the genomic make-up of subsequent human influenza A viruses (IAV). Here, we analyze both the first 1918 IAV genomes from Europe and the first from samples prior to the autumn peak. 1918 IAV genomic diversity is consistent with a combination of local transmission and long-distance dispersal events. Comparison of genomes before and during the pandemic peak shows variation at two sites in the nucleoprotein gene associated with resistance to host antiviral response, pointing at a possible adaptation of 1918 IAV to humans. Finally, local molecular clock modeling suggests a pure pandemic descent of seasonal H1N1 IAV as an alternative to the hypothesis of origination through an intrasubtype reassortment.}, }
@article {pmid35537882, year = {2022}, author = {Oláh, P and Szlávicz, E and Kuchner, M and Nemmer, J and Zeeuwen, P and Lefèvre-Utile, A and Fyhrquist, N and Prast-Nielsen, S and Skoog, T and Serra, A and Rodríguez, E and Raap, U and Meller, S and Gyulai, R and Hupé, P and Kere, J and Levi-Schaffer, F and Tsoka, S and Alexander, H and Nestle, FO and Schröder, JM and Weidinger, S and van den Bogaard, E and Soumelis, V and Greco, D and Barker, J and Lauerma, A and Ranki, A and Andersson, B and Alenius, H and Homey, B}, title = {Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation.}, journal = {Journal of dermatological science}, volume = {106}, number = {3}, pages = {132-140}, doi = {10.1016/j.jdermsci.2022.04.007}, pmid = {35537882}, issn = {1873-569X}, mesh = {*Dermatitis, Atopic/metabolism ; Filaggrin Proteins/*metabolism ; Host Microbial Interactions/genetics ; Humans ; Inflammation/genetics/metabolism ; Intermediate Filament Proteins/genetics/metabolism ; Mutation ; Skin/metabolism ; Staphylococcus aureus ; }, abstract = {BACKGROUND: Loss-of-function mutations in the filaggrin (FLG) gene directly alter skin barrier function and critically influence atopic inflammation. While skin barrier dysfunction, Th2-associated inflammation and bacterial dysbiosis are well-known characteristics of atopic dermatitis (AD), the mechanisms interconnecting genotype, transcriptome and microbiome remain largely elusive.<br><br>OBJECTIVE: In-depth analysis of FLG genotype-associated skin gene expression alterations and host-microbe interactions in AD.<br><br>METHODS: Multi-omics characterization of a cohort of AD patients carrying heterozygous loss-of-function mutations in the FLG gene (AD[Mut]) (n&#xa0;=&#xa0;15), along with matched wild-type (AD[Wt]) patients and healthy controls. Detailed clinical characterization, microarray gene expression and 16&#xa0;S rRNA-based microbial marker gene data were generated and analyzed.<br><br>RESULTS: In the context of filaggrin dysfunction, the transcriptome was characterized by dysregulation of barrier function and water homeostasis, while the lesional skin of AD[Wt] demonstrated the specific upregulation of pro-inflammatory cytokines and T-cell proliferation. S. aureus dominated the microbiome in both patient groups, however, shifting microbial communities could be observed when comparing healthy with non-lesional AD[Wt] or AD[Mut] skin, offering the opportunity to identify microbe-associated transcriptomic signatures. Moreover, an AD core signature with 28 genes, including CCL13, CCL18, BTC, SCIN, RAB31 and PCLO was identified.<br><br>CONCLUSIONS: Our integrative approach provides molecular insights for the concept that FLG loss-of-function mutations are a genetic shortcut to atopic inflammation and unravels the complex interplay between genotype, transcriptome and microbiome in the human holobiont.}, }
@article {pmid35537462, year = {2022}, author = {Cowen, LJ and Putnam, HM}, title = {Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.}, journal = {Annual review of biomedical data science}, volume = {5}, number = {}, pages = {205-231}, doi = {10.1146/annurev-biodatasci-122120-030732}, pmid = {35537462}, issn = {2574-3414}, mesh = {Animals ; *Anthozoa/genetics ; Computational Biology ; Coral Reefs ; *Microbiota/genetics ; Symbiosis/genetics ; }, abstract = {Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience.}, }
@article {pmid35524305, year = {2022}, author = {Carrier, TJ and Maldonado, M and Schmittmann, L and Pita, L and Bosch, TCG and Hentschel, U}, title = {Symbiont transmission in marine sponges: reproduction, development, and metamorphosis.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {100}, pmid = {35524305}, issn = {1741-7007}, mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S ; Reproduction ; Symbiosis ; }, abstract = {Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.}, }
@article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0067922}, pmid = {35502903}, issn = {2150-7511}, mesh = {Animals ; Bacteria/genetics ; *Cestoda/genetics ; Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Parasites ; }, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, }
@article {pmid35482345, year = {2022}, author = {Gennery, AR}, title = {Seek and you shall find: immune lymphoid cells in holobiont health.}, journal = {Blood}, volume = {139}, number = {17}, pages = {2577-2578}, doi = {10.1182/blood.2022015801}, pmid = {35482345}, issn = {1528-0020}, mesh = {*Dysbiosis ; Humans ; Immunity, Mucosal ; Interleukin Receptor Common gamma Subunit ; Janus Kinase 3 ; Lymphocytes ; Severe Combined Immunodeficiency ; *Transplants ; }, }
@article {pmid35481756, year = {2022}, author = {Bell, JK and Mamet, SD and Helgason, B and Siciliano, SD}, title = {Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {10}, pages = {e0027322}, pmid = {35481756}, issn = {1098-5336}, mesh = {*Brassica napus/microbiology ; Plant Breeding ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection. IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.}, }
@article {pmid35480035, year = {2022}, author = {Zhang, XY and Wang, DH}, title = {Gut Microbial Community and Host Thermoregulation in Small Mammals.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {888324}, pmid = {35480035}, issn = {1664-042X}, abstract = {The endotherms, particularly the small mammals living in the polar region and temperate zone, are faced with extreme challenges for maintaining stable core body temperatures in harsh cold winter. The non-hibernating small mammals increase metabolic rate including obligatory thermogenesis (basal/resting metabolic rate, BMR/RMR) and regulatory thermogenesis (mainly nonshivering thermogenesis, NST, in brown adipose tissue and skeletal muscle) to maintain thermal homeostasis in cold conditions. A substantial amount of evidence indicates that the symbiotic gut microbiota are sensitive to air temperature, and play an important function in cold-induced thermoregulation, via bacterial metabolites and byproducts such as short-chain fatty acids and secondary bile acids. Cold signal is sensed by specific thermosensitive transient receptor potential channels (thermo-TRPs), and then norepinephrine (NE) is released from sympathetic nervous system (SNS) and thyroid hormones also increase to induce NST. Meanwhile, these neurotransmitters and hormones can regulate the diversity and compositions of the gut microbiota. Therefore, cold-induced NST is controlled by both Thermo-TRPs-SNS-gut microbiota axis and thyroid-gut microbiota axis. Besides physiological thermoregulation, small mammals also rely on behavioral regulation, such as huddling and coprophagy, to maintain energy and thermal homeostasis, and the gut microbial community is involved in these processes. The present review summarized the recent progress in the gut microbiota and host physiological and behavioral thermoregulation in small mammals for better understanding the evolution and adaption of holobionts (host and symbiotic microorganism). The coevolution of host-microorganism symbionts promotes individual survival, population maintenance, and species coexistence in the ecosystems with complicated, variable environments.}, }
@article {pmid35476981, year = {2022}, author = {Weagley, JS and Zaydman, M and Venkatesh, S and Sasaki, Y and Damaraju, N and Yenkin, A and Buchser, W and Rodionov, DA and Osterman, A and Ahmed, T and Barratt, MJ and DiAntonio, A and Milbrandt, J and Gordon, JI}, title = {Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.}, journal = {Cell reports}, volume = {39}, number = {4}, pages = {110738}, pmid = {35476981}, issn = {2211-1247}, support = {R37 NS065053/NS/NINDS NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 NS087632/NS/NINDS NIH HHS/United States ; RF1 AG013730/AG/NIA NIH HHS/United States ; P30 DK056341/DK/NIDDK NIH HHS/United States ; R01 NS119812/NS/NINDS NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; U2C DK119886/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/metabolism ; Child ; Cyclic ADP-Ribose ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; *Malnutrition ; Mice ; NAD/metabolism ; NAD+ Nucleosidase/metabolism ; Receptors, Interleukin-1 ; }, abstract = {Perturbed gut microbiome development has been linked to childhood malnutrition. Here, we characterize bacterial Toll/interleukin-1 receptor (TIR) protein domains that metabolize nicotinamide adenine dinucleotide (NAD), a co-enzyme with far-reaching effects on human physiology. A consortium of 26 human gut bacterial strains, representing the diversity of TIRs observed in the microbiome and the NAD hydrolase (NADase) activities of a subset of 152 bacterial TIRs assayed in vitro, was introduced into germ-free mice. Integrating mass spectrometry and microbial RNA sequencing (RNA-seq) with consortium membership manipulation disclosed that a variant of cyclic-ADPR (v-cADPR-x) is a specific product of TIR NADase activity and a prominent, colonization-discriminatory, taxon-specific metabolite. Guided by bioinformatic analyses of biochemically validated TIRs, we find that acute malnutrition is associated with decreased fecal levels of genes encoding TIRs known or predicted to generate v-cADPR-x, as well as decreased levels of the metabolite itself. These results underscore the need to consider microbiome TIR NADases when evaluating NAD metabolism in the human holobiont.}, }
@article {pmid35459887, year = {2022}, author = {Yang, J and Shin, TS and Kim, JS and Jee, YK and Kim, YK}, title = {A new horizon of precision medicine: combination of the microbiome and extracellular vesicles.}, journal = {Experimental &amp; molecular medicine}, volume = {54}, number = {4}, pages = {466-482}, pmid = {35459887}, issn = {2092-6413}, mesh = {Cell Communication ; *Exosomes/metabolism ; *Extracellular Vesicles/metabolism ; Humans ; *Microbiota ; Precision Medicine ; }, abstract = {Over several decades, the disease pattern of intractable disease has changed from acute infection to chronic disease accompanied by immune and metabolic dysfunction. In addition, scientific evidence has shown that humans are holobionts; of the DNA in humans, 1% is derived from the human genome, and 99% is derived from microbial genomes (the microbiome). Extracellular vesicles (EVs) are lipid bilayer-delimited nanoparticles and key messengers in cell-to-cell communication. Many publications indicate that microbial EVs are both positively and negatively involved in the pathogenesis of various intractable diseases, including inflammatory diseases, metabolic disorders, and cancers. Microbial EVs in feces, blood, and urine show significant differences in their profiles between patients with a particular disease and healthy subjects, demonstrating the potential of microbial EVs as biomarkers for disease diagnosis, especially for assessing disease risk. Furthermore, microbial EV therapy offers a variety of advantages over live biotherapeutics and human cell EV (or exosome) therapy for the treatment of intractable diseases. In summary, microbial EVs are a new tool in medicine, and microbial EV technology might provide us with innovative diagnostic and therapeutic solutions in precision medicine.}, }
@article {pmid35452284, year = {2022}, author = {Field, MA and Yadav, S and Dudchenko, O and Esvaran, M and Rosen, BD and Skvortsova, K and Edwards, RJ and Keilwagen, J and Cochran, BJ and Manandhar, B and Bustamante, S and Rasmussen, JA and Melvin, RG and Chernoff, B and Omer, A and Colaric, Z and Chan, EKF and Minoche, AE and Smith, TPL and Gilbert, MTP and Bogdanovic, O and Zammit, RA and Thomas, T and Aiden, EL and Ballard, JWO}, title = {The Australian dingo is an early offshoot of modern breed dogs.}, journal = {Science advances}, volume = {8}, number = {16}, pages = {eabm5944}, pmid = {35452284}, issn = {2375-2548}, support = {RM1 HG011016/HG/NHGRI NIH HHS/United States ; U01 HL130010/HL/NHLBI NIH HHS/United States ; U01 HL156059/HL/NHLBI NIH HHS/United States ; UM1 HG009375/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Australia ; Breeding ; *Canidae/genetics ; Dogs ; Phylogeny ; *Wolves/genetics ; }, abstract = {Dogs are uniquely associated with human dispersal and bring transformational insight into the domestication process. Dingoes represent an intriguing case within canine evolution being geographically isolated for thousands of years. Here, we present a high-quality de novo assembly of a pure dingo (CanFam_DDS). We identified large chromosomal differences relative to the current dog reference (CanFam3.1) and confirmed no expanded pancreatic amylase gene as found in breed dogs. Phylogenetic analyses using variant pairwise matrices show that the dingo is distinct from five breed dogs with 100% bootstrap support when using Greenland wolf as the outgroup. Functionally, we observe differences in methylation patterns between the dingo and German shepherd dog genomes and differences in serum biochemistry and microbiome makeup. Our results suggest that distinct demographic and environmental conditions have shaped the dingo genome. In contrast, artificial human selection has likely shaped the genomes of domestic breed dogs after divergence from the dingo.}, }
@article {pmid35444618, year = {2022}, author = {Happel, L and Rondon, R and Font, A and González-Aravena, M and Cárdenas, CA}, title = {Stability of the Microbiome of the Sponge Mycale (Oxymycale) acerata in the Western Antarctic Peninsula.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {827863}, pmid = {35444618}, issn = {1664-302X}, abstract = {The sponge microbiome, especially in Low Microbial Abundance (LMA) species, is expected to be influenced by the local environment; however, contrasting results exist with evidence showing that host specificity is also important, hence suggesting that the microbiome is influenced by host-specific and environmental factors. Despite sponges being important members of Southern Ocean benthic communities, their relationships with the microbial communities they host remain poorly studied. Here, we studied the spatial and temporal patterns of the microbiota associated with the ecologically important LMA sponge M. acerata at sites along ∼400 km of the Western Antarctic Peninsula (WAP) to assess patterns in the core and variable microbial components of the symbiont communities of this sponge species. The analyses of 31 samples revealed that the microbiome of M. acerata is composed of 35 prokaryotic phyla (3 Archaea, 31 Bacteria, and one unaffiliated), being mainly dominated by Proteobacteria with Gammaproteobacteria as the most dominant class. The core community was composed of six prokaryotic OTUs, with gammaproteobacterial OTU (EC94 Family), showing a mean abundance over 65% of the total abundance. Despite some differences in rare OTUs, the core community did not show clear patterns in diversity and abundance associated with specific sites/environmental conditions, confirming a low variability in community structure of this species along the WAP. The analysis at small scale (Doumer Island, Palmer Archipelago) showed no differences in space and time in the microbiome M. acerata collected at sites around the island, sampled in three consecutive years (2016-2018). Our results highlight the existence of a low spatial and temporal variability in the microbiome of M. acerata, supporting previous suggestions based on limited studies on this and other Antarctic sponges.}, }
@article {pmid35444262, year = {2022}, author = {Pogoreutz, C and Oakley, CA and Rädecker, N and Cárdenas, A and Perna, G and Xiang, N and Peng, L and Davy, SK and Ngugi, DK and Voolstra, CR}, title = {Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1883-1895}, pmid = {35444262}, issn = {1751-7370}, support = {URF/1/3400-01-01//King Abdullah University of Science and Technology (KAUST)/ ; 15902919 FP 029/19//Universit&#xe4;t Konstanz (University of Konstanz)/ ; 19-VUW-086//Royal Marsden NHS Foundation Trust (Royal Marsden)/ ; 201807565016//China Scholarship Council (CSC)/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; Cues ; *Gammaproteobacteria/genetics ; Proteomics ; Symbiosis ; Tissue Extracts ; }, abstract = {Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.}, }
@article {pmid35435631, year = {2022}, author = {Roggatz, CC and Hardege, JD and Saha, M}, title = {Correction to: Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions.}, journal = {Journal of chemical ecology}, volume = {48}, number = {4}, pages = {474}, doi = {10.1007/s10886-022-01357-3}, pmid = {35435631}, issn = {1573-1561}, }
@article {pmid35432258, year = {2022}, author = {Zhu, W and Liu, X and Zhu, M and Li, X and Yin, H and Huang, J and Wang, A and Li, X}, title = {Responses of Symbiodiniaceae Shuffling and Microbial Community Assembly in Thermally Stressed Acropora hyacinthus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {832081}, pmid = {35432258}, issn = {1664-302X}, abstract = {Although the importance of coral holobionts is widely accepted, the relationship between the flexibility of the microbial structure and the coral host is very complicated. Particularly, the community dynamics of holobionts and the stability of host-microbe interactions under different thermal stresses remain largely unknown. In the present study, we holistically explored the physiology and growth of Acropora hyacinthus in response to increased temperatures (from 26 to 33°C). We observed that bleaching corals with loss of algal symbionts reduced lipids and proteins to maintain their survival, leading to decreased tissue biomass and retarded growth. The diversity of Symbiodiniaceae and symbiont shuffling in the community structure was mainly caused by alterations in the relative abundance of the thermally sensitive but dominant clade C symbionts and low abundance of "background types." Bacterial diversity showed a decreasing trend with increasing temperature, whereas no significant shifts were observed in the bacterial community structure. This finding might be attributed to the local adjustment of specific microbial community members that did not affect the overall metabolic state of the coral holobiont, and there was no increase in the proportion of sequences identified as typically pathogenic or opportunistic taxa. The Sloan neutral community model showed that neutral processes could explain 42.37-58.43% of bacterial community variation. The Stegen null model analysis indicates that the stochastic processes explain a significantly higher proportion of community assembly than deterministic processes when the temperature was elevated. The weak effect of temperature on the bacterial community structure and assembly might be related to an increase in stochastic dominance. The interaction of bacterial communities exhibits a fluctuating and simplistic trend with increasing temperature. Moreover, temperature increases were sufficient to establish the high stability of bacterial networks, and a non-linear response was found between the complexity and stability of the networks. Our findings collectively provide new insights into successive changes in the scleractinian coral host and holobionts in response to elevated seawater temperatures, especially the contribution of the community assembly process and species coexistence patterns to the maintenance of the coral-associated bacterial community.}, }
@article {pmid35432234, year = {2022}, author = {Quintanilla, E and Rodrigues, CF and Henriques, I and Hilário, A}, title = {Microbial Associations of Abyssal Gorgonians and Anemones (&gt;4,000 m Depth) at the Clarion-Clipperton Fracture Zone.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828469}, pmid = {35432234}, issn = {1664-302X}, abstract = {Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.}, }
@article {pmid35428831, year = {2022}, author = {Berlinghof, J and Peiffer, F and Marzocchi, U and Munari, M and Quero, GM and Dennis, L and Wild, C and Cardini, U}, title = {The role of epiphytes in seagrass productivity under ocean acidification.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6249}, pmid = {35428831}, issn = {2045-2322}, mesh = {*Alismatales/physiology ; Carbon Dioxide ; Hydrogen-Ion Concentration ; Plant Leaves ; *Seawater/chemistry ; }, abstract = {Ocean Acidification (OA), due to rising atmospheric CO2, can affect the seagrass holobiont by changing the plant's ecophysiology and the composition and functioning of its epiphytic community. However, our knowledge of the role of epiphytes in the productivity of the seagrass holobiont in response to environmental changes is still very limited. CO2 vents off Ischia Island (Italy) naturally reduce seawater pH, allowing to investigate the adaptation of the seagrass Posidonia oceanica L. (Delile) to OA. Here, we analyzed the percent cover of different epiphytic groups and the epiphytic biomass of P. oceanica leaves, collected inside (pH 6.9-7.9) and outside (pH 8.1-8.2) the CO2 vents. We estimated the contribution of epiphytes to net primary production (NPP) and respiration (R) of leaf sections collected from the vent and ambient pH sites in laboratory incubations. Additionally, we quantified net community production (NCP) and community respiration (CR) of seagrass communities in situ at vent and ambient pH sites using benthic chambers. Leaves at ambient pH sites had a 25% higher total epiphytic cover with encrusting red algae (32%) dominating the community, while leaves at vent pH sites were dominated by hydrozoans (21%). Leaf sections with and without epiphytes from the vent pH site produced and respired significantly more oxygen than leaf sections from the ambient pH site, showing an average increase of 47 ± 21% (mean ± SE) in NPP and 50 ± 4% in R, respectively. Epiphytes contributed little to the increase in R; however, their contribution to NPP was important (56 ± 6% of the total flux). The increase in productivity of seagrass leaves adapted to OA was only marginally reflected by the results from the in situ benthic chambers, underlining the complexity of the seagrass community response to naturally occurring OA conditions.}, }
@article {pmid35428367, year = {2022}, author = {Szitenberg, A and Beca-Carretero, P and Azcárate-García, T and Yergaliyev, T and Alexander-Shani, R and Winters, G}, title = {Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {18}, pmid = {35428367}, issn = {2524-6372}, support = {3-15152//Italy-Israel binational fund/ ; 03-16-06a//ICA in Israel/ ; }, abstract = {BACKGROUND: Halophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf epiphytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host.<br><br>RESULTS: In this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface.<br><br>CONCLUSIONS: Our results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.}, }
@article {pmid35418670, year = {2022}, author = {Titus, BM and Daly, M}, title = {Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?.}, journal = {Heredity}, volume = {128}, number = {5}, pages = {338-351}, pmid = {35418670}, issn = {1365-2540}, mesh = {Animals ; Genome/genetics ; Genomics/methods ; Humans ; *Metagenomics/methods ; Phylogeny ; *Sea Anemones/genetics ; Sequence Analysis, DNA ; }, abstract = {Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.}, }
@article {pmid35398946, year = {2023}, author = {Rolshausen, G and Dal Grande, F and Otte, J and Schmitt, I}, title = {Lichen holobionts show compositional structure along elevation.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6619-6630}, doi = {10.1111/mec.16471}, pmid = {35398946}, issn = {1365-294X}, mesh = {*Lichens/genetics/microbiology ; Ecosystem ; Environment ; Altitude ; Bacteria/genetics ; }, abstract = {Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.}, }
@article {pmid35397610, year = {2022}, author = {Strehlow, BW and Schuster, A and Francis, WR and Canfield, DE}, title = {Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {135}, pmid = {35397610}, issn = {1756-0500}, support = {16518//Villum Fonden/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; *Microbiota ; *Nanopore Sequencing ; *Porifera/genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.<br><br>DATA DESCRIPTION: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea-one Illumina MiSeq (2&#x2009;&#xd7;&#x2009;300&#xa0;bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the 'best' assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.}, }
@article {pmid35396623, year = {2023}, author = {Koide, RT}, title = {On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1143-1149}, pmid = {35396623}, issn = {1432-184X}, mesh = {Phylogeny ; *Symbiosis ; *Adaptation, Physiological ; Eukaryota ; Biological Evolution ; }, abstract = {My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.}, }
@article {pmid35393600, year = {2022}, author = {Sabrina Pankey, M and Plachetzki, DC and Macartney, KJ and Gastaldi, M and Slattery, M and Gochfeld, DJ and Lesser, MP}, title = {Cophylogeny and convergence shape holobiont evolution in sponge-microbe symbioses.}, journal = {Nature ecology &amp; evolution}, volume = {6}, number = {6}, pages = {750-762}, pmid = {35393600}, issn = {2397-334X}, mesh = {*Bacteria ; Biodiversity ; *Microbiota ; Phylogeny ; Symbiosis ; }, abstract = {Symbiotic microbial communities of sponges serve critical functions that have shaped the evolution of reef ecosystems since their origins. Symbiont abundance varies tremendously among sponges, with many species classified as either low microbial abundance (LMA) or high microbial abundance (HMA), but the evolutionary dynamics of these symbiotic states remain unknown. This study examines the LMA/HMA dichotomy across an exhaustive sampling of Caribbean sponge biodiversity and predicts that the LMA symbiotic state is the ancestral state among sponges. Conversely, HMA symbioses, consisting of more specialized microorganisms, have evolved multiple times by recruiting similar assemblages, mostly since the rise of scleractinian-dominated reefs. Additionally, HMA symbioses show stronger signals of phylosymbiosis and cophylogeny, consistent with stronger co-evolutionary interaction in these complex holobionts. These results indicate that HMA holobionts are characterized by increased endemism, metabolic dependence and chemical defences. The selective forces driving these patterns may include the concurrent increase in dissolved organic matter in reef ecosystems or the diversification of spongivorous fishes.}, }
@article {pmid35365219, year = {2022}, author = {Marasco, R and Fusi, M and Mosqueira, M and Booth, JM and Rossi, F and Cardinale, M and Michoud, G and Rolli, E and Mugnai, G and Vergani, L and Borin, S and De Philippis, R and Cherif, A and Daffonchio, D}, title = {Rhizosheath-root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {14}, pmid = {35365219}, issn = {2524-6372}, support = {CSA-SA REGPOT-2008-2//seventh framework programme/ ; Baseline research funds//king abdullah university of science and technology/ ; 841317//horizon 2020 framework programme/ ; 841317//horizon 2020 framework programme/ ; }, abstract = {BACKGROUND: In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath-root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert.<br><br>RESULTS: The belowground rhizosheath-root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath-root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath-root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment.<br><br>CONCLUSIONS: Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.}, }
@article {pmid35342582, year = {2022}, author = {Herrán, N and Narayan, GR and Doo, SS and Klicpera, A and Freiwald, A and Westphal, H}, title = {High-resolution imaging sheds new light on a multi-tier symbiotic partnership between a "walking" solitary coral, a sipunculan, and a bivalve from East Africa.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8633}, pmid = {35342582}, issn = {2045-7758}, abstract = {Marine symbioses are integral to the persistence of ecosystem functioning in coral reefs. Solitary corals of the species Heteropsammia cochlea and Heterocyathus aequicostatus have been observed to live in symbiosis with the sipunculan worm Aspidosiphon muelleri muelleri, which inhabits a cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these photosymbiotic corals enables the coral holobiont to move, in fine to coarse unconsolidated substrata, a process termed as "walking." This allows the coral to escape sediment cover in turbid conditions which is crucial for these light-dependent species. An additional commensalistic symbiosis of this coral-worm holobiont is found between the Aspidosiphon worm and the cryptoendolithic bivalve Jousseaumiella sp., which resides within the cavity of the coral skeleton. To understand the morphological alterations caused by these symbioses, interspecific relationships, with respect to the carbonate structures between these three organisms, are documented using high-resolution imaging techniques (scanning electron microscopy and µCT scanning). Documenting multi-layered symbioses can shed light on how morphological plasticity interacts with environmental conditions to contribute to species persistence.}, }
@article {pmid35341677, year = {2023}, author = {Tandon, K and Pasella, MM and Iha, C and Ricci, F and Hu, J and O'Kelly, CJ and Medina, M and Kühl, M and Verbruggen, H}, title = {Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business.}, journal = {Seminars in cell &amp; developmental biology}, volume = {134}, number = {}, pages = {27-36}, doi = {10.1016/j.semcdb.2022.03.010}, pmid = {35341677}, issn = {1096-3634}, mesh = {Animals ; *Chlorophyta ; *Anthozoa ; Coral Reefs ; Ecosystem ; }, abstract = {Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.}, }
@article {pmid35336242, year = {2022}, author = {Ratiner, K and Abdeen, SK and Goldenberg, K and Elinav, E}, title = {Utilization of Host and Microbiome Features in Determination of Biological Aging.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336242}, issn = {2076-2607}, abstract = {The term 'old age' generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person's life. Despite the conventional definition of old age as exceeding the age of 65 years old, quantifying aging as a function of life years does not necessarily reflect how the human body ages. In contrast, characterizing biological (or physiological) aging based on functional parameters may better reflect a person's temporal physiological status and associated disease susceptibility state. As such, differentiating 'chronological aging' from 'biological aging' holds the key to identifying individuals featuring accelerated aging processes despite having a young chronological age and stratifying them to tailored surveillance, diagnosis, prevention, and treatment. Emerging evidence suggests that the gut microbiome changes along with physiological aging and may play a pivotal role in a variety of age-related diseases, in a manner that does not necessarily correlate with chronological age. Harnessing of individualized gut microbiome data and integration of host and microbiome parameters using artificial intelligence and machine learning pipelines may enable us to more accurately define aging clocks. Such holobiont-based estimates of a person's physiological age may facilitate prediction of age-related physiological status and risk of development of age-associated diseases.}, }
@article {pmid35336184, year = {2022}, author = {Ducousso-Détrez, A and Fontaine, J and Lounès-Hadj Sahraoui, A and Hijri, M}, title = {Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336184}, issn = {2076-2607}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council/ ; Support for the A.D-D. Ph.D. thesis//R&#xe9;gion des Hauts de France/ ; }, abstract = {In many soils, the bioavailability of Phosphorus (P), an essential macronutrient is a limiting factor for crop production. Among the mechanisms developed to facilitate the absorption of phosphorus, the plant, as a holobiont, can rely on its rhizospheric microbial partners. Therefore, microbial P-solubilizing inoculants are proposed to improve soil P fertility in agriculture. However, a better understanding of the interactions of the soil-plant-microorganism continuum with the phosphorus cycle is needed to propose efficient inoculants. Before proposing further methods of research, we carried out a critical review of the literature in two parts. First, we focused on the diversity of P-chemical forms. After a review of P forms in soils, we describe multiple factors that shape these forms in soil and their turnover. Second, we provide an analysis of P as a driver of microbial community diversity in soil. Even if no rule enabling to explain the changes in the composition of microbial communities according to phosphorus has been shown, this element has been perfectly targeted as linked to the presence/absence and/or abundance of particular bacterial taxa. In conclusion, we point out the need to link soil phosphorus chemistry with soil microbiology in order to understand the variations in the composition of microbial communities as a function of P bioavailability. This knowledge will make it possible to propose advanced microbial-based inoculant engineering for the improvement of bioavailable P for plants in sustainable agriculture.}, }
@article {pmid35336179, year = {2022}, author = {Zommiti, M and Chevalier, S and Feuilloley, MGJ and Connil, N}, title = {Special Issue "Enterococci for Probiotic Use: Safety and Risk": Editorial.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336179}, issn = {2076-2607}, abstract = {Microorganisms, their activity, and metabolites are now considered as intrinsic elements of the human body and this awareness gave was leading to the concept of holobiont [...].}, }
@article {pmid35334142, year = {2022}, author = {Derežanin, L and Blažytė, A and Dobrynin, P and Duchêne, DA and Grau, JH and Jeon, S and Kliver, S and Koepfli, KP and Meneghini, D and Preick, M and Tomarovsky, A and Totikov, A and Fickel, J and Förster, DW}, title = {Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae.}, journal = {Molecular ecology}, volume = {31}, number = {10}, pages = {2898-2919}, doi = {10.1111/mec.16443}, pmid = {35334142}, issn = {1365-294X}, mesh = {Adaptation, Physiological/genetics ; Animals ; Genome ; Genomics ; *Mustelidae/genetics ; Phenotype ; }, abstract = {Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.}, }
@article {pmid35322689, year = {2022}, author = {Omae, N and Tsuda, K}, title = {Plant-Microbiota Interactions in Abiotic Stress Environments.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {35}, number = {7}, pages = {511-526}, doi = {10.1094/MPMI-11-21-0281-FI}, pmid = {35322689}, issn = {0894-0282}, mesh = {Agriculture ; Crops, Agricultural ; Humans ; *Microbiota ; Plant Development ; Stress, Physiological ; }, abstract = {Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid35310651, year = {2022}, author = {Chen, P and He, W and Shen, Y and Zhu, L and Yao, X and Sun, R and Dai, C and Sun, B and Chen, Y}, title = {Interspecific Neighbor Stimulates Peanut Growth Through Modulating Root Endophytic Microbial Community Construction.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {830666}, pmid = {35310651}, issn = {1664-462X}, abstract = {Plants have evolved the capability to respond to interspecific neighbors by changing morphological performance and reshaping belowground microbiota. However, whether neighboring plants influence the microbial colonization of the host's root and further affect host performance is less understood. In this study, using 16S rRNA high-throughput sequencing of peanut (Arachis hypogaea L.) roots from over 5 years of mono- and intercropping field systems, we found that neighbor maize can alter the peanut root microbial composition and re-shape microbial community assembly. Interspecific maize coexistence increased the colonization of genera Bradyrhizobium and Streptomyces in intercropped peanut roots. Through endophytic bacterial isolation and isolate back inoculation experiments, we demonstrated that the functional potentials of available nutrient accumulation and phytohormones production from Bradyrhizobium and Streptomyces endowed them with the ability to act as keystones in the microbial network to benefit peanut growth and production with neighbor competition. Our results support the idea that plants establish a plant-endophytic microbial holobiont through root selective filtration to enhance host competitive dominance, and provide a promising direction to develop modern diversified planting for harnessing crop microbiomes for the promotion of crop growth and productivity in sustainable agriculture.}, }
@article {pmid35308397, year = {2022}, author = {Taubenheim, J and Miklós, M and Tökölyi, J and Fraune, S}, title = {Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {799333}, pmid = {35308397}, issn = {1664-302X}, abstract = {Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.}, }
@article {pmid35303955, year = {2022}, author = {Cambon-Bonavita, MA and Aubé, J and Cueff-Gauchard, V and Reveillaud, J}, title = {Correction to: Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {51}, pmid = {35303955}, issn = {2049-2618}, }
@article {pmid35299055, year = {2022}, author = {Burgunter-Delamare, B and Tanguy, G and Legeay, E and Boyen, C and Dittami, SM}, title = {Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100944}, doi = {10.1016/j.margen.2022.100944}, pmid = {35299055}, issn = {1876-7478}, mesh = {DNA, Ribosomal ; *Kelp/genetics ; *Microbiota ; Nitrogen ; RNA ; RNA, Ribosomal, 16S/genetics ; *Seaweed ; Silica Gel ; }, abstract = {Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.}, }
@article {pmid35276225, year = {2022}, author = {Detmer, AR and Cunning, R and Pfab, F and Brown, AL and Stier, AC and Nisbet, RM and Moeller, HV}, title = {Fertilization by coral-dwelling fish promotes coral growth but can exacerbate bleaching response.}, journal = {Journal of theoretical biology}, volume = {541}, number = {}, pages = {111087}, doi = {10.1016/j.jtbi.2022.111087}, pmid = {35276225}, issn = {1095-8541}, mesh = {Animals ; *Anthozoa ; Carbon ; Coral Reefs ; Fertilization ; Fishes ; Nitrogen ; Symbiosis/physiology ; }, abstract = {Many corals form close associations with a diverse assortment of coral-dwelling fishes and other fauna. As coral reefs around the world are increasingly threatened by mass bleaching events, it is important to understand how these biotic interactions influence corals' susceptibility to bleaching. We used dynamic energy budget modeling to explore how nitrogen excreted by coral-dwelling fish affects the physiological performance of host corals. In our model, fish presence influenced the functioning of the coral-Symbiodiniaceae symbiosis by altering nitrogen availability, and the magnitude and sign of these effects depended on environmental conditions. Although our model predicted that fish-derived nitrogen can promote coral growth, the relationship between fish presence and coral tolerance of photo-oxidative stress was non-linear. Fish excretions supported denser symbiont populations that provided protection from incident light through self-shading. However, these symbionts also used more of their photosynthetic products for their own growth, rather than sharing with the coral host, putting the coral holobiont at a higher risk of becoming carbon-limited and bleaching. The balance between the benefits of increased symbiont shading and costs of reduced carbon sharing depended on environmental conditions. Thus, while there were some scenarios under which fish presence increased corals' tolerance of light stress, fish could also exacerbate bleaching and slow or prevent subsequent recovery. We discuss how the contrast between the potentially harmful effects of fish predicted by our model and results of empirical studies may relate to key model assumptions that warrant further investigation. Overall, this study provides a foundation for future work on how coral-associated fauna influence the bioenergetics of their host corals, which in turn has implications for how these corals respond to bleaching-inducing stressors.}, }
@article {pmid35273199, year = {2022}, author = {McLachlan, RH and Price, JT and Muñoz-Garcia, A and Weisleder, NL and Levas, SJ and Jury, CP and Toonen, RJ and Grottoli, AG}, title = {Physiological acclimatization in Hawaiian corals following a 22-month shift in baseline seawater temperature and pH.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {3712}, pmid = {35273199}, issn = {2045-2322}, mesh = {Acclimatization ; Animals ; *Anthozoa/physiology ; Coral Reefs ; Ecosystem ; Hawaii ; Hydrogen-Ion Concentration ; Lipids ; Seawater ; Temperature ; }, abstract = {Climate change poses a major threat to coral reefs. We conducted an outdoor 22-month experiment to investigate if coral could not just survive, but also physiologically cope, with chronic ocean warming and acidification conditions expected later this century under the Paris Climate Agreement. We recorded survivorship and measured eleven phenotypic traits to evaluate the holobiont responses of Hawaiian coral: color, Symbiodiniaceae density, calcification, photosynthesis, respiration, total organic carbon flux, carbon budget, biomass, lipids, protein, and maximum Artemia capture rate. Survivorship was lowest in Montipora capitata and only some survivors were able to meet metabolic demand and physiologically cope with future ocean conditions. Most M. capitata survivors bleached through loss of chlorophyll pigments and simultaneously experienced increased respiration rates and negative carbon budgets due to a 236% increase in total organic carbon losses under combined future ocean conditions. Porites compressa and Porites lobata had the highest survivorship and coped well under future ocean conditions with positive calcification and increased biomass, maintenance of lipids, and the capacity to exceed their metabolic demand through photosynthesis and heterotrophy. Thus, our findings show that significant biological diversity within resilient corals like Porites, and some genotypes of sensitive species, will persist this century provided atmospheric carbon dioxide levels are controlled. Since Porites corals are ubiquitous throughout the world's oceans and often major reef builders, the persistence of this resilient genus provides hope for future reef ecosystem function globally.}, }
@article {pmid35271794, year = {2022}, author = {Lin, J and Duchêne, D and Carøe, C and Smith, O and Ciucani, MM and Niemann, J and Richmond, D and Greenwood, AD and MacPhee, R and Zhang, G and Gopalakrishnan, S and Gilbert, MTP}, title = {Probing the genomic limits of de-extinction in the Christmas Island rat.}, journal = {Current biology : CB}, volume = {32}, number = {7}, pages = {1650-1656.e3}, pmid = {35271794}, issn = {1879-0445}, mesh = {Animals ; Australia ; Biological Evolution ; Extinction, Biological ; *Genome ; *Genomics ; Norway ; Phylogeny ; Rats ; }, abstract = {Three principal methods are under discussion as possible pathways to "true" de-extinction; i.e., back-breeding, cloning, and genetic engineering.[1,2] Of these, while the latter approach is most likely to apply to the largest number of extinct species, its potential is constrained by the degree to which the extinct species genome can be reconstructed. We explore this question using the extinct Christmas Island rat (Rattus macleari) as a model, an endemic rat species that was driven extinct between 1898 and 1908.[3-5] We first re-sequenced its genome to an average of >60× coverage, then mapped it to the reference genomes of different Rattus species. We then explored how evolutionary divergence from the extant reference genome affected the fraction of the Christmas Island rat genome that could be recovered. Our analyses show that even when the extremely high-quality Norway brown rat (R. norvegicus) is used as a reference, nearly 5% of the genome sequence is unrecoverable, with 1,661 genes recovered at lower than 90% completeness, and 26 completely absent. Furthermore, we find the distribution of regions affected is not random, but for example, if 90% completeness is used as the cutoff, genes related to immune response and olfaction are excessively affected. Ultimately, our approach demonstrates the importance of applying similar analyses to candidates for de-extinction through genome editing in order to provide critical baseline information about how representative the edited form would be of the extinct species.}, }
@article {pmid35269523, year = {2022}, author = {Kriaa, A and Mariaule, V and Jablaoui, A and Rhimi, S and Mkaouar, H and Hernandez, J and Korkmaz, B and Lesner, A and Maguin, E and Aghdassi, A and Rhimi, M}, title = {Bile Acids: Key Players in Inflammatory Bowel Diseases?.}, journal = {Cells}, volume = {11}, number = {5}, pages = {}, pmid = {35269523}, issn = {2073-4409}, support = {MICA department//National Research Institute for Agriculture, Food and Environment/ ; Animal microbiota analysis project//Oniris/ ; MICAfrica//European Commission/ ; }, mesh = {Bile Acids and Salts ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation ; *Inflammatory Bowel Diseases ; }, abstract = {Inflammatory bowel diseases (IBDs) have emerged as a public health problem worldwide with a limited number of efficient therapeutic options despite advances in medical therapy. Although changes in the gut microbiota composition are recognized as key drivers of dysregulated intestinal immunity, alterations in bile acids (BAs) have been shown to influence gut homeostasis and contribute to the pathogenesis of the disease. In this review, we explore the interactions involving BAs and gut microbiota in IBDs, and discuss how the gut microbiota-BA-host axis may influence digestive inflammation.}, }
@article {pmid35261041, year = {2022}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Paus, R and Bosch, TCG}, title = {Hydra and the hair follicle - An unconventional comparative biology approach to exploring the human holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {5}, pages = {e2100233}, doi = {10.1002/bies.202100233}, pmid = {35261041}, issn = {1521-1878}, mesh = {Animals ; Biology ; Hair Follicle ; Humans ; *Hydra/physiology ; Microbial Interactions ; *Microbiota/physiology ; }, abstract = {The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in-depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host-associated microbes, microbial metabolism, microbe-microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host-microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF - microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome-targeting therapeutic interventions in human skin disease.}, }
@article {pmid35260076, year = {2022}, author = {Haas, V and Vollmar, S and Preuß, S and Rodehutscord, M and Camarinha-Silva, A and Bennewitz, J}, title = {Composition of the ileum microbiota is a mediator between the host genome and phosphorus utilization and other efficiency traits in Japanese quail (Coturnix japonica).}, journal = {Genetics, selection, evolution : GSE}, volume = {54}, number = {1}, pages = {20}, pmid = {35260076}, issn = {1297-9686}, support = {BE3703/12-1//deutsche forschungsgemeinschaft/ ; CA1708/2-1//deutsche forschungsgemeinschaft/ ; }, mesh = {Animals ; *Coturnix/genetics/microbiology ; *Gastrointestinal Microbiome ; Genome ; Genotype ; Ileum/*microbiology ; Phenotype ; Phosphorus/*metabolism ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; }, abstract = {BACKGROUND: Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.<br><br>RESULTS: Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p&#x2009;&#x2264;&#x2009;0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host's quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host's quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs.<br><br>CONCLUSIONS: Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host's quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.}, }
@article {pmid35253476, year = {2022}, author = {Ricci, F and Tandon, K and Black, JR and Lê Cao, KA and Blackall, LL and Verbruggen, H}, title = {Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0004422}, pmid = {35253476}, issn = {2379-5077}, mesh = {Animals ; *Anthozoa ; Phylogeny ; Bacteria ; *Microbiota ; Symbiosis ; }, abstract = {The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence of host phylogeny, skeletal architecture, and reproductive mode on the microbiome composition, and further investigated the structure of the tissue and skeleton bacterial communities. Our results show that host phylogeny and traits explained 14% of the tissue and 13% of the skeletal microbiome composition, providing evidence that these predictors contributed to shaping the holobiont in terms of presence and relative abundance of bacterial symbionts. Based on our data, we conclude that host phylogeny affects the presence of specific microbial lineages, reproductive mode predictably influences the microbiome composition, and skeletal architecture works like a filter that affects bacterial relative abundance. We show that the β-diversity of coral tissue and skeleton microbiomes differed, but we found that a large overlapping fraction of bacterial sequences were recovered from both anatomical compartments, supporting the hypothesis that the skeleton can function as a microbial reservoir. Additionally, our analysis of the microbiome structure shows that 99.6% of tissue and 99.7% of skeletal amplicon sequence variants (ASVs) were not consistently present in at least 30% of the samples, suggesting that the coral tissue and skeleton are dominated by rare bacteria. Together, these results provide novel insights into the processes driving coral-bacterial symbioses, along with an improved understanding of the scleractinian microbiome.}, }
@article {pmid35242117, year = {2022}, author = {Gómez-Lama Cabanás, C and Wentzien, NM and Zorrilla-Fontanesi, Y and Valverde-Corredor, A and Fernández-González, AJ and Fernández-López, M and Mercado-Blanco, J}, title = {Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {809126}, pmid = {35242117}, issn = {1664-302X}, abstract = {The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.}, }
@article {pmid35237241, year = {2021}, author = {Li, J and Wei, X and Huang, D and Xiao, J}, title = {The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {800190}, pmid = {35237241}, issn = {1664-302X}, abstract = {Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities. Most of the previous studies on phylosymbiosis were conducted across the host families or genera. However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels. In this study, 54 individuals from six species of the fig wasp genus Ceratosolen (Hymenoptera: Agaonidae) collected from nine natural populations and their associated microbiota were investigated. The fig wasp species were morphologically identified and further determined by mitochondrial CO1 gene fragments and nuclear ITS2 sequences, and the V4 region of 16S rRNA gene was sequenced to analyze the bacterial communities. The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus. Moreover, we found that the endosymbiotic Wolbachia carried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities. This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.}, }
@article {pmid35229422, year = {2022}, author = {Taylor, JA and Díez-Vives, C and Nielsen, S and Wemheuer, B and Thomas, T}, title = {Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts.}, journal = {Environmental microbiology}, volume = {24}, number = {5}, pages = {2299-2314}, doi = {10.1111/1462-2920.15962}, pmid = {35229422}, issn = {1462-2920}, mesh = {Animals ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Phylogeny ; *Porifera ; Symbiosis/physiology ; }, abstract = {The diversity and function of sponge-associated symbionts is now increasingly understood; however, we lack an understanding of how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here, we performed a metatransciptomic analysis on three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidizing Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidizing archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our time-series study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change.}, }
@article {pmid35223211, year = {2022}, author = {Nyholm, L and Odriozola, I and Martin Bideguren, G and Aizpurua, O and Alberdi, A}, title = {Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e12992}, pmid = {35223211}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Fishes/microbiology ; Intestines/microbiology ; *Microbiota ; Bacteria/genetics ; }, abstract = {The microbial gut communities of fish are receiving increased attention for their relevance, among others, in a growing aquaculture industry. The members of these communities are often split into resident (long-term colonisers specialised to grow in and adhere to the mucus lining of the gut) and transient (short-term colonisers originated from food items and the surrounding water) microorganisms. Separating these two communities in small fish are impeded by the small size and fragility of the gastrointestinal tract. With the aim of testing whether it is possible to recover two distinct communities in small species of fish using a simple sampling technique, we used 16S amplicon sequencing of paired intestinal wall and digesta samples from three small Cyprinodontiformes fish. We examined the diversity and compositional variation of the two recovered communities, and we used joint species distribution modelling to identify microbes that are most likely to be a part of the resident community. For all three species we found that the diversity of intestinal wall samples was significantly lower compared to digesta samples and that the community composition between sample types was significantly different. Across the three species we found seven unique families of bacteria to be significantly enriched in samples from the intestinal wall, encompassing most of the 89 ASVs enriched in intestinal wall samples. We conclude that it is possible to characterise two different microbial communities and identify potentially resident microbes through separately analysing samples from the intestinal wall and digesta from small species of fish. We encourage researchers to be aware that different sampling procedures for gut microbiome characterization will capture different parts of the microbiome and that this should be taken into consideration when reporting results from such studies on small species of fish.}, }
@article {pmid35222085, year = {2022}, author = {Cotinat, P and Fricano, C and Toullec, G and Röttinger, E and Barnay-Verdier, S and Furla, P}, title = {Intrinsically High Capacity of Animal Cells From a Symbiotic Cnidarian to Deal With Pro-Oxidative Conditions.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {819111}, pmid = {35222085}, issn = {1664-042X}, abstract = {The cnidarian-dinoflagellate symbiosis is a mutualistic intracellular association based on the photosynthetic activity of the endosymbiont. This relationship involves significant constraints and requires co-evolution processes, such as an extensive capacity of the holobiont to counteract pro-oxidative conditions induced by hyperoxia generated during photosynthesis. In this study, we analyzed the capacity of Anemonia viridis cells to deal with pro-oxidative conditions by in vivo and in vitro approaches. Whole specimens and animal primary cell cultures were submitted to 200 and 500 μM of H2O2 during 7 days. Then, we monitored global health parameters (symbiotic state, viability, and cell growth) and stress biomarkers (global antioxidant capacity, oxidative protein damages, and protein ubiquitination). In animal primary cell cultures, the intracellular reactive oxygen species (ROS) levels were also evaluated under H2O2 treatments. At the whole organism scale, both H2O2 concentrations didn't affect the survival and animal tissues exhibited a high resistance to H2O2 treatments. Moreover, no bleaching has been observed, even at high H2O2 concentration and after long exposure (7 days). Although, the community has suggested the role of ROS as the cause of bleaching, our results indicating the absence of bleaching under high H2O2 concentration may exculpate this specific ROS from being involved in the molecular processes inducing bleaching. However, counterintuitively, the symbiont compartment appeared sensitive to an H2O2 burst as it displayed oxidative protein damages, despite an enhancement of antioxidant capacity. The in vitro assays allowed highlighting an intrinsic high capacity of isolated animal cells to deal with pro-oxidative conditions, although we observed differences on tolerance between H2O2 treatments. The 200 μM H2O2 concentration appeared to correspond to the tolerance threshold of animal cells. Indeed, no disequilibrium on redox state was observed and only a cell growth decrease was measured. Contrarily, the 500 μM H2O2 concentration induced a stress state, characterized by a cell viability decrease from 1 day and a drastic cell growth arrest after 7 days leading to an uncomplete recovery after treatment. In conclusion, this study highlights the overall high capacity of cnidarian cells to cope with H2O2 and opens new perspective to investigate the molecular mechanisms involved in this peculiar resistance.}, }
@article {pmid35218086, year = {2022}, author = {Rosenberg, Y and Simon-Blecher, N and Lalzar, M and Yam, R and Shemesh, A and Alon, S and Perna, G and Cárdenas, A and Voolstra, CR and Miller, DJ and Levy, O}, title = {Urbanization comprehensively impairs biological rhythms in coral holobionts.}, journal = {Global change biology}, volume = {28}, number = {10}, pages = {3349-3364}, pmid = {35218086}, issn = {1365-2486}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota ; Periodicity ; Urbanization ; }, abstract = {Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology &amp; Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.}, }
@article {pmid35215934, year = {2022}, author = {Yukgehnaish, K and Rajandas, H and Parimannan, S and Manickam, R and Marimuthu, K and Petersen, B and Clokie, MRJ and Millard, A and Sicheritz-Pontén, T}, title = {PhageLeads: Rapid Assessment of Phage Therapeutic Suitability Using an Ensemble Machine Learning Approach.}, journal = {Viruses}, volume = {14}, number = {2}, pages = {}, pmid = {35215934}, issn = {1999-4915}, mesh = {Bacteria/virology ; Bacterial Infections/microbiology/*therapy ; Bacterial Physiological Phenomena ; Bacteriophages/classification/*genetics/physiology ; Genome, Viral ; Humans ; Lysogeny ; *Machine Learning ; *Phage Therapy ; Viral Proteins/genetics/metabolism ; }, abstract = {The characterization of therapeutic phage genomes plays a crucial role in the success rate of phage therapies. There are three checkpoints that need to be examined for the selection of phage candidates, namely, the presence of temperate markers, antimicrobial resistance (AMR) genes, and virulence genes. However, currently, no single-step tools are available for this purpose. Hence, we have developed a tool capable of checking all three conditions required for the selection of suitable therapeutic phage candidates. This tool consists of an ensemble of machine-learning-based predictors for determining the presence of temperate markers (integrase, Cro/CI repressor, immunity repressor, DNA partitioning protein A, and antirepressor) along with the integration of the ABRicate tool to determine the presence of antibiotic resistance genes and virulence genes. Using the biological features of the temperate markers, we were able to predict the presence of the temperate markers with high MCC scores (>0.70), corresponding to the lifestyle of the phages with an accuracy of 96.5%. Additionally, the screening of 183 lytic phage genomes revealed that six phages were found to contain AMR or virulence genes, showing that not all lytic phages are suitable to be used for therapy. The suite of predictors, PhageLeads, along with the integrated ABRicate tool, can be accessed online for in silico selection of suitable therapeutic phage candidates from single genome or metagenomic contigs.}, }
@article {pmid35208935, year = {2022}, author = {Butina, TV and Petrushin, IS and Khanaev, IV and Bukin, YS}, title = {Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208935}, issn = {2076-2607}, support = {17-44-388080//Russian Foundation for Basic Research/ ; }, abstract = {Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.}, }
@article {pmid35208684, year = {2022}, author = {Dietert, RR and Dietert, JM}, title = {Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan following Adverse Childhood Experiences.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208684}, issn = {2076-2607}, abstract = {Adverse childhood experiences (ACEs), which can include child trafficking, are known to program children for disrupted biological cycles, premature aging, microbiome dysbiosis, immune-inflammatory misregulation, and chronic disease multimorbidity. To date, the microbiome has not been a major focus of deprogramming efforts despite its emerging role in every aspect of ACE-related dysbiosis and dysfunction. This article examines: (1) the utility of incorporating microorganism-based, anti-aging approaches to combat ACE-programmed chronic diseases (also known as noncommunicable diseases and conditions, NCDs) and (2) microbiome regulation of core systems biology cycles that affect NCD comorbid risk. In this review, microbiota influence over three key cyclic rhythms (circadian cycles, the sleep cycle, and the lifespan/longevity cycle) as well as tissue inflammation and oxidative stress are discussed as an opportunity to deprogram ACE-driven chronic disorders. Microbiota, particularly those in the gut, have been shown to affect host-microbe interactions regulating the circadian clock, sleep quality, as well as immune function/senescence, and regulation of tissue inflammation. The microimmunosome is one of several systems biology targets of gut microbiota regulation. Furthermore, correcting misregulated inflammation and increased oxidative stress is key to protecting telomere length and lifespan/longevity and extending what has become known as the healthspan. This review article concludes that to reverse the tragedy of ACE-programmed NCDs and premature aging, managing the human holobiont microbiome should become a routine part of healthcare and preventative medicine across the life course.}, }
@article {pmid35208662, year = {2022}, author = {Qin, Z and Yu, K and Chen, S and Chen, B and Yao, Q and Yu, X and Pan, N and Wei, X}, title = {Significant Changes in Bacterial Communities Associated with Pocillopora Corals Ingestion by Crown-of-Thorns Starfish: An Important Factor Affecting the Coral's Health.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208662}, issn = {2076-2607}, support = {42030502//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; AD17129063//Guangxi scientific projects/ ; AA17204074//Guangxi scientific projects/ ; 2014BGXZGX03//Bagui Fellowship from Guangxi Province of China/ ; }, abstract = {Coral ingestion by crown-of-thorns starfish (COTS) is an important cause of coral reef degradation, although the impacts of COTS feeding on coral-associated microbial communities are not well understood. Therefore, in this study, we analyzed the coral tissue-weight, Symbiodiniaceae density (SD), bacterial community composition, and the predicted functions of bacterial genes associated with Pocillopora corals in healthy portions and feeding scars, following COTS feeding. Coral tissue-weight loss rate in the feeding scars was 71.3-94.95%. The SDs were significantly lower in the feeding scars, and the SD-loss rate was 92.05% ± 2.12%. The relative abundances of bacterial communities associated with Pocillopora corals after COTS feeding changed significantly and were almost completely reorganized at the phylum and genus levels. Analysis of the microbial metagenomic-functional capacities showed that numerous physiological functions of the coral-bacterial holobionts in the feeding scars were different, including amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, membrane transport, signal transduction, and cell motility, and all these capacities could be corroborated based on metagenomic, transcriptomic or proteomic technologies. Overall, our research suggests that coral holobionts may be destroyed by COTS, and our findings imply that bacterial communities in feeding scars could affect the health of Pocillopora corals.}, }
@article {pmid35202673, year = {2022}, author = {Tougeron, K}, title = {Homeostasis theory: What can we learn from dormancy and symbiotic associations?.}, journal = {Physiology &amp; behavior}, volume = {249}, number = {}, pages = {113749}, doi = {10.1016/j.physbeh.2022.113749}, pmid = {35202673}, issn = {1873-507X}, mesh = {Animals ; *Diapause/physiology ; Homeostasis ; *Symbiosis ; }, abstract = {In this letter, I discuss the notion of dormancy that De Luca Jr. relies on to criticize the theory of homeostasis. In particular, I try to qualify the issues related to the fact that dormancy is not always a free behavior but is in most situations under the influence of environmental factors. To this end, I discuss diapause in arthropods, which can be obligatory (under the influence of endogenous commands) but which is in most cases facultative (under external command). I emphasize that the notion of stability of a dormant organism must be taken with caution. I briefly mention what the study of sleep in animals can contribute to the notion of homeostasis. Finally, I focus on the role of microbial symbionts and the notion of holobiont. Through this, I question the future of the notions of internal environment and homeostasis and I propose to revisit them in the context of the effects of species interactions on the physiology of organisms.}, }
@article {pmid35191335, year = {2022}, author = {Folkers, A and Opitz, S}, title = {Low-carbon cows: From microbial metabolism to the symbiotic planet.}, journal = {Social studies of science}, volume = {52}, number = {3}, pages = {330-352}, pmid = {35191335}, issn = {1460-3659}, mesh = {Animals ; *Carbon ; Cattle ; Climate Change ; *Planets ; Symbiosis ; }, abstract = {This article focuses on two projects - one at a large chemical company and the other at a small start-up - to intervene in the relations between cows and ruminal microbes to reduce bovine methane emissions. It describes these interventions as 'symbiotic engineering': a biopolitical technique targeting holobionts and becoming effective by working on interlaced sets of living things. Based on the analysis of these cases, the article elucidates a planetary symbiopolitics (Helmreich) that connects 'molecular biopolitics' (Rose) and 'microbiopolitics' (Paxson) to 'bovine biopolitics' (Lorimer, Driessen) and the politics of climate change. We critically investigate the spatial imaginaries of symbiotic engineering practices that single out the microbial realm as an Archimedean point to address planetary problems. This technoscientific vision resonates with the notion of the 'symbiotic planet' advanced by Lynn Margulis that depicts the Earth System, or Gaia, as a vast set of relations among living things down to the tiniest microbes. Margulis' concept, as well as the 'symbiotic view of life' (Gilbert, Scott, Sapp) has been embraced in recent debates in STS as a way to think of multispecies worldings. The article contributes critically to these debates by showing what happens when the topology of the symbiotic Earth becomes the operating space for symbiotic engineering practices.}, }
@article {pmid35187610, year = {2022}, author = {Roggatz, CC and Hardege, JD and Saha, M}, title = {Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions.}, journal = {Journal of chemical ecology}, volume = {48}, number = {4}, pages = {455-473}, pmid = {35187610}, issn = {1573-1561}, support = {PML Fellowship//Plymouth Marine Laboratory/ ; ERC-2016-COG GEOSTICK/ERC_/European Research Council/International ; }, mesh = {Bacteria/metabolism ; *Biofouling/prevention &amp; control ; Ecosystem ; Hydrogen-Ion Concentration ; Phylogeny ; Seawater/chemistry ; *Seaweed/microbiology ; }, abstract = {Marine macroalgae are important ecosystem engineers in marine coastal habitats. Macroalgae can be negatively impacted through excessive colonization by harmful bacteria, fungi, microalgae, and macro-colonisers and thus employ a range of chemical compounds to minimize such colonization. Recent research suggests that environmental pH conditions potentially impact the functionality of such chemical compounds. Here we predict if and how naturally fluctuating pH conditions and future conditions caused by ocean acidification will affect macroalgal (antifouling) compounds and thereby potentially alter the chemical defence mediated by these compounds. We defined the relevant ecological pH range, analysed and scored the pH-sensitivity of compounds with antifouling functions based on their modelled chemical properties before assessing their distribution across the phylogenetic macroalgal groups, and the proportion of sensitive compounds for each investigated function. For some key compounds, we also predicted in detail how the associated ecological function may develop across the pH range. The majority of compounds were unaffected by pH, but compounds containing phenolic and amine groups were found to be particularly sensitive to pH. Future pH changes due to predicted average open ocean acidification pH were found to have little effect. Compounds from Rhodophyta were mainly pH-stable. However, key algal species amongst Phaeophyceae and Chlorophyta were found to rely on highly pH-sensitive compounds for their chemical defence against harmful bacteria, microalgae, fungi, and biofouling by macro-organisms. All quorum sensing disruptive compounds were found the be unaffected by pH, but the other ecological functions were all conveyed in part by pH-sensitive compounds. For some ecological keystone species, all of their compounds mediating defence functions were found to be pH-sensitive based on our calculations, which may not only affect the health and fitness of the host alga resulting in host breakdown but also alter the associated ecological interactions of the macroalgal holobiont with micro and macrocolonisers, eventually causing ecosystem restructuring and the functions (e.g. habitat provision) provided by macroalgal hosts. Our study investigates a question of fundamental importance because environments with fluctuating or changing pH are common and apply not only to coastal marine habitats and estuaries but also to freshwater environments or terrestrial systems that are subject to acid rain. Hence, whilst warranting experimental validation, this investigation with macroalgae as model organisms can serve as a basis for future investigations in other aquatic or even terrestrial systems.}, }
@article {pmid35182765, year = {2022}, author = {Neves, RC and Møbjerg, A and Kodama, M and Ramos-Madrigal, J and Gilbert, MTP and Møbjerg, N}, title = {Differential expression profiling of heat stressed tardigrades reveals major shift in the transcriptome.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {267}, number = {}, pages = {111169}, doi = {10.1016/j.cbpa.2022.111169}, pmid = {35182765}, issn = {1531-4332}, mesh = {Animals ; Heat-Shock Proteins/genetics ; Heat-Shock Response/genetics ; RNA-Seq ; *Tardigrada/genetics ; *Transcriptome ; }, abstract = {Tardigrades are renowned for their extreme stress tolerance, which includes the ability to endure complete desiccation, high levels of radiation and very low sub-zero temperatures. Nevertheless, tardigrades appear to be vulnerable to high temperatures and thus the potential effects of global warming. Here, we provide the first analysis of transcriptome data obtained from heat stressed specimens of the eutardigrade Ramazzottius varieornatus, with the aim of providing new insights into the molecular processes affected by high temperatures. Specifically, we compare RNA-seq datasets obtained from active, heat-exposed (35 °C) tardigrades to that of active controls kept at 5 °C. Our data reveal a surprising shift in transcription, involving 9634 differentially expressed transcripts, corresponding to >35% of the transcriptome. The latter data are in striking contrast to the hitherto observed constitutive expression underlying tardigrade extreme stress tolerance and entrance into the latent state of life, known as cryptobiosis. Thus, when examining the molecular response, heat-stress appears to be more stressful for R. varieornatus than extreme conditions, such as desiccation or freezing. A gene ontology analysis reveals that the heat stress response involves a change in transcription and presumably translation, including an adjustment of metabolism, and, putatively, preparation for encystment and subsequent diapause. Among the differentially expressed transcripts we find heat-shock proteins as well as the eutardigrade specific proteins (CAHS, SAHS, MAHS, RvLEAM, and Dsup). The latter proteins thus seem to contribute to a general stress response, and may not be directly related to cryptobiosis.}, }
@article {pmid35182319, year = {2022}, author = {Ünüvar, &#xd6;C and Zencirci, N and Ünlü, ES}, title = {Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture.}, journal = {Molecular biology reports}, volume = {49}, number = {6}, pages = {5389-5395}, pmid = {35182319}, issn = {1573-4978}, support = {2180200//T&#xdc;B&#x130;TAK (TEYDEB)/ ; }, mesh = {Agriculture ; Bacteria/genetics ; DNA, Ribosomal ; Phosphates ; *Plant Breeding ; Plant Roots ; *Triticum/genetics ; }, abstract = {BACKGROUND: Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadağ Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed.<br><br>METHODS AND RESULTS: The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805&#x2009;&#xb1;&#x2009;0.439.<br><br>CONCLUSIONS: All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.}, }
@article {pmid35153869, year = {2021}, author = {Martínez, M and Postolache, TT and García-Bueno, B and Leza, JC and Figuero, E and Lowry, CA and Malan-Müller, S}, title = {The Role of the Oral Microbiota Related to Periodontal Diseases in Anxiety, Mood and Trauma- and Stress-Related Disorders.}, journal = {Frontiers in psychiatry}, volume = {12}, number = {}, pages = {814177}, pmid = {35153869}, issn = {1664-0640}, abstract = {The prevalence of anxiety, mood and trauma- and stress-related disorders are on the rise; however, efforts to develop new and effective treatment strategies have had limited success. To identify novel therapeutic targets, a comprehensive understanding of the disease etiology is needed, especially in the context of the holobiont, i.e., the superorganism consisting of a human and its microbiotas. Much emphasis has been placed on the role of the gut microbiota in the development, exacerbation, and persistence of psychiatric disorders; however, data for the oral microbiota are limited. The oral cavity houses the second most diverse microbial community in the body, with over 700 bacterial species that colonize the soft and hard tissues. Periodontal diseases encompass a group of infectious and inflammatory diseases that affect the periodontium. Among them, periodontitis is defined as a chronic, multi-bacterial infection that elicits low-grade systemic inflammation via the release of pro-inflammatory cytokines, as well as local invasion and long-distance translocation of periodontal pathogens. Periodontitis can also induce or exacerbate other chronic systemic inflammatory diseases such as atherosclerosis and diabetes and can lead to adverse pregnancy outcomes. Recently, periodontal pathogens have been implicated in the etiology and pathophysiology of neuropsychiatric disorders (such as depression and schizophrenia), especially as dysregulation of the immune system also plays an integral role in the etiology and pathophysiology of these disorders. This review will discuss the role of the oral microbiota associated with periodontal diseases in anxiety, mood and trauma- and stress-related disorders. Epidemiological data of periodontal diseases in individuals with these disorders will be presented, followed by a discussion of the microbiological and immunological links between the oral microbiota and the central nervous system. Pre-clinical and clinical findings on the oral microbiota related to periodontal diseases in anxiety, mood and trauma- and stress-related phenotypes will be reviewed, followed by a discussion on the bi-directionality of the oral-brain axis. Lastly, we will focus on the oral microbiota associated with periodontal diseases as a target for future therapeutic interventions to alleviate symptoms of these debilitating psychiatric disorders.}, }
@article {pmid35150917, year = {2022}, author = {Shigenobu, S and Yorimoto, S}, title = {Aphid hologenomics: current status and future challenges.}, journal = {Current opinion in insect science}, volume = {50}, number = {}, pages = {100882}, doi = {10.1016/j.cois.2022.100882}, pmid = {35150917}, issn = {2214-5753}, mesh = {Animals ; *Aphids/genetics ; *Buchnera/genetics ; Genomics ; Symbiosis ; }, abstract = {Aphids are important model organisms in ecological, developmental, and evolutionary studies of, for example, symbiosis, insect-plant interactions, pest management, and developmental polyphenism. Here, we review the recent progress made in the genomics of aphids and their symbionts: hologenomics. The reference genome of Acyrthosiphon pisum has been greatly improved, and chromosome-level assembly is now available. The genomes of over 20 aphid species have been sequenced, and comparative genomic analyses have revealed pervasive gene duplication and dynamic chromosomal rearrangements. Over 120 symbiont genomes (both obligate and facultative) have been sequenced, and modern deep-sequencing technologies have identified novel symbionts. The advances in hologenomics have helped to elucidate the dynamic evolution of facultative and co-obligate symbionts with the ancient obligate symbiont Buchnera.}, }
@article {pmid35147188, year = {2022}, author = {Zouache, K and Martin, E and Rahola, N and Gangue, MF and Minard, G and Dubost, A and Van, VT and Dickson, L and Ayala, D and Lambrechts, L and Moro, CV}, title = {Larval habitat determines the bacterial and fungal microbiota of the mosquito vector Aedes aegypti.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {1}, pages = {}, doi = {10.1093/femsec/fiac016}, pmid = {35147188}, issn = {1574-6941}, mesh = {*Aedes/microbiology ; Animals ; Bacteria/genetics ; Larva/microbiology ; *Microbiota ; Mosquito Vectors/microbiology ; *Mycobiome ; Plant Breeding ; }, abstract = {Mosquito larvae are naturally exposed to microbial communities present in a variety of larval development sites. Several earlier studies have highlighted that the larval habitat influences the composition of the larval bacterial microbiota. However, little information is available on their fungal microbiota, i.e. the mycobiota. In this study, we provide the first simultaneous characterization of the bacterial and fungal microbiota in field-collected Aedes aegypti larvae and their respective aquatic habitats. We evaluated whether the microbial communities associated with the breeding site may affect the composition of both the bacterial and fungal communities in Ae. aegypti larvae. Our results show a higher similarity in microbial community structure for both bacteria and fungi between larvae and the water in which larvae develop than between larvae from different breeding sites. This supports the hypothesis that larval habitat is a major factor driving microbial composition in mosquito larvae. Since the microbiota plays an important role in mosquito biology, unravelling the network of interactions that operate between bacteria and fungi is essential to better understand the functioning of the mosquito holobiont.}, }
@article {pmid35138928, year = {2022}, author = {Riva, V and Mapelli, F and Bagnasco, A and Mengoni, A and Borin, S}, title = {A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0253721}, pmid = {35138928}, issn = {1098-5336}, mesh = {*Bacteria ; Endophytes ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.}, }
@article {pmid35137526, year = {2022}, author = {Ren, CG and Liu, ZY and Wang, XL and Qin, S}, title = {The seaweed holobiont: from microecology to biotechnological applications.}, journal = {Microbial biotechnology}, volume = {15}, number = {3}, pages = {738-754}, pmid = {35137526}, issn = {1751-7915}, mesh = {*Seaweed/chemistry ; }, abstract = {In the ocean, seaweed and microorganisms have coexisted since the earliest stages of evolution and formed an inextricable relationship. Recently, seaweed has attracted extensive attention worldwide for ecological and industrial purposes, but the function of its closely related microbes is often ignored. Microbes play an indispensable role in different stages of seaweed growth, development and maturity. A very diverse group of seaweed-associated microbes have important functions and are dynamically reconstructed as the marine environment fluctuates, forming an inseparable 'holobiont' with their host. To further understand the function and significance of holobionts, this review first reports on recent advances in revealing seaweed-associated microbe spatial and temporal distribution. Then, this review discusses the microbe and seaweed interactions and their ecological significance, and summarizes the current applications of the seaweed-microbe relationship in various environmental and biological technologies. Sustainable industries based on seaweed holobionts could become an integral part of the future bioeconomy because they can provide more resource-efficient food, high-value chemicals and medical materials. Moreover, holobionts may provide a new approach to marine environment restoration.}, }
@article {pmid35136196, year = {2022}, author = {Bertorelle, G and Raffini, F and Bosse, M and Bortoluzzi, C and Iannucci, A and Trucchi, E and Morales, HE and van Oosterhout, C}, title = {Genetic load: genomic estimates and applications in non-model animals.}, journal = {Nature reviews. Genetics}, volume = {23}, number = {8}, pages = {492-503}, pmid = {35136196}, issn = {1471-0064}, support = {WT207492/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Genetic Load ; Genetic Variation ; *Genetics, Population ; Genome ; Genomics ; Inbreeding ; Mutation ; }, abstract = {Genetic variation, which is generated by mutation, recombination and gene flow, can reduce the mean fitness of a population, both now and in the future. This 'genetic load' has been estimated in a wide range of animal taxa using various approaches. Advances in genome sequencing and computational techniques now enable us to estimate the genetic load in populations and individuals without direct fitness estimates. Here, we review the classic and contemporary literature of genetic load. We describe approaches to quantify the genetic load in whole-genome sequence data based on evolutionary conservation and annotations. We show that splitting the load into its two components - the realized load (or expressed load) and the masked load (or inbreeding load) - can improve our understanding of the population genetics of deleterious mutations.}, }
@article {pmid35135352, year = {2022}, author = {Frank, HER and Amato, K and Trautwein, M and Maia, P and Liman, ER and Nichols, LM and Schwenk, K and Breslin, PAS and Dunn, RR}, title = {The evolution of sour taste.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1968}, pages = {20211918}, pmid = {35135352}, issn = {1471-2954}, support = {R01 DC013741/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Humans ; Phylogeny ; *Taste ; }, abstract = {The evolutionary history of sour taste has been little studied. Through a combination of literature review and trait mapping on the vertebrate phylogenetic tree, we consider the origin of sour taste, potential cases of the loss of sour taste, and those factors that might have favoured changes in the valence of sour taste-from aversive to appealing. We reconstruct sour taste as having evolved in ancient fish. By contrast to other tastes, sour taste does not appear to have been lost in any major vertebrate taxa. For most species, sour taste is aversive. Animals, including humans, that enjoy the sour taste triggered by acidic foods are exceptional. We conclude by considering why sour taste evolved, why it might have persisted as vertebrates made the transition to land and what factors might have favoured the preference for sour-tasting, acidic foods, particularly in hominins, such as humans.}, }
@article {pmid35134420, year = {2022}, author = {Corinaldesi, C and Varrella, S and Tangherlini, M and Dell'Anno, A and Canensi, S and Cerrano, C and Danovaro, R}, title = {Changes in coral forest microbiomes predict the impact of marine heatwaves on habitat-forming species down to mesophotic depths.}, journal = {The Science of the total environment}, volume = {823}, number = {}, pages = {153701}, doi = {10.1016/j.scitotenv.2022.153701}, pmid = {35134420}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/physiology ; Bacteria ; Coral Reefs ; Ecosystem ; Forests ; *Microbiota ; Seawater/microbiology ; }, abstract = {Global warming is causing the increase in intensity and frequency of heatwaves, which are often associated with mass mortality events of marine organisms from shallow and mesophotic rocky habitats, including gorgonians and other sessile organisms. We investigated the microbiome responses of the gorgonians Paramuricea clavata, Eunicella cavolini, and the red coral Corallium rubrum to the episodic temperature anomalies detected in the North Western Mediterranean, during August 2011. Although the investigated corals showed no signs of visible necrosis, the abundance of associated Bacteria and Archaea increased with increasing seawater temperature, suggesting their temperature-dependent proliferation. Coral microbiomes were highly sensitive to thermal anomaly amplitude and exhibited increased bacterial diversity to greater thermal shifts. This effect was explained by the decline of dominant bacterial members and the increase of new, rare and opportunistic taxa, including pathogens, revealing a direct effect of heatwave-induced alteration of the microbiomes and not a secondary consequence of coral necrosis.}, }
@article {pmid35119475, year = {2022}, author = {Tran, C}, title = {Coral-microbe interactions: their importance to reef function and survival.}, journal = {Emerging topics in life sciences}, volume = {6}, number = {1}, pages = {33-44}, doi = {10.1042/ETLS20210229}, pmid = {35119475}, issn = {2397-8554}, mesh = {*Anemone ; Animals ; *Anthozoa ; Host Microbial Interactions ; Hypochlorous Acid ; *Microbiota ; *Scyphozoa ; Sodium Compounds ; }, abstract = {Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.}, }
@article {pmid35112871, year = {2022}, author = {Deutsch, JM and Mandelare-Ruiz, P and Yang, Y and Foster, G and Routhu, A and Houk, J and De La Flor, YT and Ushijima, B and Meyer, JL and Paul, VJ and Garg, N}, title = {Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria.}, journal = {Journal of natural products}, volume = {85}, number = {3}, pages = {462-478}, doi = {10.1021/acs.jnatprod.1c01110}, pmid = {35112871}, issn = {1520-6025}, mesh = {Animals ; *Anthozoa/microbiology ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/genetics ; *Biological Products/metabolism/pharmacology ; Metabolomics ; Symbiosis ; }, abstract = {Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.}, }
@article {pmid35108095, year = {2022}, author = {Tignat-Perrier, R and van de Water, JAJM and Guillemain, D and Aurelle, D and Allemand, D and Ferrier-Pagès, C}, title = {The Effect of Thermal Stress on the Physiology and Bacterial Communities of Two Key Mediterranean Gorgonians.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0234021}, pmid = {35108095}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Mediterranean Sea ; *Microbiota ; Seawater/microbiology ; }, abstract = {Gorgonians are important habitat-providing species in the Mediterranean Sea, but their populations are declining due to microbial diseases and repeated mass mortality events caused by summer heat waves. Elevated seawater temperatures may impact the stress tolerance and disease resistance of gorgonians and lead to disturbances in their microbiota. However, our knowledge of the biological response of the gorgonian holobiont (i.e., the host and its microbiota) to thermal stress remains limited. Here, we investigated how the holobiont of two gorgonian species (Paramuricea clavata and Eunicella cavolini) are affected throughout a 7-week thermal stress event by following both the corals' physiology and the composition of their bacterial communities. We found that P. clavata was more sensitive to elevated seawater temperatures than E. cavolini, showing a greater loss in energy reserves, reduced feeding ability, and partial mortality. This lower thermotolerance may be linked to the ∼20× lower antioxidant defense capacity in P. clavata compared with E. cavolini. In the first 4 weeks of thermal stress, we also observed minor shifts in the microbiota of both species, suggesting that the microbiota likely plays a limited role in thermal acclimation of the holobiont. However, major stochastic changes occurred later on in some colonies, which were of a transient nature in E. cavolini, but were linked to partial colony mortality in P. clavata. Overall, our results show significant, but differential, effects of thermal stress on the holobionts of both E. cavolini and P. clavata and predict potentially severe impacts on gorgonian populations under future climate scenarios. IMPORTANCE In the Mediterranean Sea, the tree-shaped gorgonian corals form large forests that provide a place to live for many species. Because of this important ecological role, it is crucial to understand how common habitat-forming gorgonians, like Eunicella cavolini and Paramuricea clavata, are affected by high seawater temperatures that are expected in the future due to climate change. We found that both species lost biomass, but P. clavata was more affected, being also unable to feed and showing signs of mortality. The microbiota of both gorgonians also changed substantively under high temperatures. Although this could be linked to partial colony mortality in P. clavata, the changes were temporary in E. cavolini. The overall higher resistance of E. cavolini may be related to its much higher antioxidant defense levels than P. clavata. Climate change may thus have severe impacts on gorgonian populations and the habitats they provide.}, }
@article {pmid35106548, year = {2022}, author = {Nerva, L and Garcia, JF and Favaretto, F and Giudice, G and Moffa, L and Sandrini, M and Cantu, D and Zanzotto, A and Gardiman, M and Velasco, R and Gambino, G and Chitarra, W}, title = {The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes.}, journal = {Journal of experimental botany}, volume = {73}, number = {8}, pages = {2682-2697}, doi = {10.1093/jxb/erac032}, pmid = {35106548}, issn = {1460-2431}, support = {C94E19000770008//Italian Ministry for Agriculture and Forestry/ ; }, mesh = {Bacteria/genetics ; *Endophytes ; *Microbiota ; Plants ; Wood ; }, abstract = {The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.}, }
@article {pmid35105377, year = {2022}, author = {Zhang, S and Song, W and Nothias, LF and Couvillion, SP and Webster, N and Thomas, T}, title = {Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {22}, pmid = {35105377}, issn = {2049-2618}, mesh = {Chromatography, Liquid ; *Metabolomics ; *Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species.<br><br>RESULTS: Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms.<br><br>CONCLUSIONS: This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.}, }
@article {pmid35104474, year = {2022}, author = {Yoksan, R and Boontanimitr, A and Klompong, N and Phothongsurakun, T}, title = {Poly(lactic acid)/thermoplastic cassava starch blends filled with duckweed biomass.}, journal = {International journal of biological macromolecules}, volume = {203}, number = {}, pages = {369-378}, doi = {10.1016/j.ijbiomac.2022.01.159}, pmid = {35104474}, issn = {1879-0003}, mesh = {*Araceae ; Biomass ; *Manihot/metabolism ; Polyesters ; Starch/metabolism ; }, abstract = {Duckweed (DW) is a highly small, free-floating aquatic plant. It grows and reproduces rapidly, comprises mainly protein and carbohydrate, and has substantial potential as a feedstock to produce bioplastics due to its renewability and having very little impact on the food chain. The aim of this work was to analyze the effect of DW biomass on the characteristics and properties of bio-based and biodegradable plastics based on a poly(lactic acid)/thermoplastic cassava starch (PLA/TPS) blend. Various amounts of DW biomass were compounded with PLA and TPS in a twin-screw extruder and then converted into dumbbell-shaped specimens using an injection molding machine. The obtained PLA/TPS blends filled with DW biomass exhibited a lower melt flow ability, higher moisture content, and increased surface hydrophilicity than the neat PLA/TPS blend. Incorporation of DW with low concentrations of 2.3 and 4.6 wt% increased the tensile strength, Young's modulus, and hardness of the PLA/TPS blend. Moisture and glycerol from DW and TPS played important roles in reducing the Tg, Tcc, Tm, and Td of PLA in the blends. The current work demonstrated that DW could be used as a biofiller for PLA/TPS blends, and the resulting PLA/TPS blends filled with DW biomass have potential in manufacturing injection-molded articles for sustainable, biodegradable, and short-term use.}, }
@article {pmid35104027, year = {2022}, author = {Dungan, AM and Hartman, LM and Blackall, LL and van Oppen, MJH}, title = {Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana.}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {2940-2956}, pmid = {35104027}, issn = {1365-2672}, support = {DP160101468//Australian Research Council/ ; FL180100036//Australian Research Council/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; *Microbiota ; *Rhodobacteraceae ; Seawater/microbiology ; }, abstract = {AIMS: Fourteen percent of all living coral, equivalent to more than all the coral on the Great Barrier Reef, has died in the past decade as a result of climate change-driven bleaching. Inspired by the 'oxidative stress theory of coral bleaching', we investigated whether a bacterial consortium designed to scavenge free radicals could integrate into the host microbiome and improve thermal tolerance of the coral model, Exaiptasia diaphana.<br><br>METHODS AND RESULTS: E.&#xa0;diaphana anemones were inoculated with a consortium of high free radical scavenging (FRS) bacteria, a consortium of congeneric low FRS bacteria, or sterile seawater as a control, then exposed to elevated temperature. Increases in the relative abundance of Labrenzia during the first 2&#xa0;weeks following the last inoculation provided evidence for temporary inoculum integration into the E.&#xa0;diaphana microbiome. Initial uptake of other consortium members was inconsistent, and these bacteria did not persist either in E. diaphana's microbiome over time. Given their non-integration into the host microbiome, the ability of the FRS consortium to mitigate thermal stress could not be assessed. Importantly, there were no physiological impacts (negative or positive) of the bacterial inoculations on the holobiont.<br><br>CONCLUSIONS: The introduced bacteria were not maintained in the anemone microbiome over time, thus, their protective effect is unknown. Achieving long-term integration of bacteria into cnidarian microbiomes remains a research priority.<br><br>Microbiome engineering strategies to mitigate coral bleaching may assist coral reefs in their persistence until climate change has been curbed. This study provides insights that will inform microbiome manipulation approaches in coral bleaching mitigation research.}, }
@article {pmid35104026, year = {2022}, author = {Wood, G and Steinberg, PD and Campbell, AH and Vergés, A and Coleman, MA and Marzinelli, EM}, title = {Host genetics, phenotype and geography structure the microbiome of a foundational seaweed.}, journal = {Molecular ecology}, volume = {31}, number = {7}, pages = {2189-2206}, pmid = {35104026}, issn = {1365-294X}, mesh = {Geography ; *Microbiota/genetics ; *Phaeophyceae/genetics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; *Seaweed/genetics ; }, abstract = {Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.}, }
@article {pmid35095978, year = {2021}, author = {Abdullaeva, Y and Ratering, S and Ambika Manirajan, B and Rosado-Porto, D and Schnell, S and Cardinale, M}, title = {Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {806915}, pmid = {35095978}, issn = {1664-462X}, abstract = {The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.}, }
@article {pmid35094708, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and Ernst, M and Hansen, M and Forberg, T and Gopalakrishnan, S and Gilbert, MTP and Bojesen, AM and Kristiansen, K and Limborg, MT}, title = {A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss).}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {21}, pmid = {35094708}, issn = {2049-2618}, mesh = {Animals ; Metagenome ; Metagenomics ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Synbiotics ; }, abstract = {BACKGROUND: Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. Here, we investigate the functional effects of bacteria-based pro- and synbiotic feed additives on microbiome-associated functions in relation to growth performance in the commercially important rainbow trout (Oncorhynchus mykiss). We combine complementary insights from multiple omics datasets from gut content samples, including 16S bacterial profiling, whole metagenomes, and untargeted metabolomics, to investigate bacterial metagenome-assembled genomes (MAGs) and their molecular interactions with host metabolism.<br><br>RESULTS: Our findings reveal that (I) feed additives changed the microbiome and that rainbow trout reared with feed additives had a significantly reduced relative abundance of the salmonid related Candidatus Mycoplasma salmoninae in both the mid and distal gut content, (II) genome resolved metagenomics revealed that alterations of microbial arginine biosynthesis and terpenoid backbone synthesis pathways were directly associated with the presence of Candidatus Mycoplasma salmoninae, and (III) differences in the composition of intestinal microbiota among feed types were directly associated with significant changes of the metabolomic landscape, including lipids and lipid-like metabolites, amino acids, bile acids, and steroid-related metabolites.<br><br>CONCLUSION: Our results demonstrate how the use of multi-omics to investigate complex host-microbiome interactions enable us to better evaluate the functional potential of probiotics compared to studies that only measure overall growth performance or that only characterise the microbial composition in intestinal environments. Video Abstract.}, }
@article {pmid35090190, year = {2022}, author = {Bonthond, G and Barilo, A and Allen, RJ and Cunliffe, M and Krueger-Hadfield, SA}, title = {Fungal endophytes vary by species, tissue type, and life cycle stage in intertidal macroalgae.}, journal = {Journal of phycology}, volume = {58}, number = {2}, pages = {330-342}, doi = {10.1111/jpy.13237}, pmid = {35090190}, issn = {1529-8817}, mesh = {Animals ; *Chondrus ; Ecosystem ; Endophytes ; Life Cycle Stages ; *Seaweed ; }, abstract = {Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.}, }
@article {pmid35086740, year = {2022}, author = {Jensen, EL and Díez-Del-Molino, D and Gilbert, MTP and Bertola, LD and Borges, F and Cubric-Curik, V and de Navascués, M and Frandsen, P and Heuertz, M and Hvilsom, C and Jiménez-Mena, B and Miettinen, A and Moest, M and Pečnerová, P and Barnes, I and Vernesi, C}, title = {Ancient and historical DNA in conservation policy.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {5}, pages = {420-429}, doi = {10.1016/j.tree.2021.12.010}, pmid = {35086740}, issn = {1872-8383}, mesh = {*Biodiversity ; *Conservation of Natural Resources ; DNA ; Policy ; }, abstract = {Although genetic diversity has been recognized as a key component of biodiversity since the first Convention on Biological Diversity (CBD) in 1993, it has rarely been included in conservation policies and regulations. Even less appreciated is the role that ancient and historical DNA (aDNA and hDNA, respectively) could play in unlocking the temporal dimension of genetic diversity, allowing key conservation issues to be resolved, including setting baselines for intraspecies genetic diversity, estimating changes in effective population size (Ne), and identifying the genealogical continuity of populations. Here, we discuss how genetic information from ancient and historical specimens can play a central role in preserving biodiversity and highlight specific conservation policies that could incorporate such data to help countries meet their CBD obligations.}, }
@article {pmid35086739, year = {2022}, author = {Formenti, G and Theissinger, K and Fernandes, C and Bista, I and Bombarely, A and Bleidorn, C and Ciofi, C and Crottini, A and Godoy, JA and Höglund, J and Malukiewicz, J and Mouton, A and Oomen, RA and Paez, S and Palsbøll, PJ and Pampoulie, C and Ruiz-López, MJ and Svardal, H and Theofanopoulou, C and de Vries, J and Waldvogel, AM and Zhang, G and Mazzoni, CJ and Jarvis, ED and Bálint, M and , }, title = {The era of reference genomes in conservation genomics.}, journal = {Trends in ecology &amp; evolution}, volume = {37}, number = {3}, pages = {197-202}, doi = {10.1016/j.tree.2021.11.008}, pmid = {35086739}, issn = {1872-8383}, mesh = {Biodiversity ; *Genome ; *Genomics ; }, abstract = {Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics.}, }
@article {pmid35056519, year = {2021}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations.}, journal = {Microorganisms}, volume = {10}, number = {1}, pages = {}, pmid = {35056519}, issn = {2076-2607}, abstract = {Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.}, }
@article {pmid35054418, year = {2021}, author = {Rusanova, A and Fedorchuk, V and Toshchakov, S and Dubiley, S and Sutormin, D}, title = {An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {35054418}, issn = {2075-1729}, abstract = {Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus-host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.}, }
@article {pmid35050172, year = {2022}, author = {Ortega, MA and Alvarez-Mon, MA and García-Montero, C and Fraile-Martinez, O and Guijarro, LG and Lahera, G and Monserrat, J and Valls, P and Mora, F and Rodríguez-Jiménez, R and Quintero, J and Álvarez-Mon, M}, title = {Gut Microbiota Metabolites in Major Depressive Disorder-Deep Insights into Their Pathophysiological Role and Potential Translational Applications.}, journal = {Metabolites}, volume = {12}, number = {1}, pages = {}, pmid = {35050172}, issn = {2218-1989}, support = {B2017/BMD3804//Comunidad de Madrid/ ; }, abstract = {The gut microbiota is a complex and dynamic ecosystem essential for the proper functioning of the organism, affecting the health and disease status of the individuals. There is continuous and bidirectional communication between gut microbiota and the host, conforming to a unique entity known as "holobiont". Among these crosstalk mechanisms, the gut microbiota synthesizes a broad spectrum of bioactive compounds or metabolites which exert pleiotropic effects on the human organism. Many of these microbial metabolites can cross the blood-brain barrier (BBB) or have significant effects on the brain, playing a key role in the so-called microbiota-gut-brain axis. An altered microbiota-gut-brain (MGB) axis is a major characteristic of many neuropsychiatric disorders, including major depressive disorder (MDD). Significative differences between gut eubiosis and dysbiosis in mental disorders like MDD with their different metabolite composition and concentrations are being discussed. In the present review, the main microbial metabolites (short-chain fatty acids -SCFAs-, bile acids, amino acids, tryptophan -trp- derivatives, and more), their signaling pathways and functions will be summarized to explain part of MDD pathophysiology. Conclusions from promising translational approaches related to microbial metabolome will be addressed in more depth to discuss their possible clinical value in the management of MDD patients.}, }
@article {pmid35050140, year = {2021}, author = {Liang, J and Luo, W and Yu, K and Xu, Y and Chen, J and Deng, C and Ge, R and Su, H and Huang, W and Wang, G}, title = {Multi-Omics Revealing the Response Patterns of Symbiotic Microorganisms and Host Metabolism in Scleractinian Coral Pavona minuta to Temperature Stresses.}, journal = {Metabolites}, volume = {12}, number = {1}, pages = {}, pmid = {35050140}, issn = {2218-1989}, support = {42030502//National Natural Science Foundation of China/ ; }, abstract = {Global climate change has resulted in large-scale coral reef decline worldwide, for which the ocean warming has paid more attention. Coral is a typical mutually beneficial symbiotic organism with diverse symbiotic microorganisms, which maintain the stability of physiological functions. This study compared the responses of symbiotic microorganisms and host metabolism in a common coral species, Pavona minuta, under indoor simulated thermal and cold temperatures. The results showed that abnormal temperature stresses had unfavorable impact on the phenotypes of corals, resulting in bleaching and color change. The compositions of symbiotic bacteria and dinoflagellate communities only presented tiny changes under temperature stresses. However, some rare symbiotic members have been showed to be significantly influenced by water temperatures. Finally, by using ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS) method, we found that different temperature stresses had very different impacts on the metabolism of coral holobiont. The thermal and cold stresses induced the decrease of anti-oxidation metabolites, several monogalactosyldiacylglycerols (MGDGs), and the increase of lipotoxic metabolite, 10-oxo-nonadecanoic acid, in the coral holobiont, respectively. Our study indicated the response patterns of symbiotic microorganisms and host metabolism in coral to the thermal and cold stresses, providing theoretical data for the adaptation and evolution of coral to a different climate in the future.}, }
@article {pmid35043221, year = {2023}, author = {Kanisan, DP and Quek, ZBR and Oh, RM and Afiq-Rosli, L and Lee, JN and Huang, D and Wainwright, BJ}, title = {Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.}, journal = {Microbial ecology}, volume = {85}, number = {1}, pages = {37-48}, pmid = {35043221}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Malaysia ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria/genetics ; Coral Reefs ; }, abstract = {Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.}, }
@article {pmid35042418, year = {2022}, author = {Kriefall, NG and Kanke, MR and Aglyamova, GV and Davies, SW}, title = {Reef environments shape microbial partners in a highly connected coral population.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1967}, pages = {20212459}, pmid = {35042418}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/genetics/microbiology ; Bacteria/genetics ; Coral Reefs ; Polynesia ; }, abstract = {Evidence is mounting that composition of microorganisms within a host can play an essential role in total holobiont health. In corals, for instance, studies have identified algal and bacterial taxa that can significantly influence coral host function and these communities depend on environmental context. However, few studies have linked host genetics to algal and microbial partners across environments within a single coral population. Here, using 2b-RAD sequencing of corals and metabarcoding of their associated algal (ITS2) and bacterial (16S) communities, we show evidence that reef zones (locales that differ in proximity to shore and other environmental characteristics) structure algal and bacterial communities at different scales in a highly connected coral population (Acropora hyacinthus) in French Polynesia. Fore reef (FR) algal communities in Mo'orea were more diverse than back reef (BR) communities, suggesting that these BR conditions constrain diversity. Interestingly, in FR corals, host genetic diversity correlated with bacterial diversity, which could imply genotype by genotype interactions between these holobiont members. Our results illuminate that local reef conditions play an important role in shaping unique host-microbial partner combinations, which may have fitness consequences for dispersive coral populations arriving in novel environments.}, }
@article {pmid35032344, year = {2022}, author = {Rasmussen, JA and Villumsen, KR and von Gersdorff Jørgensen, L and Forberg, T and Zuo, S and Kania, PW and Buchmann, K and Kristiansen, K and Bojesen, AM and Limborg, MT}, title = {Integrative analyses of probiotics, pathogenic infections and host immune response highlight the importance of gut microbiota in understanding disease recovery in rainbow trout (Oncorhynchus mykiss).}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {3201-3216}, doi = {10.1111/jam.15433}, pmid = {35032344}, issn = {1365-2672}, support = {DNRF143//Danmarks Grundforskningsfond/ ; 34009-17-1218//Milj&#xf8;styrelsen/ ; 8022-00005B//Det Frie Forskningsr&#xe5;d/ ; }, mesh = {Animals ; *Fish Diseases/microbiology ; *Gastrointestinal Microbiome ; Immunity ; *Oncorhynchus mykiss/microbiology ; *Probiotics ; *Yersinia Infections/microbiology/veterinary ; Yersinia ruckeri ; }, abstract = {AIMS: Given the pivotal role played by the gut microbiota in regulating the host immune system, great interest has arisen in the possibility of controlling fish health by modulating the gut microbiota. Hence, there is a need to better understand of the host-microbiota interactions after disease responses to optimize the use of probiotics to strengthen disease resilience and recovery.<br><br>METHODS AND RESULTS: We tested the effects of a probiotic feed additive in rainbow trout and challenged the fish with the causative agent for enteric red mouth disease, Yersinia ruckeri. We evaluated the survival, host immune gene expression and the gut microbiota composition. Results revealed that provision of probiotics and exposure to Y. ruckeri induced immune gene expression in the host, which were associated with changes in the gut microbiota. Subsequently, infection with Y. ruckeri had very little effect on microbiota composition when probiotics were applied, indicating that probiotics increased stabilisation of the microbiota. Our analysis revealed potential biomarkers for monitoring infection status and fish health. Finally, we used modelling approaches to decipher interactions between gut bacteria and the host immune gene responses, indicating removal of endogenous bacteria elicited by non-specific immune responses.<br><br>CONCLUSIONS: We discuss the relevance of these results emphasizing the importance of host-microbiota interactions, including the protective potential of the gut microbiota in disease responses.<br><br>Our results highlight the functional consequences of probiotic-induced changes in the gut microbiota post infection and the resulting host immune response.}, }
@article {pmid35014869, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Dai, R and He, C and Xu, K and Luo, L and Xiao, L and Zheng, Y and Han, C and Akinyemi, FT and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0126121}, pmid = {35014869}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome ; Chickens/genetics ; Body Weight/genetics ; RNA, Messenger/genetics ; *Somatomedins ; *MicroRNAs ; }, abstract = {Multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts and variation in DNA methylation, mRNA expression, and microRNA profiles in the ceca. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by the upregulation of expression of gga-miR-2128 and a methylated region near its transcription start site (388 bp). Correlation analysis showed that IGF2BP1 expression was associated with an abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in adapting to long-term artificial selection for body weight. Our study provides evidence that adaptation of the holobiont can occur in the microbiome as well as in the epigenetic profile of the host. IMPORTANCE The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts, and variation in DNA methylation, mRNA expression, and microRNA profiles in ceca. The insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by a methylated region near its transcription start site and the upregulation of expression of gga-miR-2128. Correlation analysis also showed that IGF2BP1 expression was associated with the abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in response to long-term artificial selection for body weight. Our study shows that the holobiont may adapt in both the microbiome and the host's epigenetic profile.}, }
@article {pmid34987542, year = {2021}, author = {Lombardi, N and Woo, SL and Vinale, F and Turrà, D and Marra, R}, title = {Editorial: The Plant Holobiont Volume II: Impacts of the Rhizosphere on Plant Health.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {809291}, pmid = {34987542}, issn = {1664-462X}, }
@article {pmid34985334, year = {2022}, author = {Marasco, R and Fusi, M and Callegari, M and Jucker, C and Mapelli, F and Borin, S and Savoldelli, S and Daffonchio, D and Crotti, E}, title = {Destabilization of the Bacterial Interactome Identifies Nutrient Restriction-Induced Dysbiosis in Insect Guts.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0158021}, pmid = {34985334}, issn = {2165-0497}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; *Gastrointestinal Microbiome ; Nutrients/analysis/*metabolism ; Simuliidae/growth &amp; development/metabolism/*microbiology ; }, abstract = {Stress-associated dysbiosis of microbiome can have several configurations that, under an energy landscape conceptual framework, can change from one configuration to another due to different alternating selective forces. It has been proposed-according to the Anna Karenina Principle-that in stressed individuals the microbiome are more dispersed (i.e., with a higher within-beta diversity), evidencing the grade of dispersion as indicator of microbiome dysbiosis. We hypothesize that although dysbiosis leads to different microbial communities in terms of beta diversity, these are not necessarily differently dispersed (within-beta diversity), but they form disrupted networks that make them less resilient to stress. To test our hypothesis, we select nutrient restriction (NR) stress that impairs host fitness but does not introduce overt microbiome selectors, such as toxic compounds and pathogens. We fed the polyphagous black soldier fly, Hermetia illucens, with two NR diets and a control full-nutrient (FN) diet. NR diets were dysbiotic because they strongly affected insect growth and development, inducing significant microscale changes in physiochemical conditions of the gut compartments. NR diets established new configurations of the gut microbiome compared to FN-fed guts but with similar dispersion. However, these new configurations driven by the deterministic changes induced by NR diets were reflected in rarefied, less structured, and less connected bacterial interactomes. These results suggested that while the dispersion cannot be considered a consistent indicator of the unhealthy state of dysbiotic microbiomes, the capacity of the community members to maintain network connections and stability can be an indicator of the microbial dysbiotic conditions and their incapacity to sustain the holobiont resilience and host homeostasis. IMPORTANCE Changes in diet play a role in reshaping the gut microbiome in animals, inducing dysbiotic configurations of the associated microbiome. Although studies have reported on the effects of specific nutrient contents on the diet, studies regarding the conditions altering the microbiome configurations and networking in response to diet changes are limited. Our results showed that nutrient poor diets determine dysbiotic states of the host with reduction of insect weight and size, and increase of the times for developmental stage. Moreover, the poor nutrient diets lead to changes in the compositional diversity and network interaction properties of the gut microbial communities. Our study adds a new component to the understanding of the ecological processes associated with dysbiosis, by disentangling consequences of diets on microbiome dysbiosis that is manifested with the disruption of microbiome networking properties rather than changes in microbiome dispersion and beta diversity.}, }
@article {pmid34977575, year = {2021}, author = {Jomori, T and Matsuda, K and Egami, Y and Abe, I and Takai, A and Wakimoto, T}, title = {Insights into phosphatase-activated chemical defense in a marine sponge holobiont.}, journal = {RSC chemical biology}, volume = {2}, number = {6}, pages = {1600-1607}, pmid = {34977575}, issn = {2633-0679}, abstract = {Marine sponges often contain potent cytotoxic compounds, which in turn evokes the principle question of how marine sponges avoid self-toxicity. In a marine sponge Discodermia calyx, the highly toxic calyculin A is detoxified by the phosphorylation, which is catalyzed by the phosphotransferase CalQ of a producer symbiont, "Candidatus Entotheonella" sp. Here we show the activating mechanism to dephosphorylate the stored phosphocalyculin A protoxin. The phosphatase specific to phosphocalyculin A is CalL, which is also encoded in the calyculin biosynthetic gene cluster. CalL represents a new clade and unprecedently coordinates the heteronuclear metals Cu and Zn. CalL is localized in the periplasmic space of the sponge symbiont, where it is ready for the on-demand production of calyculin A in response to sponge tissue disruption.}, }
@article {pmid34975794, year = {2021}, author = {Ge, R and Liang, J and Yu, K and Chen, B and Yu, X and Deng, C and Chen, J and Xu, Y and Qin, L}, title = {Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {767174}, pmid = {34975794}, issn = {1664-302X}, abstract = {Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.}, }
@article {pmid38993286, year = {2022}, author = {Reynoso-García, J and Miranda-Santiago, AE and Meléndez-Vázquez, NM and Acosta-Pagán, K and Sánchez-Rosado, M and Díaz-Rivera, J and Rosado-Quiñones, AM and Acevedo-Márquez, L and Cruz-Roldán, L and Tosado-Rodríguez, EL and Figueroa-Gispert, MDM and Godoy-Vitorino, F}, title = {A complete guide to human microbiomes: Body niches, transmission, development, dysbiosis, and restoration.}, journal = {Frontiers in systems biology}, volume = {2}, number = {}, pages = {}, pmid = {38993286}, issn = {2674-0702}, support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; U54 CA096297/CA/NCI NIH HHS/United States ; R25 GM061838/GM/NIGMS NIH HHS/United States ; U54 MD007587/MD/NIMHD NIH HHS/United States ; S21 MD001830/MD/NIMHD NIH HHS/United States ; R25 GM061151/GM/NIGMS NIH HHS/United States ; }, abstract = {Humans are supra-organisms co-evolved with microbial communities (Prokaryotic and Eukaryotic), named the microbiome. These microbiomes supply essential ecosystem services that play critical roles in human health. A loss of indigenous microbes through modern lifestyles leads to microbial extinctions, associated with many diseases and epidemics. This narrative review conforms a complete guide to the human holobiont-comprising the host and all its symbiont populations- summarizes the latest and most significant research findings in human microbiome. It pretends to be a comprehensive resource in the field, describing all human body niches and their dominant microbial taxa while discussing common perturbations on microbial homeostasis, impacts of urbanization and restoration and humanitarian efforts to preserve good microbes from extinction.}, }
@article {pmid34959516, year = {2021}, author = {Hartmann, A and Klink, S and Rothballer, M}, title = {Importance of N-Acyl-Homoserine Lactone-Based Quorum Sensing and Quorum Quenching in Pathogen Control and Plant Growth Promotion.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34959516}, issn = {2076-0817}, support = {RO 2340/4-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe-plant interactions. Different aspects of QS systems in bacteria-plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.}, }
@article {pmid34957693, year = {2022}, author = {Cavill, EL and Liu, S and Zhou, X and Gilbert, MTP}, title = {To bee, or not to bee? One leg is the question.}, journal = {Molecular ecology resources}, volume = {22}, number = {5}, pages = {1868-1874}, doi = {10.1111/1755-0998.13578}, pmid = {34957693}, issn = {1755-0998}, support = {681396//ERC Consolidator grant/ ; }, mesh = {Animals ; Bees/genetics ; DNA/genetics ; Genome ; *Genomics/methods ; Insecta/genetics ; *Museums ; Sequence Analysis, DNA/methods ; }, abstract = {Temporal genomic studies that utilise museum insects are invaluable for understanding changes in ecological processes in which insects are essential, such as wild and agricultural pollination, seed dispersal, nutrient cycling, and food web architecture, to name a few. However, given such analyses come at the cost of physical damage to museum specimens required for such work, there is a natural interest in the development and/or application of methods to minimise the damage incurred. We explored the efficacy of a recently published single stranded library construction protocol, on DNA extracted from single legs taken from eight dry-preserved historic bee specimens collected 150 years ago. Specifically, the DNA was extracted using a "minimally destructive" method that leaves the samples' exterior intact. Our sequencing data revealed not only that the endogenous DNA recovered from some of the samples was at a relatively high level (up to 58%), but that the complexity of the libraries was sufficient in the best samples to theoretically allow deeper sequencing to a predicted level of 69x genome coverage. As such, these combined protocols offer the possibility to generate sequencing data at levels that are suitable for many common evolutionary genomic analyses, while simultaneously minimising the damage conferred to the valuable dried museum bee samples. Furthermore, we anticipate that these methods may have much wider application on many other invertebrate taxa stored in a similar way. We hope that the results from this research may be able to contribute to the increased willingness of museums to loan much needed dry-preserved insects for future genomic studies.}, }
@article {pmid34951090, year = {2022}, author = {Rolli, E and de Zélicourt, A and Alzubaidy, H and Karampelias, M and Parween, S and Rayapuram, N and Han, B and Froehlich, K and Abulfaraj, AA and Alhoraibi, H and Mariappan, K and Andrés-Barrao, C and Colcombet, J and Hirt, H}, title = {The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {223-239}, pmid = {34951090}, issn = {1462-2920}, mesh = {*Arabidopsis/genetics/microbiology ; *Arabidopsis Proteins/genetics ; Enterobacter/genetics ; Plant Immunity ; Salt Tolerance ; }, abstract = {Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>10[8] CFUs ml[-1]), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant-microbe interaction.}, }
@article {pmid34950234, year = {2021}, author = {Iannello, M and Mezzelani, M and Dalla Rovere, G and Smits, M and Patarnello, T and Ciofi, C and Carraro, L and Boffo, L and Ferraresso, S and Babbucci, M and Mazzariol, S and Centelleghe, C and Cardazzo, B and Carrer, C and Varagnolo, M and Nardi, A and Pittura, L and Benedetti, M and Fattorini, D and Regoli, F and Ghiselli, F and Gorbi, S and Bargelloni, L and Milan, M}, title = {Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam.}, journal = {Evolutionary applications}, volume = {14}, number = {12}, pages = {2864-2880}, pmid = {34950234}, issn = {1752-4571}, abstract = {Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.}, }
@article {pmid34946024, year = {2021}, author = {Singh, S and Singh, A and Baweja, V and Roy, A and Chakraborty, A and Singh, IK}, title = {Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946024}, issn = {2076-2607}, abstract = {Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host-microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota-brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect-microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect-microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.}, }
@article {pmid34943189, year = {2021}, author = {Liu, Y and Liao, X and Han, T and Su, A and Guo, Z and Lu, N and He, C and Lu, Z}, title = {Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont.}, journal = {Biology}, volume = {10}, number = {12}, pages = {}, pmid = {34943189}, issn = {2079-7737}, abstract = {Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.}, }
@article {pmid34933781, year = {2022}, author = {Bianciotto, V and Selosse, MA and Martos, F and Marmeisse, R}, title = {Herbaria preserve plant microbiota responses to environmental changes.}, journal = {Trends in plant science}, volume = {27}, number = {2}, pages = {120-123}, doi = {10.1016/j.tplants.2021.11.012}, pmid = {34933781}, issn = {1878-4372}, mesh = {*Microbiota ; *Plants ; }, abstract = {Interaction between plants and their microbiota is a central theme to understand adaptation of plants to their environment. Considering herbaria as repositories of holobionts that preserved traces of ancient plant-associated microbial communities, we propose to explore these historical collections to evaluate the impact of long-lasting global changes on plant-microbiota interactions.}, }
@article {pmid34932575, year = {2021}, author = {Maltseva, AL and Varfolomeeva, MA and Gafarova, ER and Panova, MAZ and Mikhailova, NA and Granovitch, AI}, title = {Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260792}, pmid = {34932575}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Environmental Microbiology ; *Genetic Variation ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/classification/*microbiology ; Species Specificity ; }, abstract = {Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207-603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species-specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome ("scaffolding enterotype") is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.}, }
@article {pmid34931883, year = {2021}, author = {Der Sarkissian, C and Velsko, IM and Fotakis, AK and Vågene, &#xc5;J and Hübner, A and Fellows Yates, JA}, title = {Ancient Metagenomic Studies: Considerations for the Wider Scientific Community.}, journal = {mSystems}, volume = {6}, number = {6}, pages = {e0131521}, pmid = {34931883}, issn = {2379-5077}, support = {Paleobiotechnology//Werner Siemens-Stiftung/ ; CEH - DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; CF18-1109//Carlsbergfondet (Carlsberg Foundation)/ ; //Centre National de la Recherche Scientifique (CNRS)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; ERC-2015-StG 678901-FoodTransforms//EC | H2020 | H2020 Priority Excellent Science | H2020 European Research Council (ERC)/ ; //Max-Planck-Gesellschaft (MPG)/ ; }, abstract = {Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with finite sample sizes, which impedes optimal experimental design and control of confounding factors, and with ethically sensitive samples necessitating the consideration of additional guidelines. In September 2020, early career researchers in the field of ancient metagenomics met (Standards, Precautions &amp; Advances in Ancient Metagenomics 2 [SPAAM2] community meeting) to discuss the state of the field and how to address current challenges. Here, in an effort to bridge the gap between ancient and modern metagenomics, we highlight and reflect upon some common misconceptions, provide a brief overview of the challenges in our field, and point toward useful resources for potential reviewers and newcomers to the field.}, }
@article {pmid34927107, year = {2021}, author = {Cáceres, PFF and Vélez, LP and Junca, H and Moreno-Herrera, CX}, title = {Theobroma cacao L. agricultural soils with natural low and high cadmium (Cd) in Santander (Colombia), contain a persistent shared bacterial composition shaped by multiple soil variables and bacterial isolates highly resistant to Cd concentrations.}, journal = {Current research in microbial sciences}, volume = {2}, number = {}, pages = {100086}, pmid = {34927107}, issn = {2666-5174}, abstract = {Heavy metals can be found in soil as natural components or as product of contaminations events; plants growing in soils are prone to bioaccumulate heavy metals on their biomass. Theobroma cacao L. can bioaccumulate cadmium (Cd) in the seed and could be in derived food products, it considered a human health risk; therefore, removal of Cd is desirable but not vet technically and economically feasible; only to avoid Cd in cocoa is by selecting lands plots exhibiting lower Cd concentrations in soils, imposing a serious limitation to farmers and regulators. The study of bacterial communities and isolation bacteria with tolerance and mechanisms to counteract the translocation of Cd to the parts of cocoa plant exhibits high relevance in Colombia economy and especially to companies producing chocolate and derivatives. Here, we explore bacterial communities associated with soils having relatively high natural Cd concentrations in a large agricultural cocoa plot located in the Santander region. We characterized the bacterial communities' compositions by amplicon 16S rRNA sequencing from metagenomics soil DNA and by culturing-based enumeration and isolation approaches. Culture-dependent techniques allowed the isolation of bacteria tolerant to Cd concentration, complement the information for Colombia, and expand the number of strains characterized with adaptive capacity against Cd with tolerance in a concentration of 120 mg/L, which represents the first capacity for Exiguobacterium sp., Ralstonia sp., Serratia sp., Dermacoccus sp., Klebsiella sp., Lactococcus sp. and Staphylococcus sp. In addition to confirming that there is a greater diversity of Cd-tolerant bacteria present in soils of farms cultivated with cocoa in Colombia. As for the results of new generation sequencing, they revealed that, the alpha-diversity in bacterial composition, according to the ANOVA, there are statistically significant differences of the bacterial communities present in the samples. Regarding Pearson correlation analysis, it was found the Shannon Simpson indices, have a positive correlation against OM, C, pH, Mn, C.E.C.I., Ca, P and negatively correlated with S; respect to bacterial community structure, a principal component analysis, which revealed that independent of the concentration of Cd present in soil samples, separates them according to pH value. Phyla to high abundance relative in all samples were Proteobacteria, Acidobacteriota, Actinobacteriota, Verrucomicrobiota, Myxococcota, Chloroflexi, Plactomycetota, Bacteroidota, Gemmatimonadota, Nitrospirota, Firmicutes and NB1_J; the bacteria genera with higher relative abundance (>0.5%) Nitrospira, candidatus Udaeobacter, Haliangium, Cupriavidus, MND1, Bacillus, Kitasatospora, Niveibacterium, Acidothermus, Burkholderia, Acidibacter, Terrimonas, Gaiella, candidatus Solibacter, Kitasatospora, Sphingomonas, Streptomyces, this genus with a relationship with the Cd tolerance process. After it, redundancy analysis was performed between the variation of the bacterial communities identified by dependent and independent techniques and edaphic soil variables, where their positive correlation was found against K, OM, C, Ca, pH (p<0.01) and P, C.E.C.I (p<0.05). For soil samples, the bacterial genera that make up the core community were identified, which are present in all samples as Nitrospira sp., Cupriavidus sp., Burkholderia sp., Haliangium sp., candidatus Udaeobacter, MND1, Kitasatospora, Acidothermus, Acidibacter, Streptomyces, Gaiella, candidatus Solibacter and Terramonas; the genera identified has a different and fundamental role in ecosystem functioning. The combination of different approaches offers new clues regarding the assessment of bacterial communities in soils cultivated with cocoa in soils with elevated Cd content in Colombia, and the ecological role and interplay of soil components and bacterial communities that contribute to modulate the effect of bioaccumulation in products.}, }
@article {pmid34926833, year = {2021}, author = {Sinding, MS and Gopalakrishnan, S and Raundrup, K and Dalén, L and Threlfall, J and ,  and ,  and ,  and ,  and ,  and Gilbert, T}, title = {The genome sequence of the grey wolf, Canis lupus Linnaeus 1758.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {310}, pmid = {34926833}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; }, abstract = {We present a genome assembly from an individual male Canis lupus orion (the grey wolf, subspecies: Greenland wolf; Chordata; Mammalia; Carnivora; Canidae). The genome sequence is 2,447 megabases in span. The majority of the assembly (98.91%) is scaffolded into 40 chromosomal pseudomolecules, with the X and Y sex chromosomes assembled.}, }
@article {pmid34922182, year = {2022}, author = {Formosinho, J and Bencard, A and Whiteley, L}, title = {Environmentality in biomedicine: microbiome research and the perspectival body.}, journal = {Studies in history and philosophy of science}, volume = {91}, number = {}, pages = {148-158}, doi = {10.1016/j.shpsa.2021.11.005}, pmid = {34922182}, issn = {0039-3681}, mesh = {Causality ; Ecology ; Humans ; *Microbiota ; }, abstract = {Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool - environmentality - to think through this problem. Environmentality is the state or quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health.}, }
@article {pmid34917118, year = {2021}, author = {Cesaro, P and Gamalero, E and Zhang, J and Pivato, B}, title = {Editorial: The Plant Holobiont Volume I: Microbiota as Part of the Holobiont; Challenges for Agriculture.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {799168}, pmid = {34917118}, issn = {1664-462X}, }
@article {pmid34912564, year = {2021}, author = {Watson, SA and Neo, ML}, title = {Conserving threatened species during rapid environmental change: using biological responses to inform management strategies of giant clams.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coab082}, pmid = {34912564}, issn = {2051-1434}, abstract = {Giant clams are threatened by overexploitation for human consumption, their valuable shells and the aquarium trade. Consequently, these iconic coral reef megafauna are extinct in some former areas of their range and are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and Convention on International Trade in Endangered Species of Wild Fauna and Flora. Now, giant clams are also threatened by rapid environmental change from both a suite of local and regional scale stressors and global change, including climate change, global warming, marine heatwaves and ocean acidification. The interplay between local- to regional-scale and global-scale drivers is likely to cause an array of lethal and sub-lethal effects on giant clams, potentially limiting their depth distribution on coral reefs and decreasing suitable habitat area within natural ranges of species. Global change stressors, pervasive both in unprotected and protected areas, threaten to diminish conservation efforts to date. International efforts urgently need to reduce carbon dioxide emissions to avoid lethal and sub-lethal effects of global change on giant clams. Meanwhile, knowledge of giant clam physiological and ecological responses to local-regional and global stressors could play a critical role in conservation strategies of these threatened species through rapid environmental change. Further work on how biological responses translate into habitat requirements as global change progresses, selective breeding for resilience, the capacity for rapid adaptive responses of the giant clam holobiont and valuing tourism potential, including recognizing giant clams as a flagship species for coral reefs, may help improve the prospects of these charismatic megafauna over the coming decades.}, }
@article {pmid34911766, year = {2021}, author = {Jaspers, C and Ehrlich, M and Pujolar, JM and Künzel, S and Bayer, T and Limborg, MT and Lombard, F and Browne, WE and Stefanova, K and Reusch, TBH}, title = {Invasion genomics uncover contrasting scenarios of genetic diversity in a widespread marine invader.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {51}, pages = {}, pmid = {34911766}, issn = {1091-6490}, mesh = {Animal Distribution ; Animals ; Ctenophora/*genetics/physiology ; *Genetic Variation ; Genome ; *Genomics ; Introduced Species ; }, abstract = {Invasion rates have increased in the past 100 y irrespective of international conventions. What characterizes a successful invasion event? And how does genetic diversity translate into invasion success? Employing a whole-genome perspective using one of the most successful marine invasive species world-wide as a model, we resolve temporal invasion dynamics during independent invasion events in Eurasia. We reveal complex regionally independent invasion histories including cases of recurrent translocations, time-limited translocations, and stepping-stone range expansions with severe bottlenecks within the same species. Irrespective of these different invasion dynamics, which lead to contrasting patterns of genetic diversity, all nonindigenous populations are similarly successful. This illustrates that genetic diversity, per se, is not necessarily the driving force behind invasion success. Other factors such as propagule pressure and repeated introductions are an important contribution to facilitate successful invasions. This calls into question the dominant paradigm of the genetic paradox of invasions, i.e., the successful establishment of nonindigenous populations with low levels of genetic diversity.}, }
@article {pmid34905712, year = {2021}, author = {Chapron, L and Galand, PE and Pruski, AM and Peru, E and Vétion, G and Robin, S and Lartaud, F}, title = {Resilience of cold-water coral holobionts to thermal stress.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1965}, pages = {20212117}, pmid = {34905712}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; Mediterranean Sea ; *Microbiota ; Seawater ; Water ; }, abstract = {Cold-water corals are threatened by global warming, especially in the Mediterranean Sea where they live close to their upper known thermal limit (i.e. 13°C), yet their response to rising temperatures is not well known. Here, temperature effects on Lophelia pertusa and Madrepora oculata holobionts (i.e. the host and its associated microbiome) were investigated. We found that at warmer seawater temperature (+2°C), L. pertusa showed a modification of its microbiome prior to a change in behaviour, leading to lower energy reserves and skeletal growth, whereas M. oculata was more resilient. At extreme temperature (+4°C), both species quickly lost their specific bacterial signature followed by lower physiological activity prior to death. In addition, our results showing the holobionts' negative response to colder temperatures (-3°C), suggest that Mediterranean corals live close to their thermal optimum. The species-specific response to temperature change highlights that global warming may affect dramatically the main deep-sea reef-builders, which would alter the associated biodiversity and related ecosystem services.}, }
@article {pmid34899619, year = {2021}, author = {Barreto, MM and Ziegler, M and Venn, A and Tambutté, E and Zoccola, D and Tambutté, S and Allemand, D and Antony, CP and Voolstra, CR and Aranda, M}, title = {Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {707674}, pmid = {34899619}, issn = {1664-302X}, abstract = {Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.}, }
@article {pmid34896508, year = {2022}, author = {Lin, Z and Wang, L and Chen, M and Zheng, X and Chen, J}, title = {Proteome and microbiota analyses characterizing dynamic coral-algae-microbe tripartite interactions under simulated rapid ocean acidification.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152266}, doi = {10.1016/j.scitotenv.2021.152266}, pmid = {34896508}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Homeostasis ; Hydrogen-Ion Concentration ; *Microbiota ; Oceans and Seas ; Proteome ; Seawater ; }, abstract = {Ocean acidification (OA) is a pressing issue currently and in the future for coral reefs. The importance of maintenance interactions among partners of the holobiont association in the stress response is well appreciated; however, the candidate molecular and microbial mechanisms that underlie holobiont stress resilience or susceptibility remain unclear. Here, to assess the effects of rapid pH change on coral holobionts at both the protein and microbe levels, combined proteomics and microbiota analyses of the scleractinian coral Galaxea fascicularis exposed to three relevant OA scenarios, including current (pHT = 8.15), preindustrial (pHT = 8.45) and future IPCC-2100 scenarios (pHT = 7.85), were conducted. The results demonstrated that pH changes had no significant effect on the physiological calcification rate of G. fascicularis in a 10-day experiment; however, significant differences were recorded in the proteome and 16S profiling. Proteome variance analysis identified some of the core biological pathways in coral holobionts, including coral host infection and immune defence, and maintaining metabolic compatibility involved in energy homeostasis, nutrient cycling, antibiotic activity and carbon budgets of coral-Symbiodiniaceae interactions were key mechanisms in the early OA stress response. Furthermore, microbiota changes indicate substantial microbial community and functional disturbances in response to OA stress, potentially compromising holobiont health and fitness. Our results may help to elucidate many complex mechanisms to describe scleractinian coral holobiont responses to OA and raise interesting questions for future studies.}, }
@article {pmid36619855, year = {2021}, author = {Puetz, LC and Delmont, TO and Aizpurua, O and Guo, C and Zhang, G and Katajamaa, R and Jensen, P and Gilbert, MTP}, title = {Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {4}, pages = {2100018}, pmid = {36619855}, issn = {2641-6573}, abstract = {Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.}, }
@article {pmid34861476, year = {2022}, author = {van de Water, JA and Tignat-Perrier, R and Allemand, D and Ferrier-Pagès, C}, title = {Coral holobionts and biotechnology: from Blue Economy to coral reef conservation.}, journal = {Current opinion in biotechnology}, volume = {74}, number = {}, pages = {110-121}, doi = {10.1016/j.copbio.2021.10.013}, pmid = {34861476}, issn = {1879-0429}, mesh = {Animals ; *Anthozoa ; Bionics ; *Coral Reefs ; Ecosystem ; Photosynthesis ; }, abstract = {Corals are of ecological and economic importance, providing habitat for species and contributing to coastal protection, fisheries, and tourism. Their biotechnological potential is also increasingly recognized. Particularly, the production of pharmaceutically interesting compounds by corals and their microbial associates stimulated natural product-based drug discovery. The efficient light distribution by coral skeletons for optimal photosynthesis by algal symbionts has led to 3D-printed bionic corals that may be used to upscale micro-algal cultivation for bioenergy generation. However, corals are under threat from climate change and pollution, and biotechnological approaches to increase their resilience, like 'probiotics' and 'assisted evolution', are being evaluated. In this review, we summarize the recent biotechnological developments related to corals with an emphasis on coral conservation, drug discovery and bioenergy.}, }
@article {pmid34861071, year = {2022}, author = {Armstrong, EE and Perez-Lamarque, B and Bi, K and Chen, C and Becking, LE and Lim, JY and Linderoth, T and Krehenwinkel, H and Gillespie, RG}, title = {A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates.}, journal = {Molecular ecology}, volume = {31}, number = {4}, pages = {1299-1316}, doi = {10.1111/mec.16301}, pmid = {34861071}, issn = {1365-294X}, mesh = {Animals ; Geography ; Hawaii ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Spiders/genetics ; }, abstract = {The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawai'i, and outgroup taxa on older islands, we tested whether each component of the "holobiont" (spider hosts, intracellular endosymbionts and gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. To investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. The results showed that the host A. waikula is indeed structured by geographical isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawai'i. Conversely, the gut microbiota, which we suspect is generally environmentally derived, was largely conserved across all populations and species. Our results show that different components of the holobiont respond in distinct ways to the dynamic environment of the volcanic archipelago. This highlights the necessity of understanding the interplay between different components of the holobiont, to properly characterize its evolution.}, }
@article {pmid34857934, year = {2022}, author = {Rädecker, N and Pogoreutz, C and Gegner, HM and Cárdenas, A and Perna, G and Geißler, L and Roth, F and Bougoure, J and Guagliardo, P and Struck, U and Wild, C and Pernice, M and Raina, JB and Meibom, A and Voolstra, CR}, title = {Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1110-1118}, pmid = {34857934}, issn = {1751-7370}, support = {200021_179092//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 433042944//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 458901010//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Anthozoa/metabolism ; Coral Reefs ; Heat-Shock Response ; Nitrogen/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Symbiosis ; }, abstract = {Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.}, }
@article {pmid34853170, year = {2021}, author = {Wolinska, KW and Vannier, N and Thiergart, T and Pickel, B and Gremmen, S and Piasecka, A and Piślewska-Bednarek, M and Nakano, RT and Belkhadir, Y and Bednarek, P and Hacquard, S}, title = {Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {49}, pages = {}, pmid = {34853170}, issn = {1091-6490}, mesh = {Arabidopsis/*metabolism/microbiology ; Arabidopsis Proteins/metabolism ; Bacteria/metabolism ; Dysbiosis/metabolism ; Fungi/metabolism ; Microbiota/genetics/physiology ; Mycoses/metabolism ; Oomycetes/metabolism ; Plant Development ; Plant Roots/*growth &amp; development/metabolism/microbiology ; Soil Microbiology ; Symbiosis/physiology ; Tryptophan/*metabolism ; }, abstract = {In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host-microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.}, }
@article {pmid34835139, year = {2021}, author = {Olesen, AS and Kodama, M and Lohse, L and Accensi, F and Rasmussen, TB and Lazov, CM and Limborg, MT and Gilbert, MTP and Bøtner, A and Belsham, GJ}, title = {Identification of African Swine Fever Virus Transcription within Peripheral Blood Mononuclear Cells of Acutely Infected Pigs.}, journal = {Viruses}, volume = {13}, number = {11}, pages = {}, pmid = {34835139}, issn = {1999-4915}, mesh = {African Swine Fever/*virology ; *African Swine Fever Virus/genetics/isolation &amp; purification ; Animals ; Gene Expression Regulation, Viral ; *Genome, Viral ; Leukocytes, Mononuclear ; Male ; Swine ; }, abstract = {African swine fever virus (ASFV) has become widespread in Europe, Asia and elsewhere, thereby causing extensive economic losses. The viral genome includes nearly 200 genes, but their expression within infected pigs has not been well characterized previously. In this study, four pigs were infected with a genotype II strain (ASFV POL/2015/Podlaskie); blood samples were collected before inoculation and at both 3 and 6 days later. During this period, a range of clinical signs of infection became apparent in the pigs. From the blood, peripheral blood mononuclear cells (PBMCs) were isolated. The transcription of the ASFV genes was determined using RNAseq on poly(A)+ mRNAs isolated from these cells. Only very low levels of virus transcription were detected in the PBMCs at 3 days post-inoculation (dpi) but, at 6 dpi, extensive transcription was apparent. This was co-incident with a large increase in the level of ASFV DNA within these cells. The pattern of the virus gene expression was very reproducible between the individual pigs. Many highly expressed genes have undefined roles. Surprisingly, some genes with key roles in virus replication were expressed at only low levels. As the functions of individual genes are identified, information about their expression becomes important for understanding their contribution to virus biology.}, }
@article {pmid34821475, year = {2021}, author = {Kopprio, GA and Luyen, ND and Cuong, LH and Duc, TM and Fricke, A and Kunzmann, A and Huong, LM and Gärdes, A}, title = {Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1253}, pmid = {34821475}, issn = {2045-8827}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Caulerpa/*microbiology/physiology ; Host Microbial Interactions ; *Microbiota ; Plant Diseases/*microbiology ; }, abstract = {The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.}, }
@article {pmid34820166, year = {2021}, author = {Price, DC and Brennan, JR and Wagner, NE and Egizi, AM}, title = {Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12313}, pmid = {34820166}, issn = {2167-8359}, abstract = {Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome-the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick's own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.}, }
@article {pmid34820163, year = {2021}, author = {Liu, S and Zhang, SM and Buddenborg, SK and Loker, ES and Bonning, BC}, title = {Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12290}, pmid = {34820163}, issn = {2167-8359}, support = {P30 GM110907/GM/NIGMS NIH HHS/United States ; R37 AI101438/AI/NIAID NIH HHS/United States ; }, abstract = {Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.}, }
@article {pmid34811423, year = {2021}, author = {Alberdi, A and Martin Bideguren, G and Aizpurua, O}, title = {Diversity and compositional changes in the gut microbiota of wild and captive vertebrates: a meta-analysis.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {22660}, pmid = {34811423}, issn = {2045-2322}, support = {DNRF143//Danmarks Grundforskningsfond/ ; }, mesh = {Animals ; Animals, Wild ; Animals, Zoo/*microbiology ; Bacteria/classification ; Cluster Analysis ; Computational Biology ; Ecology ; *Gastrointestinal Microbiome ; Humans ; Mammals/*microbiology ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Species Specificity ; Vertebrates ; }, abstract = {The gut microbiota is recognised as an essential asset for the normal functioning of animal biology. When wild animals are moved into captivity, the modified environmental pressures are expected to rewire the gut microbiota, yet whether this transition follows similar patterns across vertebrates is still unresolved due to the absence of systematic multi-species analyses. We performed a meta-analysis of gut microbiota profiles of 322 captive and 322 wild specimens from 24 vertebrate species. Our analyses yielded no overall pattern of diversity and compositional variation between wild and captive vertebrates, but a heterogeneous landscape of responses, which differed depending on the components of diversity considered. Captive populations showed enrichment patterns of human-associated microorganisms, and the minimal host phylogenetic signal suggests that changes between wild and captive populations are mainly driven by case-specific captivity conditions. Finally, we show that microbiota differences between wild and captive populations can impact evolutionary and ecological inferences that rely on hierarchical clustering-based comparative analyses of gut microbial communities across species.}, }
@article {pmid34802818, year = {2022}, author = {Marana, MH and Poulsen, R and Thormar, EA and Clausen, CG and Thit, A and Mathiessen, H and Jaafar, R and Korbut, R and Hansen, AMB and Hansen, M and Limborg, MT and Syberg, K and von Gersdorff Jørgensen, L}, title = {Plastic nanoparticles cause mild inflammation, disrupt metabolic pathways, change the gut microbiota and affect reproduction in zebrafish: A full generation multi-omics study.}, journal = {Journal of hazardous materials}, volume = {424}, number = {Pt D}, pages = {127705}, doi = {10.1016/j.jhazmat.2021.127705}, pmid = {34802818}, issn = {1873-3336}, mesh = {Animals ; Ecosystem ; *Gastrointestinal Microbiome ; Inflammation/chemically induced ; Male ; Metabolic Networks and Pathways ; *Microplastics ; Reproduction ; Zebrafish ; }, abstract = {Plastic pollution has become a major concern on a global scale. The plastic is broken down into minuscule particles, which have an impact on the biosystems, however long-term impacts through an entire generation is largely unknown. Here, we present the first whole generation study exposing fish to a 500 nm polystyrene plastic particle at environmentally relevant concentrations. Short- and long-term adverse effects were investigated in the zebrafish model organism using a holistic multi-omics approach. The particles accumulated in the yolk sac of young larvae and short-term biological impacts included immune-relevant gene regulation related to inflammation and tolerance as well as disruption of metabolic processes, such as the fatty acid and lipid pathways. The long-term effects comprised gene regulations pointing towards skin and/or gill inflammation, dysbiosis of the gut microbiota, a tendency towards decreased condition factor in adult males as well as a lowered reproductive capability. From this study, it can be concluded that exposures to plastic nanoparticles have an impact on population as well as ecosystem level in fish and likely also in other vertebrates.}, }
@article {pmid34800848, year = {2022}, author = {Cerrano, C and Giovine, M and Steindler, L}, title = {Petrosia ficiformis (Poiret, 1789): an excellent model for holobiont and biotechnological studies.}, journal = {Current opinion in biotechnology}, volume = {74}, number = {}, pages = {61-65}, doi = {10.1016/j.copbio.2021.10.022}, pmid = {34800848}, issn = {1879-0429}, mesh = {Animals ; Biotechnology ; *Petrosia ; Phylogeny ; *Porifera ; Symbiosis ; }, }
@article {pmid34798282, year = {2022}, author = {Decroës, A and Li, JM and Richardson, L and Mutasa-Gottgens, E and Lima-Mendez, G and Mahillon, M and Bragard, C and Finn, RD and Legrève, A}, title = {Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.}, journal = {Genomics}, volume = {114}, number = {1}, pages = {9-22}, doi = {10.1016/j.ygeno.2021.11.018}, pmid = {34798282}, issn = {1089-8646}, mesh = {*Genome, Mitochondrial ; Genomics ; Metagenomics ; *Plasmodiophorida/genetics ; }, abstract = {Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.}, }
@article {pmid34788073, year = {2022}, author = {Xiang, N and Hassenrück, C and Pogoreutz, C and Rädecker, N and Simancas-Giraldo, SM and Voolstra, CR and Wild, C and Gärdes, A}, title = {Contrasting Microbiome Dynamics of Putative Denitrifying Bacteria in Two Octocoral Species Exposed to Dissolved Organic Carbon (DOC) and Warming.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {2}, pages = {e0188621}, pmid = {34788073}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Coral Reefs ; Dissolved Organic Matter ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.}, }
@article {pmid34765156, year = {2021}, author = {Morrissey, KL and Iveša, L and Delva, S and D'Hondt, S and Willems, A and De Clerck, O}, title = {Impacts of environmental stress on resistance and resilience of algal-associated bacterial communities.}, journal = {Ecology and evolution}, volume = {11}, number = {21}, pages = {15004-15019}, pmid = {34765156}, issn = {2045-7758}, abstract = {Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche-specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea. Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo-, epi-, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes.}, }
@article {pmid34749049, year = {2022}, author = {Thatcher, C and Høj, L and Bourne, DG}, title = {Probiotics for coral aquaculture: challenges and considerations.}, journal = {Current opinion in biotechnology}, volume = {73}, number = {}, pages = {380-386}, doi = {10.1016/j.copbio.2021.09.009}, pmid = {34749049}, issn = {1879-0429}, mesh = {Animals ; *Anthozoa/microbiology ; Aquaculture ; Climate Change ; Coral Reefs ; *Probiotics ; }, abstract = {Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.}, }
@article {pmid34737272, year = {2021}, author = {Dubé, CE and Ziegler, M and Mercière, A and Boissin, E and Planes, S and Bourmaud, CA and Voolstra, CR}, title = {Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6402}, pmid = {34737272}, issn = {2041-1723}, mesh = {Coral Reefs ; Ecosystem ; Genotype ; Microbiota/genetics/*physiology ; }, abstract = {Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.}, }
@article {pmid34734290, year = {2021}, author = {Higuita Palacio, MF and Montoya, OI and Saldamando, CI and García-Bonilla, E and Junca, H and Cadavid-Restrepo, GE and Moreno-Herrera, CX}, title = {Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia.}, journal = {Journal of insect science (Online)}, volume = {21}, number = {6}, pages = {}, pmid = {34734290}, issn = {1536-2442}, mesh = {Animals ; Colombia ; *Enterococcus ; *Gastrointestinal Microbiome ; Larva ; *Seasons ; Spodoptera/*microbiology ; Zea mays ; }, abstract = {Spodoptera frugiperda is a polyphagous pest of several crops of economic importance. Nowadays, the insect is broadly distributed in America and, recently, in Africa, Asia, and Australia. The species has diverged into corn and rice strains. The role of the gut microbiota in insect physiology is relevant due to its participation in crucial functions. However, knowledge of seasonal variations that alter the gut microbiome in pests is limited. Gut microbiome composition between the dry and rainy seasons was analyzed with cultured and uncultured approaches in S. frugiperda corn strain larvae collected at Northwest Colombia, as seasonal microbiome changes might fluctuate due to environmental changes. On the basis of culture-dependent methods, results show well-defined microbiota with bacterial isolates belonging to Enterococcus, Klebsiella (Enterobacteriales: Enterobacteriaceae), Enterobacter (Enterobacterales: Enterobacteriaceae), and Bacillus (Bacillales: Bacillaceae) genera. The community composition displayed a low bacterial diversity across all samples. The core community detected with uncultured methods was composed of Enterococcus, Erysipelatoclostridium (Erysipelotrichales: Erysipelotrichaceae), Rasltonia (Burkholderiales: Burkholderiaceae), and Rhizobium (Hyphomicrobiales: Rhizobiaceae) genera, and Enterobacteriaceae family members. Significant differences in microbiome diversity were observed between the two seasons. The relative abundance of Erysipelatoclostridium was high in the dry season, while in the phylotype ZOR0006 (Erysipelotrichales: Erysipelotrichaceae) and Tyzzerella (Lachnospirales: Lachnospiraceae) genus, the relative abundance was high in the rainy season. The overall low gut bacterial diversity observed in the S. frugiperda corn strain suggests a strong presence of antagonist activity as a selection factor possibly arising from the host, the dominant bacterial types, or the material ingested. Targeting the stability and predominance of this core microbiome could be an additional alternative to pest control strategies, particularly in this moth.}, }
@article {pmid34721372, year = {2021}, author = {Wale, M and Daffonchio, D and Fusi, M and Marasco, R and Garuglieri, E and Diele, K}, title = {The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {770245}, pmid = {34721372}, issn = {1664-302X}, }
@article {pmid34718260, year = {2021}, author = {Banić, M and Pleško, S and Urek, M and Babić, &#x17d; and Kardum, D}, title = {Immunosenescence, Inflammaging and Resilience: An Evolutionary Perspective of Adaptation in the Light of COVID-19 Pandemic.}, journal = {Psychiatria Danubina}, volume = {33}, number = {Suppl 4}, pages = {427-431}, pmid = {34718260}, issn = {0353-5053}, mesh = {Aged ; Aging ; *COVID-19 ; Humans ; Immunity, Innate ; *Immunosenescence ; Inflammation ; Lymphocytes ; Pandemics ; SARS-CoV-2 ; }, abstract = {The evolution of immunology enabled the study of role of innate and adaptive immunity in systems biology network of immunosenescence and inflammaging. Due to global reduction in birth rates and reduced mortality, in year 2025 there will be about 1.2 billion of people over age of sixty, worldwide. The notion that the real age is not chronological, but the biological one led to the concept of "bioage", defining the biologic reactivity and resilience, including the immune competence of an individual. A competent immune network, systemic and mucosal is intrinsic to resilience and homeostasis of the human holobiont as the unit of evolution. In elderly, the immunosenescence could be associated with higher levels of proinflammatory mediators (such as IL-6), frialty and mortality. Proi-inflammatory state in elderly is denoted as inflammaging, characterized with low-grade (sterile) inflammation, as a physiologic response to life-long antigenic stimuli. When under control, inflammaging could be regarded as an efficient defense mechanism, oposed and regulated by anti-inflammatory pathways and molecules. Immunosensecence. The emerging concepts of "individual immunobiography" and "trained immunity" speak in favour that the immunological experience during the life would shape the ability of each individual to respond to various stimuli, strongly influencing the elements of innate and adaptive immunity, including macrophages and innate lymphoid cells. Older age is one of the main risk factors for the severe clinical picture and adverse outcome of COVID-19 infection, due to immunosenscence and chronic low-grade inflammation (inflammaging), both characterizing the immune reactioin in elderly. The senescent immune system, along with the advanced process of inflammaging is prone to react with uncontrolled activation of innate immune response that leads to cytokine release syndrome, tissue damage and adverse outcome of infection. Further research is aimed to nutritional and pharmacologic (immunomodulatory) interventions to influence the process of bioaging and immunosenscence, and to modulate the reaction of elderly to infection, including the COVID-19.}, }
@article {pmid34714176, year = {2021}, author = {Czernik, PJ and Golonka, RM and Chakraborty, S and Yeoh, BS and Abokor, AA and Saha, P and Yeo, JY and Mell, B and Cheng, X and Baroi, S and Tian, Y and Patterson, AD and Joe, B and Vijay-Kumar, M and Lecka-Czernik, B}, title = {Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content.}, journal = {Physiological genomics}, volume = {53}, number = {12}, pages = {518-533}, pmid = {34714176}, issn = {1531-2267}, support = {R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Adipocytes/metabolism ; Animals ; Bacteria/*genetics/*metabolism ; Bone Density/physiology ; Bone Development/*physiology ; Bone Marrow Cells/*metabolism ; Cell Proliferation/physiology ; Chondrocytes/metabolism ; Coprophagia ; Dysbiosis ; Fatty Acids, Volatile/analysis/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Germ-Free Life ; Host Microbial Interactions/*genetics ; Male ; Osteogenesis/*physiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Integration of microbiota in a host begins at birth and progresses during adolescence, forming a multidirectional system of physiological interactions. Here, we present an instantaneous effect of natural, bacterial gut colonization on the acceleration of longitudinal and radial bone growth in germ-free born, 7-wk-old male rats. Changes in bone mass and structure were analyzed after 10 days following the onset of colonization through cohousing with conventional rats and revealed unprecedented acceleration of bone accrual in cortical and trabecular compartments, increased bone tissue mineral density, improved proliferation and hypertrophy of growth plate chondrocytes, bone lengthening, and preferential deposition of periosteal bone in the tibia diaphysis. In addition, the number of small in size adipocytes increased, whereas the number of megakaryocytes decreased, in the bone marrow of conventionalized germ-free rats indicating that not only bone mass but also bone marrow environment is under control of gut microbiota signaling. The changes in bone status paralleled with a positive shift in microbiota composition toward short-chain fatty acids (SCFA)-producing microbes and a considerable increase in cecal SCFA concentrations, specifically butyrate. Furthermore, reconstitution of the host holobiont increased hepatic expression of IGF-1 and its circulating levels. Elevated serum levels of 25-hydroxy vitamin D and alkaline phosphatase pointed toward an active process of bone formation. The acute stimulatory effect on bone growth occurred independently of body mass increase. Overall, the presented model of conventionalized germ-free rats could be used to study microbiota-based therapeutics for combatting dysbiosis-related bone disorders.}, }
@article {pmid34713541, year = {2022}, author = {Iltis, C and Tougeron, K and Hance, T and Louâpre, P and Foray, V}, title = {A perspective on insect-microbe holobionts facing thermal fluctuations in a climate-change context.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {18-29}, doi = {10.1111/1462-2920.15826}, pmid = {34713541}, issn = {1462-2920}, mesh = {Animals ; *Climate Change ; Heat-Shock Response ; *Insecta ; Symbiosis ; Temperature ; }, abstract = {Temperature influences the ecology and evolution of insects and their symbionts by impacting each partner independently and their interactions, considering the holobiont as a primary unit of selection. There are sound data about the responses of these partnerships to constant temperatures and sporadic thermal stress (mostly heat shock). However, the current understanding of the thermal ecology of insect-microbe holobionts remains patchy because the complex thermal fluctuations (at different spatial and temporal scales) experienced by these organisms in nature have often been overlooked experimentally. This may drastically constrain our ability to predict the fate of mutualistic interactions under climate change, which will alter both mean temperatures and thermal variability. Here, we tackle down these issues by focusing on the effects of temperature fluctuations on the evolutionary ecology of insect-microbe holobionts. We propose potentially worth-investigating research avenues to (i) evaluate the relevance of theoretical concepts used to predict the biological impacts of temperature fluctuations when applied to holobionts; (ii) acknowledge the plastic (behavioural thermoregulation, physiological acclimation) and genetic responses (evolution) expressed by holobionts in fluctuating thermal environments; and (iii) explore the potential impacts of previously unconsidered patterns of temperature fluctuations on the outcomes and the dynamic of these insect-microbe associations.}, }
@article {pmid34712923, year = {2021}, author = {Sinding, MS and Ciucani, MM and Ramos-Madrigal, J and Carmagnini, A and Rasmussen, JA and Feng, S and Chen, G and Vieira, FG and Mattiangeli, V and Ganjoo, RK and Larson, G and Sicheritz-Pontén, T and Petersen, B and Frantz, L and Gilbert, MTP and Bradley, DG}, title = {Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos.}, journal = {iScience}, volume = {24}, number = {11}, pages = {103226}, pmid = {34712923}, issn = {2589-0042}, abstract = {The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so.}, }
@article {pmid34711286, year = {2021}, author = {Aizpurua, O and Nyholm, L and Morris, E and Chaverri, G and Herrera Montalvo, LG and Flores-Martinez, JJ and Lin, A and Razgour, O and Gilbert, MTP and Alberdi, A}, title = {The role of the gut microbiota in the dietary niche expansion of fishing bats.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {76}, pmid = {34711286}, issn = {2524-4671}, support = {CF15-0619//Carlsbergfondet/ ; DNRF143//Danmarks Grundforskningsfond/ ; 17417//Villum Fonden/ ; R250-2017-1351//Lundbeckfonden/ ; DFF 5051-00033//Natur og Univers, Det Frie Forskningsr&#xe5;d/ ; 237774//Consejo Nacional de Ciencia y Tecnolog&#xed;a/ ; NE/L002531/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet.<br><br>RESULTS: We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish.<br><br>CONCLUSIONS: Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory.}, }
@article {pmid34710723, year = {2022}, author = {Varasteh, T and Tschoeke, D and Silva-Lima, AW and Thompson, C and Thompson, F}, title = {Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100912}, doi = {10.1016/j.margen.2021.100912}, pmid = {34710723}, issn = {1876-7478}, mesh = {Animals ; *Anthozoa/genetics ; Biological Transport ; Brazil ; Transcriptome ; }, abstract = {A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.}, }
@article {pmid34709051, year = {2021}, author = {Mead, OL and Hahn, EE and Adamska, MA}, title = {Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn.}, journal = {Microbiology resource announcements}, volume = {10}, number = {43}, pages = {e0085821}, pmid = {34709051}, issn = {2576-098X}, support = {//Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; //Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; //Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; }, abstract = {Sponges have complex relationships with bacteria, the roles of which include food, important components of the holobiont, pathogens, and accidentally accumulated elements of the environment. Consequently, sponges are reservoirs of microbial genomes and novel compounds. Therefore, we isolated and sequenced the whole genomes of bacterial species from the calcareous sponge Sycon capricorn.}, }
@article {pmid34699617, year = {2022}, author = {Shoguchi, E}, title = {Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae).}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {1-11}, pmid = {34699617}, issn = {1529-8817}, mesh = {*Amino Acids/biosynthesis ; Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Gene Transfer, Horizontal ; Multigene Family ; Phylogeny ; Symbiosis ; }, abstract = {Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.}, }
@article {pmid34697892, year = {2021}, author = {Merges, D and Dal Grande, F and Greve, C and Otte, J and Schmitt, I}, title = {Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6637-6650}, doi = {10.1111/1462-2920.15802}, pmid = {34697892}, issn = {1462-2920}, mesh = {*Ascomycota/genetics ; *Bacteriophages/genetics ; Genome, Viral/genetics ; *Lichens/genetics/microbiology ; Metagenome ; Phylogeny ; Symbiosis ; }, abstract = {Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.}, }
@article {pmid34685796, year = {2021}, author = {Alotaibi, F and Lee, SJ and St-Arnaud, M and Hijri, M}, title = {Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {34685796}, issn = {2223-7747}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.}, }
@article {pmid34685638, year = {2021}, author = {Kriaa, A and Jablaoui, A and Rhimi, S and Soussou, S and Mkaouar, H and Mariaule, V and Gruba, N and Gargouri, A and Maguin, E and Lesner, A and Rhimi, M}, title = {SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice.}, journal = {Cells}, volume = {10}, number = {10}, pages = {}, pmid = {34685638}, issn = {2073-4409}, mesh = {Amino Acid Sequence ; Animals ; Colitis/chemically induced/*enzymology/*microbiology ; Conserved Sequence ; Dextran Sulfate ; Dysbiosis/*enzymology/*microbiology ; Feces/enzymology ; *Gastrointestinal Microbiome ; Inflammation/pathology ; Intestinal Mucosa/pathology ; Intestines/*pathology ; Kinetics ; Lactobacillus/enzymology ; Male ; Mice, Inbred C57BL ; Phylogeny ; Serine Proteases/administration &amp; dosage/chemistry/isolation &amp; purification/*metabolism ; Substrate Specificity ; Subtilisin/chemistry ; Mice ; }, abstract = {Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.}, }
@article {pmid34678546, year = {2021}, author = {Zhu, W and Xia, J and Ren, Y and Xie, M and Yin, H and Liu, X and Huang, J and Zhu, M and Li, X}, title = {Coastal corals during heat stress and eutrophication: A case study in Northwest Hainan coastal areas.}, journal = {Marine pollution bulletin}, volume = {173}, number = {Pt B}, pages = {113048}, doi = {10.1016/j.marpolbul.2021.113048}, pmid = {34678546}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa ; Chlorophyll A ; *Dinoflagellida ; Eutrophication ; Heat-Shock Response ; Symbiosis ; }, abstract = {This study initially investigated the coral status during the unexpected bleaching event in three coastal areas in Northwest Hainan coastal areas and analyzed changes in coral holobionts of the healthy and bleached Galaxea fascicularis. Coral coverage had declined severely, and the bleaching rate was extremely high during heat stress. The bleached corals had lower maximum photosynthetic yield, actual photosynthetic yield, zooxanthellae density, and chlorophyll a content than the healthy G. fascicularis, but there was no significant difference in protein, carbohydrate and lipid in eutrophic waters. The diversity and community composition of Symbiodiniaceae and symbiotic bacteria between healthy and bleached G. fascicularis showed no difference. Function prediction of the symbiotic bacteria revealed that the metabolism process was the main pathway of annotation. Present findings suggested that energy reserve functioning and high stability of the holobiont structure and might provide opportunities to G. fascicularis to adapt to eutrophication and heat stress.}, }
@article {pmid34675394, year = {2022}, author = {Alberdi, A and Andersen, SB and Limborg, MT and Dunn, RR and Gilbert, MTP}, title = {Disentangling host-microbiota complexity through hologenomics.}, journal = {Nature reviews. Genetics}, volume = {23}, number = {5}, pages = {281-297}, pmid = {34675394}, issn = {1471-0064}, mesh = {Animals ; Biological Evolution ; *Microbiota/genetics ; }, abstract = {Research on animal-microbiota interactions has become a central topic in biological sciences because of its relevance to basic eco-evolutionary processes and applied questions in agriculture and health. However, animal hosts and their associated microbial communities are still seldom studied in a systemic fashion. Hologenomics, the integrated study of the genetic features of a eukaryotic host alongside that of its associated microbes, is becoming a feasible - yet still underexploited - approach that overcomes this limitation. Acknowledging the biological and genetic properties of both hosts and microbes, along with the advantages and disadvantages of implemented techniques, is essential for designing optimal studies that enable some of the major questions in biology to be addressed.}, }
@article {pmid34674103, year = {2021}, author = {Bonthond, G and Shalygin, S and Bayer, T and Weinberger, F}, title = {Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont.}, journal = {Antonie van Leeuwenhoek}, volume = {114}, number = {12}, pages = {2189-2203}, pmid = {34674103}, issn = {1572-9699}, support = {WE2700/5-1//Deutsche Forschungsgemeinshaft/ ; BA5508/2-1//Deutsche Forschungsgemeinshaft/ ; }, mesh = {*Cyanobacteria/genetics ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; *Rhodophyta ; *Seaweed ; Sequence Analysis, DNA ; }, abstract = {This work introduces Waterburya agarophytonicola Bonthond and Shalygin gen. nov., sp. nov, a baeocyte producing cyanobacterium that was isolated from the rhodophyte Agarophyton vermiculophyllum (Ohmi) Gurgel et al., an invasive seaweed that has spread across the northern hemisphere. The new species genome reveals a diverse repertoire of chemotaxis and adhesion related genes, including genes coding for type IV pili assembly proteins and a high number of genes coding for filamentous hemagglutinin family (FHA) proteins. Among a genetic basis for the synthesis of siderophores, carotenoids and numerous vitamins, W. agarophytonicola is potentially capable of producing cobalamin (vitamin B12), for which A. vermiculophyllum is an auxotroph. With a taxonomic description of the genus and species and a draft genome, this study provides as a basis for future research, to uncover the nature of this geographically independent association between seaweed and cyanobiont.}, }
@article {pmid37284513, year = {2021}, author = {Mauger, S and Ricono, C and Mony, C and Chable, V and Serpolay, E and Biget, M and Vandenkoornhuyse, P}, title = {Differentiation of endospheric microbiota in ancient and modern wheat cultivar roots.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {2}, number = {5}, pages = {235-248}, pmid = {37284513}, issn = {2575-6265}, abstract = {Modern plant breeding and agrosystems artificialization could have altered plants' ability to filter and recruit beneficial microorganisms in its microbiota. Thus, compared to modern cultivars, we hypothesized that root-endosphere microbiota in modern wheat cultivars are less resistant to colonization by fungi and bacteria and thus more susceptible to also recruit more pathogens. We used an in-field experimental design including six wheat varieties (three ancient vs. three modern) grown in monoculture and in mixture (three replicates each). Endospheric microbiota of wheat roots were analyzed on four individuals sampled randomly in each plot. Composition-based clustering of sequences was then characterized from amplicon mass-sequencing. We show that the bacterial and fungal microbiota composition in wheat roots differed between ancient and modern wheat cultivar categories. However, the responses observed varied with the group considered. Modern cultivars harbored higher richness of bacterial and fungal pathogens than ancient cultivars. Both cultivar types displayed specific indicator species. A synergistic effect was identified in mixtures of modern cultivars with a higher root endospheric mycobiota richness than expected from a null model. The present study shows the effect of plant breeding on the microbiota associated plant roots. The results call for making a diagnosis of the cultivar's endospheric-microbiota composition. These new results also suggest the importance of a holobiont-vision while considering plant selection in crops and call for better integration of symbiosis in the development of next-generation agricultural practices.}, }
@article {pmid34659277, year = {2021}, author = {Bharadwaj, R and Noceda, C and Mohanapriya, G and Kumar, SR and Thiers, KLL and Costa, JH and Macedo, ES and Kumari, A and Gupta, KJ and Srivastava, S and Adholeya, A and Oliveira, M and Velada, I and Sircar, D and Sathishkumar, R and Arnholdt-Schmitt, B}, title = {Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {686274}, pmid = {34659277}, issn = {1664-462X}, abstract = {Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.}, }
@article {pmid34641951, year = {2021}, author = {Paix, B and Layglon, N and Le Poupon, C and D'Onofrio, S and Misson, B and Garnier, C and Culioli, G and Briand, JF}, title = {Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {201}, pmid = {34641951}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Copper ; Metabolome ; *Microbiota/genetics ; *Seaweed ; }, abstract = {BACKGROUND: Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms.<br><br>RESULTS: Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and &#x3b1;-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.<br><br>CONCLUSION: We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.}, }
@article {pmid34641725, year = {2021}, author = {Muller, EM and Dungan, AM and Million, WC and Eaton, KR and Petrik, C and Bartels, E and Hall, ER and Kenkel, CD}, title = {Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1960}, pages = {20210923}, pmid = {34641725}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/genetics ; *Climate Change ; Coral Reefs ; Ecosystem ; Endangered Species ; }, abstract = {Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.}, }
@article {pmid34638430, year = {2021}, author = {Oldenburg, M and Rüchel, N and Janssen, S and Borkhardt, A and Gössling, KL}, title = {The Microbiome in Childhood Acute Lymphoblastic Leukemia.}, journal = {Cancers}, volume = {13}, number = {19}, pages = {}, pmid = {34638430}, issn = {2072-6694}, support = {428917761//Deutsche Forschungsgemeinschaft/ ; 2020-24//Research Committee of the Heinrich Heine University Duesseldorf/ ; }, abstract = {For almost 30 years, the term "holobiont" has referred to an ecological unit where a host (e.g., human) and all species living in or around it are considered together. The concept highlights the complex interactions between the host and the other species, which, if disturbed may lead to disease and premature aging. Specifically, the impact of microbiome alterations on the etiology of acute lymphoblastic leukemia (ALL) in children is not fully understood, but has been the focus of much research in recent years. In ALL patients, significant reductions in microbiome diversity are already observable at disease onset. It remains unclear whether such alterations at diagnosis are etiologically linked with leukemogenesis or simply due to immunological alteration preceding ALL onset. Regardless, all chemotherapeutic treatment regimens severely affect the microbiome, accompanied by severe side effects, including mucositis, systemic inflammation, and infection. In particular, dominance of Enterococcaceae is predictive of infections during chemotherapy. Long-term dysbiosis, like depletion of Faecalibacterium, has been observed in ALL survivors. Modulation of the microbiome (e.g., by fecal microbiota transplant, probiotics, or prebiotics) is currently being researched for potential protective effects. Herein, we review the latest microbiome studies in pediatric ALL patients.}, }
@article {pmid34637727, year = {2021}, author = {Duchêne, DA}, title = {Phylogenomics.}, journal = {Current biology : CB}, volume = {31}, number = {19}, pages = {R1177-R1181}, doi = {10.1016/j.cub.2021.07.039}, pmid = {34637727}, issn = {1879-0445}, mesh = {Biological Evolution ; *Evolution, Molecular ; Genome ; *Genomics ; Phylogeny ; }, abstract = {The reconstruction of evolutionary relationships among species is fundamental for our understanding of biodiversity. Today, evolutionary relationships are closely related with the depiction of the tree of life, and research on the topic is underpinned by methods in molecular phylogenetics that have grown in popularity since the 1960s. These methods depend on our understanding of how nucleotide or amino acid sequences evolve through time and in different lineages. Armed with this knowledge, researchers can make inferences about the relationships and amount of genomic divergence among species.}, }
@article {pmid36618122, year = {2021}, author = {Margaryan, A and Sinding, MS and Carøe, C and Yamshchikov, V and Burtsev, I and Gilbert, MTP}, title = {The genomic origin of Zana of Abkhazia.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {2}, pages = {e10051}, pmid = {36618122}, issn = {2641-6573}, abstract = {Enigmatic phenomena have sparked the imagination of people around the globe into creating folkloric creatures. One prime example is Zana of Abkhazia (South Caucasus), a well-documented 19th century female who was captured living wild in the forest. Zana's appearance was sufficiently unusual, that she was referred to by locals as an Almasty-the analog of Bigfoot in the Caucasus. Although the exact location of Zana's burial site was unknown, the grave of her son, Khwit, was identified in 1971. The genomes of Khwit and the alleged Zana skeleton were sequenced to an average depth of ca. 3× using ancient DNA techniques. The identical mtDNA and parent-offspring relationship between the two indicated that the unknown woman was indeed Zana. Population genomic analyses demonstrated that Zana's immediate genetic ancestry can likely be traced to present-day East-African populations. We speculate that Zana might have had a genetic disorder such as congenital generalized hypertrichosis which could partially explain her strange behavior, lack of speech, and long body hair. Our findings elucidate Zana's unfortunate story and provide a clear example of how prejudices of the time led to notions of cryptic hominids that are still held and transmitted by some today.}, }
@article {pmid36157708, year = {2020}, author = {Wang, M and Cernava, T}, title = {Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity.}, journal = {Environmental science and ecotechnology}, volume = {4}, number = {}, pages = {100061}, pmid = {36157708}, issn = {2666-4984}, abstract = {Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.}, }
@article {pmid34635054, year = {2021}, author = {Fontsere, C and Frandsen, P and Hernandez-Rodriguez, J and Niemann, J and Scharff-Olsen, CH and Vallet, D and Le Gouar, P and Ménard, N and Navarro, A and Siegismund, HR and Hvilsom, C and Gilbert, MTP and Kuhlwilm, M and Hughes, D and Marques-Bonet, T}, title = {The genetic impact of an Ebola outbreak on a wild gorilla population.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {735}, pmid = {34635054}, issn = {1471-2164}, mesh = {Animals ; Disease Outbreaks ; *Gastrointestinal Microbiome ; Gorilla gorilla/genetics ; *Hemorrhagic Fever, Ebola/epidemiology/veterinary ; Humans ; Pan troglodytes ; }, abstract = {BACKGROUND: Numerous Ebola virus outbreaks have occurred in Equatorial Africa over the past decades. Besides human fatalities, gorillas and chimpanzees have also succumbed to the fatal virus. The 2004 outbreak at the Odzala-Kokoua National Park (Republic of Congo) alone caused a severe decline in the resident western lowland gorilla (Gorilla gorilla gorilla) population, with a 95% mortality rate. Here, we explore the immediate genetic impact of the Ebola outbreak in the western lowland gorilla population.<br><br>RESULTS: Associations with survivorship were evaluated by utilizing DNA obtained from fecal samples from 16 gorilla individuals declared missing after the outbreak (non-survivors) and 15 individuals observed before and after the epidemic (survivors). We used a target enrichment approach to capture the sequences of 123 genes previously associated with immunology and Ebola virus resistance and additionally analyzed the gut microbiome which could influence the survival after an infection. Our results indicate no changes in the population genetic diversity before and after the Ebola outbreak, and no significant differences in microbial community composition between survivors and non-survivors. However, and despite the low power for an association analysis, we do detect six nominally significant missense mutations in four genes that might be candidate variants associated with an increased chance of survival.<br><br>CONCLUSION: This study offers the first insight to the genetics of a wild great ape population before and after an Ebola outbreak using target capture experiments from fecal samples, and presents a list of candidate loci that may have facilitated their survival.}, }
@article {pmid34612522, year = {2022}, author = {Kaniewska, P and Sampayo, EM}, title = {Macro- and micro-scale adaptations allow distinct Stylophora pistillata-symbiodiniaceae holobionts to optimize performance across a broad light habitat.}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {55-70}, doi = {10.1111/jpy.13215}, pmid = {34612522}, issn = {1529-8817}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida/physiology ; Ecosystem ; Symbiosis/physiology ; }, abstract = {In sessile organisms, phenotypic plasticity represents an important strategy for dealing with environmental variability. Here we test if phenotypic plasticity enables the common coral Stylophora pistillata to occupy a broad niche. We find clear differences in the photo-physiology of four putative species of photosynthetic dinoflagellate symbionts associated with the coral S. pistillata, namely, Cladocopium 'C35a', 'C79', 'C78a' and 'C8a'. Coral phenotypic responses were also tightly linked to symbiont identity. Corals with Cladocopium 'C8a' have more "open" macro-morphology compared to colonies associating with depth-restricted Cladocopium 'C35a' or 'C78a' in the same shallow water habitat. Corals with Cladocopium 'C8a' had 40 to 60% lower symbiont cell densities compared to other holobionts but were more efficient at acclimating over a range of light levels, with clear mechanisms to dissipate excess light energy. This holobiont contains host-based green fluorescent pigments, increased concentrations of symbiont-based mycosporine amino acids, and xanthophyll cycling in high light habitats. Photosynthetic efficiency was also adjusted over the light habitat. In contrast, limited micro-scale responses were observed between three depth-restricted symbionts: Cladocopium 'C79', 'C35a', and 'C78a'. To optimize light levels reaching the photosynthetic unit, these colonies rely on a more closed macro-morphology under high light levels, which reduces incident light levels by up to 43%, and higher symbiont densities . Our results show that distinct macro- and micro-scale adaptations lead to functional differences between four distinct S. pistillata holobionts, allowing them to co-exist by filling specific niches on a small, but environmentally diverse, spatial scale. Key index words: Light, Symbiodiniaceae, coral, pigments, Stylophora pistillata, ITS2, phenotypic plasticity, niche diversification.}, }
@article {pmid34606240, year = {2021}, author = {Webster, TM and McFarland, A and Gebert, MJ and Oliverio, AM and Nichols, LM and Dunn, RR and Hartmann, EM and Fierer, N}, title = {Structure and Functional Attributes of Bacterial Communities in Premise Plumbing Across the United States.}, journal = {Environmental science &amp; technology}, volume = {55}, number = {20}, pages = {14105-14114}, doi = {10.1021/acs.est.1c03309}, pmid = {34606240}, issn = {1520-5851}, mesh = {*Drinking Water ; Humans ; *Mycobacterium ; RNA, Ribosomal, 16S/genetics ; Sanitary Engineering ; United States ; Water Microbiology ; }, abstract = {Microbes that thrive in premise plumbing can have potentially important effects on human health. Yet, how and why plumbing-associated microbial communities vary across broad spatial scales remain undetermined. We characterized the bacterial communities in 496 showerheads collected from across the continental United States. The overall community structure, determined by 16S rRNA gene amplicon sequencing, revealed high levels of bacterial diversity. Although a large fraction of the observed variation in community composition could not be explained, differences in bacterial community composition were associated with water supply (private well water vs public municipal water), water source (groundwater vs surface water), and associated differences in water chemistry (pH and chlorine). Most notably, showerheads in homes supplied with public water had higher abundances of Blastomonas, Mycobacterium, and Porphyrobacter, while Pseudorhodoplanes, Novosphingobium, and Nitrospira were more abundant in those receiving private well water. We conducted shotgun metagenomic analyses on 92 of these samples to assess differences in genomic attributes. Public water-sourced showerheads had communities enriched in genes related to lipid and xenobiotic metabolisms, virulence factors, and antibiotic resistance. In contrast, genes associated with oxidative stress and membrane transporters were over-represented in communities from private well water-sourced showerheads compared to those supplied by public water systems. These results highlight the broad diversity of bacteria found in premise plumbing across the United States and the role of the water source and treatment in shaping the microbial community structure and functional potential.}, }
@article {pmid34597574, year = {2022}, author = {Zhang, Y and Ip, JC and Xie, JY and Yeung, YH and Sun, Y and Qiu, JW}, title = {Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150656}, doi = {10.1016/j.scitotenv.2021.150656}, pmid = {34597574}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/genetics ; Chlorophyll A ; Coral Reefs ; Plant Leaves ; Symbiosis ; Transcriptome ; }, abstract = {Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.}, }
@article {pmid34593802, year = {2021}, author = {Avila-Magaña, V and Kamel, B and DeSalvo, M and Gómez-Campo, K and Enríquez, S and Kitano, H and Rohlfs, RV and Iglesias-Prieto, R and Medina, M}, title = {Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5731}, pmid = {34593802}, issn = {2041-1723}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/*microbiology/physiology ; Caribbean Region ; Coral Reefs ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; *Heat-Shock Response ; Metabolic Networks and Pathways/genetics ; Microbiota/*genetics ; Photosynthesis/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.}, }
@article {pmid34591135, year = {2022}, author = {Villegas-Plazas, M and Sanabria, J and Arbeli, Z and Vasquez, Y and Roldan, F and Junca, H}, title = {Metagenomic Analysis of Biochemical Passive Reactors During Acid Mine Drainage Bioremediation Reveals Key Co-selected Metabolic Functions.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {465-472}, pmid = {34591135}, issn = {1432-184X}, support = {Beca de Estudios Doctorales Nacionales 727//Minciencias/ ; 120377657722//Minciencias/ ; }, mesh = {Acids ; Biodegradation, Environmental ; *Metagenomics ; *Mining ; Sulfates/metabolism ; }, abstract = {Acid mine drainage (AMD) is the major pollutant generated by the mining industry, and it is characterized by low pH and high concentration of metals and sulfate. The use of biochemical passive reactors (BPRs) is a promising strategy for its bioremediation. To date, there are various studies describing the taxonomical composition of BPR microbial communities, generally consisting of an assemblage of sulfate-reducing organisms inside Deltaproteobacteria, and a diverse set of anaerobic (ligno)cellulolytic bacteria; however, insights about its functional metagenomic content are still scarce. In previous studies, a laboratory-scale AMD bioremediation using biochemical passive reactors was designed and performed, tracking operation parameters, chemical composition, and changes, together with taxonomic composition of the microbiomes harbored in these systems. In order to reveal the main functional content of these communities, we used shotgun metagenomics analyses to explore genes of higher relative frequencies and their inferred functions during the AMD bioremediation from three BPRs representing the main microbiome compositions detected in the system. Remarkably, genes encoding for two-component regulatory systems and ABC transporters related to metal and inorganic ions, cellulose degradation enzymes, dicarboxylic acid production, and sulfite reduction complex were all detected at increased frequency. Our results evidenced that higher taxonomic diversity of the microbiome was arising together with a functional redundancy of the specific metabolic roles, indicating its co-selection and suggesting that its enrichment on BPRs may be implicated in the cumulative efficiency of these systems.}, }
@article {pmid34582942, year = {2022}, author = {Ravindran, C and Raveendran, HP and Irudayarajan, L}, title = {Ciliated protozoan occurrence and association in the pathogenesis of coral disease.}, journal = {Microbial pathogenesis}, volume = {162}, number = {}, pages = {105211}, doi = {10.1016/j.micpath.2021.105211}, pmid = {34582942}, issn = {1096-1208}, mesh = {Animals ; *Anthozoa ; *Ciliophora ; }, abstract = {Various microbial infections have significantly contributed to disease progression leading to the mortality of corals. However, the holobiont and the external surfaces of coral, including the secreted mucus, provide a varied microenvironment that attracts ciliates based on their feeding preferences. Besides, some ciliates (e.g., Philasterine scuticociliate) may enter through the injuries or lesions on corals or through their indirect interactions with other types of microbes that influence coral health. Thus, ciliates occurrence and association are described with 12 different diseases worldwide. White syndrome disease lesions have diverse ciliate associations, and higher ciliate diversity was observed with diseased genera Acropora. Also, it was described, about sixteen ciliate species ingest coral Symbiodiniaceae and histophagous ciliates for coral tissue loss as secondary invaders. However, the ciliates nature of association with the coral disease remains unclear for primary or opportunistic secondary pathogenicity. Herein, we explore the urgent need to understand the complex interactions of ciliates in coral health.}, }
@article {pmid34582868, year = {2022}, author = {Kenigsberg, C and Titelboim, D and Ashckenazi-Polivoda, S and Herut, B and Kucera, M and Zukerman, Y and Hyams-Kaphzan, O and Almogi-Labin, A and Abramovich, S}, title = {The combined effects of rising temperature and salinity may halt the future proliferation of symbiont-bearing foraminifera as ecosystem engineers.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150581}, doi = {10.1016/j.scitotenv.2021.150581}, pmid = {34582868}, issn = {1879-1026}, mesh = {Cell Proliferation ; Ecosystem ; *Foraminifera ; Salinity ; Seawater ; Temperature ; }, abstract = {Rising sea surface temperatures and extreme heat waves are affecting symbiont-bearing tropical calcifiers such as corals and Large Benthic Foraminifera (LBF). In many ecosystems, parallel to warming, global change unleashes a host of additional changes to the marine environment, and the combined effect of such multiple stressors may be far greater than those of temperature alone. One such additional stressor, positively correlated to temperature in evaporation-dominated shallow-water settings is rising salinity. Here we used laboratory culture experiments to evaluate the combined thermohaline tolerance of one of the most common LBF species and carbonate producer, Amphistegina lobifera. The experiments were done under ambient (39 psu) and modified (30, 45, 50 psu) salinities and at optimum (25 °C) and warm temperatures (32 °C). Calcification of the A. lobifera holobiont was evaluated by measuring alkalinity loss in the culturing seawater, as an indication of carbonate ion uptake. The vitality of the symbionts was determined by monitoring pigment loss of the holobiont and their photosynthetic performances by measuring dissolved oxygen. We further evaluated the growth of Peneroplis (P. pertusus and P. planatus), a Rhodophyta bearing LBF, which is known to tolerate high temperatures, under elevated salinities. The results show that the A. lobifera holobiont exhibits optimal performance at 39 psu and 25 °C, and its growth is significantly reduced upon exposure to 30, 45, 50 psu and under all 32 °C treatments. Salinity and temperature exhibit a significant interaction, with synergic effects observed in most treatments. Our results confirm that Peneroplis has a higher tolerance to elevated temperature and salinity compared to A. lobifera, implying that a further increase of salinity and temperatures may result in a regime shift from Amphistegina- to Peneroplis-dominated assemblages.}, }
@article {pmid34576867, year = {2021}, author = {Liang, J and Deng, C and Yu, K and Ge, R and Xu, Y and Qin, Z and Chen, B and Wang, Y and Su, H and Huang, X and Huang, W and Wang, G and Gong, S}, title = {Cross-Linked Regulation of Coral-Associated Dinoflagellates and Bacteria in Pocillopora sp. during High-Temperature Stress and Recovery.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576867}, issn = {2076-2607}, support = {42090041, 41666005, 42030502 and 41866006//National Natural Science Foundation of China/ ; }, abstract = {As the problem of ocean warming worsens, the environmental adaptation potential of symbiotic Symbiodiniaceae and bacteria is directly related to the future and fate of corals. This study aimed to analyse the comprehensive community dynamics and physiology of these two groups of organisms in the coral Pocillopora sp. through indoor simulations of heat stress (which involved manually adjusting the temperature between both 26 °C and 34 °C). Heat treatment (≥30 °C) significantly reduced the abundance of Symbiodiniaceae and bacteria by more than 70%. After the temperature was returned to 26 °C for one month, the Symbiodiniaceae density was still low, while the absolute number of bacteria quickly recovered to 55% of that of the control. At this time point, the Fv/Fm value rose to 91% of the pretemperature value. The content of chlorophyll b associated with Cyanobacteria increased by 50% compared with that under the control conditions. Moreover, analysis of the Symbiodiniaceae subclade composition suggested that the relative abundance of C1c.C45, C1, and C1ca increased during heat treatment, indicating that they might constitute heat-resistant subgroups. We suggest that the increase in the absolute number of bacteria during the recovery period could be an important indicator of coral holobiont recovery after heat stress. This study provides insight into the cross-linked regulation of key symbiotic microbes in the coral Pocillopora sp. during high-temperature stress and recovery and provides a scientific basis for exploring the mechanism underlying coral adaptation to global warming.}, }
@article {pmid34572284, year = {2021}, author = {Dietert, RR}, title = {Microbiome First Medicine in Health and Safety.}, journal = {Biomedicines}, volume = {9}, number = {9}, pages = {}, pmid = {34572284}, issn = {2227-9059}, abstract = {Microbiome First Medicine is a suggested 21st century healthcare paradigm that prioritizes the entire human, the human superorganism, beginning with the microbiome. To date, much of medicine has protected and treated patients as if they were a single species. This has resulted in unintended damage to the microbiome and an epidemic of chronic disorders [e.g., noncommunicable diseases and conditions (NCDs)]. Along with NCDs came loss of colonization resistance, increased susceptibility to infectious diseases, and increasing multimorbidity and polypharmacy over the life course. To move toward sustainable healthcare, the human microbiome needs to be front and center. This paper presents microbiome-human physiology from the view of systems biology regulation. It also details the ongoing NCD epidemic including the role of existing drugs and other factors that damage the human microbiome. Examples are provided for two entryway NCDs, asthma and obesity, regarding their extensive network of comorbid NCDs. Finally, the challenges of ensuring safety for the microbiome are detailed. Under Microbiome-First Medicine and considering the importance of keystone bacteria and critical windows of development, changes in even a few microbiota-prioritized medical decisions could make a significant difference in health across the life course.}, }
@article {pmid34570392, year = {2021}, author = {Florez, JZ and Camus, C and Hengst, MB and Buschmann, AH}, title = {A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics.}, journal = {Journal of phycology}, volume = {57}, number = {6}, pages = {1777-1791}, doi = {10.1111/jpy.13213}, pmid = {34570392}, issn = {1529-8817}, mesh = {Bacteria/genetics ; *Kelp ; *Macrocystis ; Nitrogen ; }, abstract = {Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.}, }
@article {pmid34569131, year = {2022}, author = {Oberemok, V and Laikova, K and Golovkin, I and Kryukov, L and Kamenetsky-Goldstein, R}, title = {Biotechnology of virus eradication and plant vaccination in phytobiome context.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {24}, number = {1}, pages = {3-8}, doi = {10.1111/plb.13338}, pmid = {34569131}, issn = {1438-8677}, support = {2019-220-07-5322//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Biotechnology ; Crops, Agricultural ; Plant Diseases ; *Plant Viruses ; Vaccination ; }, abstract = {A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.}, }
@article {pmid34561754, year = {2022}, author = {Varasteh, T and Salazar, V and Tschoeke, D and Francini-Filho, RB and Swings, J and Garcia, G and Thompson, CC and Thompson, FL}, title = {Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.}, journal = {Microbial ecology}, volume = {84}, number = {2}, pages = {325-335}, pmid = {34561754}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/physiology ; Atlantic Ocean ; Coral Reefs ; DNA, Ribosomal/genetics ; *Dinoflagellida/physiology ; Phylogeny ; Symbiosis ; }, abstract = {The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.}, }
@article {pmid34561474, year = {2021}, author = {Ramos, C and Calus, M and Schokker, D}, title = {Persistence of functional microbiota composition across generations.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {19007}, pmid = {34561474}, issn = {2045-2322}, mesh = {Animals ; Culicidae/microbiology ; Datasets as Topic ; *Host Microbial Interactions ; Host Specificity ; Humans ; Microbiota/*physiology ; Plants/microbiology ; Zooplankton/microbiology ; }, abstract = {Holobionts are defined as a host and its microbiota, however, only a fraction of the bacteria are inherited vertically and thus coevolve with the host. The "it's the song, not the singer" theory proposes that functional traits, instead of taxonomical microbiota composition, could be preserved across generations if interspecies interaction patterns perpetuate themselves. We tested conservation of functional composition across generations using zooplankton, mosquito, and plant datasets. Then, we tested if there is a change of functional microbiota composition over time within a generation in human datasets. Finally, we simulated microbiota communities to investigate if (pairwise) interactions can lead to multiple stable community compositions. Our results suggest that the vertically transmitted microbiota starts a predictable change of functions performed by the microbiota over time, whose robustness depends on the arrival of diverse migrants. This succession culminates in a stable functional composition state. The results suggest that the host-microbiota interaction and higher order interactions in general have an important contribution to the robustness of the final community. If the proposed mechanism proves to be valid for a diverse array of host species, this would support the concept of holobionts being used as units of selection, including animal breeding, suggesting this has a wider applicability.}, }
@article {pmid34544484, year = {2021}, author = {Zhu, D and Delgado-Baquerizo, M and Ding, J and Gillings, MR and Zhu, YG}, title = {Trophic level drives the host microbiome of soil invertebrates at a continental scale.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {189}, pmid = {34544484}, issn = {2049-2618}, mesh = {Animals ; Biodiversity ; Ecosystem ; Invertebrates ; *Microbiota ; *Soil ; Soil Microbiology ; }, abstract = {BACKGROUND: Increasing our knowledge of soil biodiversity is fundamental to forecast changes in ecosystem functions under global change scenarios. All multicellular organisms are now known to be holobionts, containing large assemblages of microbial species. Soil fauna is now known to have thousands of species living within them. However, we know very little about the identity and function of host microbiome in contrasting soil faunal groups, across different terrestrial biomes, or at a large spatial scale. Here, we examined the microbiomes of multiple functionally important soil fauna in contrasting terrestrial ecosystems across China.<br><br>RESULTS: Different soil fauna had diverse and unique microbiomes, which were also distinct from those in surrounding soils. These unique microbiomes were maintained within taxa across diverse sampling sites and in contrasting terrestrial ecosystems. The microbiomes of nematodes, potworms, and earthworms were more difficult to predict using environmental data, compared to those of collembolans, oribatid mites, and predatory mites. Although stochastic processes were important, deterministic processes, such as host selection, also contributed to the assembly of unique microbiota in each taxon of soil fauna. Microbial biodiversity, unique microbial taxa, and microbial dark matter (defined as unidentified microbial taxa) all increased with trophic levels within the soil food web.<br><br>CONCLUSIONS: Our findings demonstrate that soil animals are important as repositories of microbial biodiversity, and those at the top of the food web harbor more diverse and unique microbiomes. This hidden source of biodiversity is rarely considered in biodiversity and conservation debates and stresses the importance of preserving key soil invertebrates. Video abstract.}, }
@article {pmid34519538, year = {2021}, author = {Waterworth, SC and Parker-Nance, S and Kwan, JC and Dorrington, RA}, title = {Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0157721}, pmid = {34519538}, issn = {2150-7511}, mesh = {Animals ; Bacteria/classification/*genetics ; *Genomics ; *Host Specificity ; Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Symbiosis ; }, abstract = {The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.}, }
@article {pmid34508605, year = {2022}, author = {Duchêne, DA and Mather, N and Van Der Wal, C and Ho, SYW}, title = {Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.}, journal = {Systematic biology}, volume = {71}, number = {3}, pages = {676-689}, pmid = {34508605}, issn = {1076-836X}, mesh = {*Biological Evolution ; *Genome ; Models, Genetic ; Phylogeny ; }, abstract = {The historical signal in nucleotide sequences becomes eroded over time by substitutions occurring repeatedly at the same sites. This phenomenon, known as substitution saturation, is recognized as one of the primary obstacles to deep-time phylogenetic inference using genome-scale data sets. We present a new test of substitution saturation and demonstrate its performance in simulated and empirical data. For some of the 36 empirical phylogenomic data sets that we examined, we detect substitution saturation in around 50% of loci. We found that saturation tends to be flagged as problematic in loci with highly discordant phylogenetic signals across sites. Within each data set, the loci with smaller numbers of informative sites are more likely to be flagged as containing problematic levels of saturation. The entropy saturation test proposed here is sensitive to high evolutionary rates relative to the evolutionary timeframe, while also being sensitive to several factors known to mislead phylogenetic inference, including short internal branches relative to external branches, short nucleotide sequences, and tree imbalance. Our study demonstrates that excluding loci with substitution saturation can be an effective means of mitigating the negative impact of multiple substitutions on phylogenetic inferences. [Phylogenetic model performance; phylogenomics; substitution model; substitution saturation; test statistics.].}, }
@article {pmid34504670, year = {2021}, author = {Fernández-González, AJ and Ramírez-Tejero, JA and Nevado-Berzosa, MP and Luque, F and Fernández-López, M and Mercado-Blanco, J}, title = {Coupling the endophytic microbiome with the host transcriptome in olive roots.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {4777-4789}, pmid = {34504670}, issn = {2001-0370}, abstract = {The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.}, }
@article {pmid34495983, year = {2021}, author = {Nobre, T}, title = {Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: Two new symbiont haplotypes in the Mediterranean basin.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0256284}, pmid = {34495983}, issn = {1932-6203}, mesh = {Animals ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Erwinia/*physiology ; Haplotypes ; Mediterranean Region ; Phylogeny ; Symbiosis ; Tephritidae/*microbiology/physiology ; }, abstract = {The olive fruit fly, specialized to become monophagous during several life stages, remains the most important olive tree pest with high direct production losses, but also affecting the quality, composition, and inherent properties of the olives. Thought to have originated in Africa is nowadays present wherever olive groves are grown. The olive fruit fly evolved to harbor a vertically transmitted and obligate bacterial symbiont -Candidatus Erwinia dacicola- leading thus to a tight evolutionary history between olive tree, fruit fly and obligate, vertical transmitted symbiotic bacterium. Considering this linkage, the genetic diversity (at a 16S fragment) of this obligate symbiont was added in the understanding of the distribution pattern of the holobiont at nine locations throughout four countries in the Mediterranean Basin. This was complemented with mitochondrial (four mtDNA fragments) and nuclear (ten microsatellites) data of the host. We focused on the previously established Iberian cluster for the B. oleae structure and hypothesised that the Tunisian samples would fall into a differentiated cluster. From the host point of view, we were unable to confirm this hypothesis. Looking at the symbiont, however, two new 16S haplotypes were found exclusively in the populations from Tunisia. This finding is discussed in the frame of host-symbiont specificity and transmission mode. To understand olive fruit fly population diversity and dispersion, the dynamics of the symbiont also needs to be taken into consideration, as it enables the fly to, so efficiently and uniquely, exploit the olive fruit resource.}, }
@article {pmid34490980, year = {2021}, author = {Paix, B and Potin, P and Schires, G and Le Poupon, C and Misson, B and Leblanc, C and Culioli, G and Briand, JF}, title = {Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6777-6797}, doi = {10.1111/1462-2920.15758}, pmid = {34490980}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Microbiota ; *Phaeophyceae ; *Seaweed/microbiology ; Temperature ; }, abstract = {In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.}, }
@article {pmid34490977, year = {2021}, author = {Marasco, R and Fusi, M and Rolli, E and Ettoumi, B and Tambone, F and Borin, S and Ouzari, HI and Boudabous, A and Sorlini, C and Cherif, A and Adani, F and Daffonchio, D}, title = {Aridity modulates belowground bacterial community dynamics in olive tree.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {6275-6291}, pmid = {34490977}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Desert Climate ; *Ecosystem ; *Olea ; Soil ; Soil Microbiology ; }, abstract = {Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.}, }
@article {pmid34481401, year = {2022}, author = {Ahmed, T and Noman, M and Rizwan, M and Ali, S and Ijaz, U and Nazir, MM and ALHaithloul, HAS and Alghanem, SM and Abdulmajeed, AM and Bin Li, }, title = {Green molybdenum nanoparticles-mediated bio-stimulation of Bacillus sp. strain ZH16 improved the wheat growth by managing in planta nutrients supply, ionic homeostasis and arsenic accumulation.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt A}, pages = {127024}, doi = {10.1016/j.jhazmat.2021.127024}, pmid = {34481401}, issn = {1873-3336}, mesh = {*Arsenic/toxicity ; *Bacillus ; Homeostasis ; Molybdenum ; *Nanoparticles ; Nutrients ; Plant Roots ; Soil Microbiology ; Triticum ; }, abstract = {The present work mechanistically addressed the problem of arsenic (As) contamination in agricultural soils by using locally isolated Bacillus sp. strain ZH16 and biogenic molybdenum nanoparticles (MoNPs) simultaneously for the first time. The interactions of MoNPs with strain ZH16 and ZH16-inoculated wheat plants were examined under As non-spiked and spiked conditions. The biogenic MoNPs showed efficient biocompatibility with strain ZH16 by promoting indole-3-acetic acid synthesis, phosphate solubilization and ACC deaminase activity without and with As stress. The results from greenhouse experiment revealed that co-application of biogenic MoNPs and bacterial strain ZH16 significantly promoted the morphological parameters, nutrients content and ionic balance of wheat plants under normal and As spiked conditions. Furthermore, combining the bacterial strain ZH16 with biogenic MoNPs dramatically reduced As translocation in plants (30.3%) as compared to ZH16-inoculated wheat plants. Conclusively, our results elucidate the importance of synergistic application of plant growth promoting rhizobacteria (PGPR) and biogenic MoNPs to counteract global food safety issues in a sustainable manner. The biogenic NPs could serve as stabilizing agent for PGPR by facilitating their colonization in plant holobiont regardless of environmental conditions. These novel advancements will provide new insights into nano-oriented PGPR research in the agricultural sector.}, }
@article {pmid34479653, year = {2021}, author = {Filek, K and Trotta, A and Gračan, R and Di Bello, A and Corrente, M and Bosak, S}, title = {Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta).}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {59}, pmid = {34479653}, issn = {2524-4671}, support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; }, abstract = {BACKGROUND: Microbial communities of wild animals are being increasingly investigated to provide information about the hosts' biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions.<br><br>RESULTS: We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities.<br><br>CONCLUSIONS: We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles' health and survival upon their return to the wild.}, }
@article {pmid34479645, year = {2021}, author = {Zhou, K and Xu, Y and Zhang, R and Qian, PY}, title = {Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {182}, pmid = {34479645}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; Genomics ; Proteomics ; Snails ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Deep-sea animals in hydrothermal vents often form endosymbioses with chemosynthetic bacteria. Endosymbionts serve essential biochemical and ecological functions, but the prokaryotic viruses (phages) that determine their fate are unknown.<br><br>RESULTS: We conducted metagenomic analysis of a deep-sea vent snail. We assembled four genome bins for Caudovirales phages that had developed dual endosymbiosis with sulphur-oxidising bacteria (SOB) and methane-oxidising bacteria (MOB). Clustered regularly interspaced short palindromic repeat (CRISPR) spacer mapping, genome comparison, and transcriptomic profiling revealed that phages Bin1, Bin2, and Bin4 infected SOB and MOB. The observation of prophages in the snail endosymbionts and expression of the phage integrase gene suggested the presence of lysogenic infection, and the expression of phage structural protein and lysozyme genes indicated active lytic infection. Furthermore, SOB and MOB appear to employ adaptive CRISPR-Cas systems to target phage DNA. Additional expressed defence systems, such as innate restriction-modification systems and dormancy-inducing toxin-antitoxin systems, may co-function and form multiple lines for anti-viral defence. To counter host defence, phages Bin1, Bin2, and Bin3 appear to have evolved anti-restriction mechanisms and expressed methyltransferase genes that potentially counterbalance host restriction activity. In addition, the high-level expression of the auxiliary metabolic genes narGH, which encode nitrate reductase subunits, may promote ATP production, thereby benefiting phage DNA packaging for replication.<br><br>CONCLUSIONS: This study provides new insights into phage-bacteria interplay in intracellular environments of a deep-sea vent snail. Video Abstract.}, }
@article {pmid34474030, year = {2022}, author = {Brennerova, MV and Zavala-Meneses, SG and Josefiova, J and Branny, P and Buriankova, K and Vetrovsky, T and Junca, H}, title = {A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons.}, journal = {Environmental research}, volume = {204}, number = {Pt A}, pages = {111954}, doi = {10.1016/j.envres.2021.111954}, pmid = {34474030}, issn = {1096-0953}, mesh = {Biodegradation, Environmental ; Oxygenases/genetics ; Phylogeny ; *Polycyclic Aromatic Hydrocarbons ; }, abstract = {Extradiol dioxygenation is a key reaction in the microbial aerobic degradation of mono- and polycyclic aromatic hydrocarbon catecholic derivatives. It has been reported that many bacterial enzymes exhibiting such converging functions act on a wide range of catecholic substrates. The present study reports a new subfamily of extradiol dioxygenases (EXDOs) with broad substrate specificity, the HrbC EXDOs. The new clade belongs to the XII cluster within family 2 of the vicinal oxygen chelate superfamily (EXDO-VC2), which is typically characterized by a preference for bicyclic substrates. Coding hrbC orthologs were isolated by activity-based screening of fosmid metagenomic libraries from large DNA fragments derived from heavily PAH-contaminated soils. They occurred as solitary genes within conserved sequences encoding enzymes for amino acid metabolism and were stably maintained in the chromosomes of the Betaproteobacteria lineages harboring them. Analysis of contaminated aquifers revealed coexpression of hrbC as a polycistronic mRNA component. The predicted open reading frames were verified by cloning and heterologous expression, confirming the expected molecular mass and meta-cleavage activity of the recombinant enzymes. Evolutionary analysis of the HrbC protein sequences grouped them into a discrete cluster of 1,2-dihydroxynaphthalene dioxygenases represented by a cultured PAH degrader, Rugosibacter aromaticivorans strain Ca6. The ecological importance and relevance of the new EXDO genes were confirmed by PCR-based mapping in different biogeographical localities contaminated with a variety of mono- and polycyclic aromatic compounds. The cosmopolitan distribution of hrbC in PAH-contaminated aquifers supports our hypothesis about its auxiliary role in the degradation of toxic catecholic intermediates, contributing to the composite EXDO catabolic capacity of the world's microbiomes.}, }
@article {pmid34473860, year = {2021}, author = {Meunier, V and Geissler, L and Bonnet, S and Rädecker, N and Perna, G and Grosso, O and Lambert, C and Rodolfo-Metalpa, R and Voolstra, CR and Houlbrèque, F}, title = {Microbes support enhanced nitrogen requirements of coral holobionts in a high CO2 environment.}, journal = {Molecular ecology}, volume = {30}, number = {22}, pages = {5888-5899}, doi = {10.1111/mec.16163}, pmid = {34473860}, issn = {1365-294X}, support = {ANR15CE02-0006-01//French National Research Agency (ANR/ ; 1598//Fonds Pacifique/ ; }, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Coral Reefs ; Hydrogen-Ion Concentration ; Nitrogen ; Seawater ; }, abstract = {Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2 seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2 site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.}, }
@article {pmid34469576, year = {2021}, author = {Kapun, M and Nunez, JCB and Bogaerts-Márquez, M and Murga-Moreno, J and Paris, M and Outten, J and Coronado-Zamora, M and Tern, C and Rota-Stabelli, O and Guerreiro, MPG and Casillas, S and Orengo, DJ and Puerma, E and Kankare, M and Ometto, L and Loeschcke, V and Onder, BS and Abbott, JK and Schaeffer, SW and Rajpurohit, S and Behrman, EL and Schou, MF and Merritt, TJS and Lazzaro, BP and Glaser-Schmitt, A and Argyridou, E and Staubach, F and Wang, Y and Tauber, E and Serga, SV and Fabian, DK and Dyer, KA and Wheat, CW and Parsch, J and Grath, S and Veselinovic, MS and Stamenkovic-Radak, M and Jelic, M and Buendía-Ruíz, AJ and Gómez-Julián, MJ and Espinosa-Jimenez, ML and Gallardo-Jiménez, FD and Patenkovic, A and Eric, K and Tanaskovic, M and Ullastres, A and Guio, L and Merenciano, M and Guirao-Rico, S and Horváth, V and Obbard, DJ and Pasyukova, E and Alatortsev, VE and Vieira, CP and Vieira, J and Torres, JR and Kozeretska, I and Maistrenko, OM and Montchamp-Moreau, C and Mukha, DV and Machado, HE and Lamb, K and Paulo, T and Yusuf, L and Barbadilla, A and Petrov, D and Schmidt, P and Gonzalez, J and Flatt, T and Bergland, AO}, title = {Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5782-5805}, pmid = {34469576}, issn = {1537-1719}, support = {R35 GM119686/GM/NIGMS NIH HHS/United States ; P 32275/FWF_/Austrian Science Fund FWF/Austria ; R35 GM118165/GM/NIGMS NIH HHS/United States ; R01 GM137430/GM/NIGMS NIH HHS/United States ; R01 GM100366/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Drosophila melanogaster/genetics ; Gene Frequency ; Genetics, Population ; Genomics ; *Metagenomics ; }, abstract = {Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.}, }
@article {pmid34459547, year = {2021}, author = {Wahdan, SFM and Tanunchai, B and Wu, YT and Sansupa, C and Schädler, M and Dawoud, TM and Buscot, F and Purahong, W}, title = {Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1217}, pmid = {34459547}, issn = {2045-8827}, mesh = {Acclimatization/*genetics ; Bacteria/classification/*genetics ; *Climate Change ; Fungi/classification/*genetics ; Germany ; Indoleacetic Acids/metabolism ; Microbiota/genetics ; Mycobiome/genetics ; Nitrogen Fixation/physiology ; Phosphorus/metabolism ; Plant Roots/microbiology ; Rhizosphere ; Siderophores/biosynthesis ; Soil Microbiology ; Trifolium/*growth &amp; development/*microbiology ; }, abstract = {The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.}, }
@article {pmid34442809, year = {2021}, author = {Rumbou, A and Vainio, EJ and Büttner, C}, title = {Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442809}, issn = {2076-2607}, abstract = {Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.}, }
@article {pmid34442634, year = {2021}, author = {Malassigné, S and Minard, G and Vallon, L and Martin, E and Valiente Moro, C and Luis, P}, title = {Diversity and Functions of Yeast Communities Associated with Insects.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442634}, issn = {2076-2607}, abstract = {Following the concept of the holobiont, insect-microbiota interactions play an important role in insect biology. Many examples of host-associated microorganisms have been reported to drastically influence insect biological processes such as development, physiology, nutrition, survival, immunity, or even vector competence. While a huge number of studies on insect-associated microbiota have focused on bacteria, other microbial partners including fungi have been comparatively neglected. Yeasts, which establish mostly commensal or symbiotic relationships with their host, can dominate the mycobiota of certain insects. This review presents key advances and progress in the research field highlighting the diversity of yeast communities associated with insects, as well as their impact on insect life-history traits, immunity, and behavior.}, }
@article {pmid34434172, year = {2021}, author = {Aires, T and Stuij, TM and Muyzer, G and Serrão, EA and Engelen, AH}, title = {Characterization and Comparison of Bacterial Communities of an Invasive and Two Native Caribbean Seagrass Species Sheds Light on the Possible Influence of the Microbiome on Invasive Mechanisms.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {653998}, pmid = {34434172}, issn = {1664-302X}, abstract = {Invasive plants, including marine macrophytes, are one of the most important threats to biodiversity by displacing native species and organisms depending on them. Invasion success is dependent on interactions among living organisms, but their study has been mostly limited to negative interactions while positive interactions are mostly underlooked. Recent studies suggested that microorganisms associated with eukaryotic hosts may play a determinant role in the invasion process. Along with the knowledge of their structure, taxonomic composition, and potential functional profile, understanding how bacterial communities are associated with the invasive species and the threatened natives (species-specific/environmentally shaped/tissue-specific) can give us a holistic insight into the invasion mechanisms. Here, we aimed to compare the bacterial communities associated with leaves and roots of two native Caribbean seagrasses (Halodule wrightii and Thalassia testudinum) with those of the successful invader Halophila stipulacea, in the Caribbean island Curaçao, using 16S rRNA gene amplicon sequencing and functional prediction. Invasive seagrass microbiomes were more diverse and included three times more species-specific core OTUs than the natives. Associated bacterial communities were seagrass-specific, with higher similarities between natives than between invasive and native seagrasses for both communities associated with leaves and roots, despite their strong tissue differentiation. However, with a higher number of OTUs in common, the core community (i.e., OTUs occurring in at least 80% of the samples) of the native H. wrightii was more similar to that of the invader H. stipulacea than T. testudinum, which could reflect more similar essential needs (e.g., nutritional, adaptive, and physiological) between native and invasive, in contrast to the two natives that might share more environment-related OTUs. Relative to native seagrass species, the invasive H. stipulacea was enriched in halotolerant bacterial genera with plant growth-promoting properties (like Halomonas sp. and Lysinibacillus sp.) and other potential beneficial effects for hosts (e.g., heavy metal detoxifiers and quorum sensing inhibitors). Predicted functional profiles also revealed some advantageous traits on the invasive species such as detoxification pathways, protection against pathogens, and stress tolerance. Despite the predictive nature of our findings concerning the functional potential of the bacteria, this investigation provides novel and important insights into native vs. invasive seagrasses microbiome. We demonstrated that the bacterial community associated with the invasive seagrass H. stipulacea is different from native seagrasses, including some potentially beneficial bacteria, suggesting the importance of considering the microbiome dynamics as a possible and important influencing factor in the colonization of non-indigenous species. We suggest further comparison of H. stipulacea microbiome from its native range with that from both the Mediterranean and Caribbean habitats where this species has a contrasting invasion success. Also, our new findings open doors to a more in-depth investigation combining meta-omics with bacterial manipulation experiments in order to confirm any functional advantage in the microbiome of this invasive seagrass.}, }
@article {pmid34432867, year = {2021}, author = {Astolfi, A and Masetti, R and Indio, V and Bertuccio, SN and Messelodi, D and Rampelli, S and Leardini, D and Carella, M and Serravalle, S and Libri, V and Bandini, J and Volinia, S and Candela, M and Pession, A}, title = {Torque teno mini virus as a cause of childhood acute promyelocytic leukemia lacking PML/RARA fusion.}, journal = {Blood}, volume = {138}, number = {18}, pages = {1773-1777}, doi = {10.1182/blood.2021011677}, pmid = {34432867}, issn = {1528-0020}, mesh = {Anelloviridae/pathogenicity/physiology ; Antineoplastic Agents/therapeutic use ; Child ; Female ; Humans ; Karyotype ; Leukemia, Promyelocytic, Acute/*genetics/pathology/therapy ; Oncogene Proteins, Fusion/*genetics ; Oncogenic Viruses/pathogenicity/*physiology ; *Retinoic Acid Receptor alpha ; Torque teno virus/pathogenicity/*physiology ; Tretinoin/therapeutic use ; }, }
@article {pmid34427504, year = {2021}, author = {Motaung, TE and Steenkamp, ET}, title = {Extracellular Vesicles in Teasing Apart Complex Plant-Microbiota Links: Implications for Microbiome-Based Biotechnology.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0073421}, pmid = {34427504}, issn = {2379-5077}, support = {129580//National Research Foundation (NRF)/ ; }, abstract = {Extracellular vesicles (EVs) are subcellular carriers of bioactive compounds with a complex array of functional effects on target cells. In mammals, circulating bodily fluid microbiota EVs (mbEVs) deliver cargo from source cells and adversely or favorably alter the physiology of the same source, neighboring, and distant recipient cells in an autocrine, paracrine, or endocrine fashion, respectively. Plant mbEVs may similarly mediate these interactive effects within the holobiont framework. However, the majority of plant EV research has focused on a small number of individual microbes, thus failing to reflect the importance of EVs in a community and consequently leaving a wide gap in scientific knowledge. Addressing this gap should entail a systems-level approach that combines vesicle characterization with microbiome analyses. This would certainly usher in a new age in microbial biotechnology entailing EVs as a microbiome manipulation strategy, a biomarker for stable microbiomes, and a diagnostic tool for plant infectious diseases.}, }
@article {pmid34427502, year = {2021}, author = {Garg, N}, title = {Metabolomics in Functional Interrogation of Individual Holobiont Members.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0084121}, pmid = {34427502}, issn = {2379-5077}, support = {2047235//National Science Foundation (NSF)/ ; }, abstract = {Eukaryotes and their environments serve as petri dishes, hosting an abundant and a rich prokaryotic microbiome. The assemblage of a eukaryotic host and its microbiome is referred to as a holobiont. The holobiont's microbiome interacts within itself, with the environment, and with the host at the chemical level through production of specialized metabolites resulting in homeostasis or dysbiosis. These interactions are triggered by a multitude of factors, such as community composition, age, presence of nutrients, xenobiotics, and change in physical conditions, such as temperature and oxygen. Understanding how holobionts respond and adapt to diverse triggers is necessary to uncover mechanisms of resilience or susceptibility to dysbiosis and to modulate the collective functioning of microbiome in health and disease. This article highlights the challenges associated with uncovering chemical contributions of individual holobiont members and the applicability of metabolomics-based approaches to uncover chemical signatures of microbial processes in the natural environment.}, }
@article {pmid34426366, year = {2021}, author = {Leite, MFA and Dimitrov, MR and Freitas-Iório, RP and de Hollander, M and Cipriano, MAP and Andrade, SAL and da Silveira, APD and Kuramae, EE}, title = {Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149493}, doi = {10.1016/j.scitotenv.2021.149493}, pmid = {34426366}, issn = {1879-1026}, mesh = {Bacteria ; Burkholderiaceae ; Enterobacteriaceae ; Herbaspirillum ; Nitrogen ; Plant Roots ; Rhizosphere ; *Saccharum ; Soil Microbiology ; }, abstract = {The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.}, }
@article {pmid34424926, year = {2021}, author = {Zacho, CM and Bager, MA and Margaryan, A and Gravlund, P and Galatius, A and Rasmussen, AR and Allentoft, ME}, title = {Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes.}, journal = {PloS one}, volume = {16}, number = {8}, pages = {e0256353}, pmid = {34424926}, issn = {1932-6203}, mesh = {Animals ; *Ethanol ; *Metagenomics/methods ; *Genomics/methods ; Snakes/genetics ; Museums ; DNA, Ancient/analysis ; Genome ; Sequence Analysis, DNA/methods ; Liver/metabolism ; Preservation, Biological/methods ; Metagenome ; }, abstract = {Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.}, }
@article {pmid34408733, year = {2021}, author = {Schapheer, C and Pellens, R and Scherson, R}, title = {Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {702763}, pmid = {34408733}, issn = {1664-302X}, abstract = {Recent reports indicate that the health of our planet is getting worse and that genuine transformative changes are pressing. So far, efforts to ameliorate Earth's ecosystem crises have been insufficient, as these often depart from current knowledge of the underlying ecological processes. Nowadays, biodiversity loss and the alterations in biogeochemical cycles are reaching thresholds that put the survival of our species at risk. Biological interactions are fundamental for achieving biological conservation and restoration of ecological processes, especially those that contribute to nutrient cycles. Microorganism are recognized as key players in ecological interactions and nutrient cycling, both free-living and in symbiotic associations with multicellular organisms. This latter assemblage work as a functional ecological unit called "holobiont." Here, we review the emergent ecosystem properties derived from holobionts, with special emphasis on detritivorous terrestrial arthropods and their symbiotic microorganisms. We revisit their relevance in the cycling of recalcitrant organic compounds (e.g., lignin and cellulose). Finally, based on the interconnection between biodiversity and nutrient cycling, we propose that a multicellular organism and its associates constitute an Ecosystem Holobiont (EH). This EH is the functional unit characterized by carrying out key ecosystem processes. We emphasize that in order to meet the challenge to restore the health of our planet it is critical to reduce anthropic pressures that may threaten not only individual entities (known as "bionts") but also the stability of the associations that give rise to EH and their ecological functions.}, }
@article {pmid34394058, year = {2021}, author = {Kostygov, AY and Alves, JMP and Yurchenko, V}, title = {Editorial: Symbioses Between Protists and Bacteria/Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {709184}, pmid = {34394058}, issn = {1664-302X}, }
@article {pmid34377966, year = {2021}, author = {Rampelli, S and Turroni, S and Debandi, F and Alberdi, A and Schnorr, SL and Hofman, CA and Taddia, A and Helg, R and Biagi, E and Brigidi, P and D'Amico, F and Cattani, M and Candela, M}, title = {The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs.}, journal = {iScience}, volume = {24}, number = {8}, pages = {102816}, pmid = {34377966}, issn = {2589-0042}, abstract = {In an attempt to explore the role of the gut microbiome during recent canine evolutionary history, we sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 years ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as also inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Of interest, the Solarolo dog microbiome was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism, thus compensating for delayed host response.}, }
@article {pmid34371395, year = {2021}, author = {Ferreira, V and Pavlaki, MD and Martins, R and Monteiro, MS and Maia, F and Tedim, J and Soares, AMVM and Calado, R and Loureiro, S}, title = {Effects of nanostructure antifouling biocides towards a coral species in the context of global changes.}, journal = {The Science of the total environment}, volume = {799}, number = {}, pages = {149324}, doi = {10.1016/j.scitotenv.2021.149324}, pmid = {34371395}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; *Biofouling/prevention &amp; control ; Coral Reefs ; *Disinfectants/toxicity ; Ecosystem ; *Nanostructures/toxicity ; Thiazoles ; }, abstract = {Biofouling prevention is one of the biggest challenges faced by the maritime industry, but antifouling agents commonly impact marine ecosystems. Advances in antifouling technology include the use of nanomaterials. Herein we test an antifouling nano-additive based on the encapsulation of the biocide 4,5-dichloro-2-octyl-4-isothiazolin-3-one (DCOIT) in engineered silica nanocontainers (SiNC). The work aims to assess the biochemical and physiological effects on the symbiotic coral Sarcophyton cf. glaucum caused by (1) thermal stress and (2) DCOIT exposure (free or nanoencapsulated forms), in a climate change scenario. Accordingly, the following hypotheses were addressed: (H1) ocean warming can cause toxicity on S. cf. glaucum; (H2) the nanoencapsulation process decreases DCOIT toxicity towards this species; (H3) the biocide toxicity, free or encapsulated forms, can be affected by ocean warming. Coral fragments were exposed for seven days to DCOIT in both free and encapsulated forms, SiNC and negative controls, under two water temperature regimes (26 °C and 30.5 °C). Coral polyp behavior and photosynthetic efficiency were determined in the holobiont, while biochemical markers were assessed individually in the endosymbiont and coral host. Results showed transient coral polyp retraction and diminished photosynthetic efficiency in the presence of heat stress or free DCOIT, with effects being magnified in the presence of both stressors. The activity of catalase and glutathione-S-transferase were modulated by temperature in each partner of the symbiosis. The shifts in enzymatic activity were more pronounced in the presence of free DCOIT, but to a lower extent for encapsulated DCOIT. Increased levels of oxidative damage were detected under heat conditions. The findings highlight the physiological constrains elicited by the increase of seawater temperature to symbiotic corals and demonstrate that DCOIT toxicity can be minimized through encapsulation in SiNC. The presence of both stressors magnifies toxicity and confirm that ocean warming enhances the vulnerability of tropical photosynthetic corals to local stressors.}, }
@article {pmid34370107, year = {2021}, author = {Schneider, T}, title = {The holobiont self: understanding immunity in context.}, journal = {History and philosophy of the life sciences}, volume = {43}, number = {3}, pages = {99}, pmid = {34370107}, issn = {1742-6316}, mesh = {Host Microbial Interactions/immunology/*physiology ; Immune System/*physiology ; Immunity/*physiology ; }, abstract = {Both concepts of the holobiont and the immune system are at the heart of an ongoing scientific and philosophical examination concerning questions of the organism's individuality and identity as well as the relations between organisms and their environment. Examining the holobiont, the question of boundaries and individuality is challenging because it is both an assemblage of organisms with physiological cohesive aspects. I discuss the concept of immunity and the immune system function from the holobiont perspective. Because of the host-microbial close relations of codependence and interdependence, the holobiont is more often than not confused with the host, as the host is the domain in which this entity exists. I discuss the holobiont unique ecological characteristics of microbial assemblages connected to a host in a network of interactions in which the host is one of the organisms in the community but also its landscape. Therefore, I suggest viewing the holobiont as a host-ecosystem and discuss the implication of such a view on the concept of immunity and the meaning of protection. Furthermore, I show that viewing the holobiont as a host ecosystem opens the possibility of using the same ecological definition of boundaries and immunity dealing with an ecological system. Thus, the holobiont's boundaries and immunity are defined by the persistence of its complex system of interactions integrating existing and new interactions. This way of thinking presents a notion of immunity that materializes as the result of the complex interdependence relations between the different organisms composing the holobiont similar to that of an ecosystem. Taking this view further, I discuss the notion of immunogenicity that is ontologically heterogeneous with various causal explanations of the processes of tolerance and targeted immune response. Finally, I discuss the possible conceptualization of already existing and new biomedical practices.}, }
@article {pmid34367078, year = {2021}, author = {Legüe, M and Aguila, B and Calixto, A}, title = {Interspecies RNA Interactome of Pathogen and Host in a Heritable Defensive Strategy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {649858}, pmid = {34367078}, issn = {1664-302X}, abstract = {Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode Caenorhabditis elegans. The chronic exposure of C. elegans to pathogens promotes the adaptive behavior in the host's progeny called pathogen-induced diapause formation (PIDF). PIDF is a pathogen avoidance strategy induced in the second generation of animals infected and can be recalled transgenerationally. This behavior requires the RNA interference machinery and specific nematode and bacteria small RNAs (sRNAs). In this work, we assume that RNAs from both species co-exist and can interact with each other. Under this principle, we explore the potential interspecies RNA interactions during PIDF-triggering conditions, using transcriptomic data from the holobiont. We study two transcriptomics datasets: first, the dual sRNA expression of Pseudomonas aeruginosa PAO1 and C. elegans in a transgenerational paradigm for six generations and second, the simultaneous expression of sRNAs and mRNA in intergenerational PIDF. We focus on those bacterial sRNAs that are systematically overexpressed in the intestines of animals compared with sRNAs expressed in host-naïve bacteria. We selected diverse in silico methods that represent putative mechanisms of RNA-mediated interspecies interaction. These interactions are as follows: heterologous perfect and incomplete pairing between bacterial RNA and host mRNA; sRNAs of similar sequence expressed in both species that could mimic each other; and known or predicted eukaryotic motifs present in bacterial transcripts. We conclude that a broad spectrum of tools can be applied for the identification of potential sRNA and mRNA targets of the interspecies RNA interaction that can be subsequently tested experimentally.}, }
@article {pmid34361898, year = {2021}, author = {Barra Caracciolo, A and Terenzi, V}, title = {Rhizosphere Microbial Communities and Heavy Metals.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34361898}, issn = {2076-2607}, abstract = {The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants' functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.}, }
@article {pmid34356947, year = {2021}, author = {Ben-Dor Cohen, E and Ilan, M and Yarden, O}, title = {The Culturable Mycobiome of Mesophotic Agelas oroides: Constituents and Changes Following Sponge Transplantation to Shallow Water.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {7}, pages = {}, pmid = {34356947}, issn = {2309-608X}, support = {888/19//Israel Science Foundation/ ; 217-17-020//Israel Ministry of Energy/ ; 01023182//Israel Nature and Parks Authority/ ; }, abstract = {Marine sponges harbor a diverse array of microorganisms and the composition of the microbial community has been suggested to be linked to holo-biont health. Most of the attention concerning sponge mycobiomes has been given to sponges present in shallow depths. Here, we describe the presence of 146 culturable mycobiome taxa isolated from mesophotic niche (100 m depth)-inhabiting samples of Agelas oroides, in the Mediterranean Sea. We identify some potential in vitro interactions between several A. oroides-associated fungi and show that sponge meso-hyl extract, but not its predominantly collagen-rich part, is sufficient to support hyphal growth. We demonstrate that changes in the diversity of culturable mycobiome constituents occur following sponge transplantation from its original mesophotic habitat to shallow (10 m) waters, where historically (60 years ago) this species was found. We conclude that among the 30 fungal genera identified as associated with A. oroides, Aspergillus, Penicillium and Trichoderma constitute the core mycobiome of A. oroides, and that they persist even when the sponge is transplanted to a suboptimal environment, indicative of the presence of constant, as well as dynamic, components of the sponge mycobiome. Other genera seemed more depth-related and appeared or disappeared upon host's transfer from 100 to 10 m.}, }
@article {pmid34349734, year = {2021}, author = {Herrera, M and Liew, YJ and Venn, A and Tambutté, E and Zoccola, D and Tambutté, S and Cui, G and Aranda, M}, title = {New Insights From Transcriptomic Data Reveal Differential Effects of CO2 Acidification Stress on Photosynthesis of an Endosymbiotic Dinoflagellate in hospite.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {666510}, pmid = {34349734}, issn = {1664-302X}, abstract = {Ocean acidification (OA) has both detrimental as well as beneficial effects on marine life; it negatively affects calcifiers while enhancing the productivity of photosynthetic organisms. To date, many studies have focused on the impacts of OA on calcification in reef-building corals, a process particularly susceptible to acidification. However, little is known about the effects of OA on their photosynthetic algal partners, with some studies suggesting potential benefits for symbiont productivity. Here, we investigated the transcriptomic response of the endosymbiont Symbiodinium microadriaticum (CCMP2467) in the Red Sea coral Stylophora pistillata subjected to different long-term (2 years) OA treatments (pH 8.0, 7.8, 7.4, 7.2). Transcriptomic analyses revealed that symbionts from corals under lower pH treatments responded to acidification by increasing the expression of genes related to photosynthesis and carbon-concentrating mechanisms. These processes were mostly up-regulated and associated metabolic pathways were significantly enriched, suggesting an overall positive effect of OA on the expression of photosynthesis-related genes. To test this conclusion on a physiological level, we analyzed the symbiont's photochemical performance across treatments. However, in contrast to the beneficial effects suggested by the observed gene expression changes, we found significant impairment of photosynthesis with increasing pCO2. Collectively, our data suggest that over-expression of photosynthesis-related genes is not a beneficial effect of OA but rather an acclimation response of the holobiont to different water chemistries. Our study highlights the complex effects of ocean acidification on these symbiotic organisms and the role of the host in determining symbiont productivity and performance.}, }
@article {pmid34342082, year = {2021}, author = {Voolstra, CR and Valenzuela, JJ and Turkarslan, S and Cárdenas, A and Hume, BCC and Perna, G and Buitrago-López, C and Rowe, K and Orellana, MV and Baliga, NS and Paranjape, S and Banc-Prandi, G and Bellworthy, J and Fine, M and Frias-Torres, S and Barshis, DJ}, title = {Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance.}, journal = {Molecular ecology}, volume = {30}, number = {18}, pages = {4466-4480}, doi = {10.1111/mec.16064}, pmid = {34342082}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; Heat-Shock Response ; Indian Ocean ; Symbiosis/genetics ; }, abstract = {Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.}, }
@article {pmid34331071, year = {2022}, author = {Haydon, TD and Suggett, DJ and Siboni, N and Kahlke, T and Camp, EF and Seymour, JR}, title = {Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1073-1087}, pmid = {34331071}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; *Gammaproteobacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.}, }
@article {pmid34326856, year = {2021}, author = {Gaete, A and Pulgar, R and Hodar, C and Maldonado, J and Pavez, L and Zamorano, D and Pastenes, C and González, M and Franck, N and Mandakovic, D}, title = {Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {688533}, pmid = {34326856}, issn = {1664-462X}, abstract = {Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible Solanum lycopersicum cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.}, }
@article {pmid34306668, year = {2021}, author = {Vecchi, M and Kossi Adakpo, L and Dunn, RR and Nichols, LM and Penick, CA and Sanders, NJ and Rebecchi, L and Guidetti, R}, title = {The toughest animals of the Earth versus global warming: Effects of long-term experimental warming on tardigrade community structure of a temperate deciduous forest.}, journal = {Ecology and evolution}, volume = {11}, number = {14}, pages = {9856-9863}, pmid = {34306668}, issn = {2045-7758}, abstract = {Understanding how different taxa respond to global warming is essential for predicting future changes and elaborating strategies to buffer them. Tardigrades are well known for their ability to survive environmental stressors, such as drying and freezing, by undergoing cryptobiosis and rapidly recovering their metabolic function after stressors cease. Determining the extent to which animals that undergo cryptobiosis are affected by environmental warming will help to understand the real magnitude climate change will have on these organisms. Here, we report on the responses of tardigrades within a five-year-long, field-based artificial warming experiment, which consisted of 12 open-top chambers heated to simulate the projected effects of global warming (ranging from 0 to 5.5°C above ambient temperature) in a temperate deciduous forest of North Carolina (USA). To elucidate the effects of warming on the tardigrade community inhabiting the soil litter, three community diversity indices (abundance, species richness, and Shannon diversity) and the abundance of the three most abundant species (Diphascon pingue, Adropion scoticum, and Mesobiotus sp.) were determined. Their relationships with air temperature, soil moisture, and the interaction between air temperature and soil moisture were tested using Bayesian generalized linear mixed models. Despite observed negative effects of warming on other ground invertebrates in previous studies at this site, long-term warming did not affect the abundance, richness, or diversity of tardigrades in this experiment. These results are in line with previous experimental studies, indicating that tardigrades may not be directly affected by ongoing global warming, possibly due to their thermotolerance and cryptobiotic abilities to avoid negative effects of stressful temperatures, and the buffering effect on temperature of the soil litter substrate.}, }
@article {pmid34294880, year = {2022}, author = {Moynihan, MA and Goodkin, NF and Morgan, KM and Kho, PYY and Lopes Dos Santos, A and Lauro, FM and Baker, DM and Martin, P}, title = {Coral-associated nitrogen fixation rates and diazotrophic diversity on a nutrient-replete equatorial reef.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {233-246}, pmid = {34294880}, issn = {1751-7370}, mesh = {Animals ; *Anthozoa/physiology ; Nitrogen ; Nitrogen Fixation ; Nutrients ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The role of diazotrophs in coral physiology and reef biogeochemistry remains poorly understood, in part because N2 fixation rates and diazotrophic community composition have only been jointly analyzed in the tissue of one tropical coral species. We performed field-based [15]N2 tracer incubations during nutrient-replete conditions to measure diazotroph-derived nitrogen (DDN) assimilation into three species of scleractinian coral (Pocillopora acuta, Goniopora columna, Platygyra sinensis). Using multi-marker metabarcoding (16S rRNA, nifH, 18S rRNA), we analyzed DNA- and RNA-based communities in coral tissue and skeleton. Despite low N2 fixation rates, DDN assimilation supplied up to 6% of the holobiont's N demand. Active coral-associated diazotrophs were chiefly Cluster I (aerobes or facultative anaerobes), suggesting that oxygen may control coral-associated diazotrophy. Highest N2 fixation rates were observed in the endolithic community (0.20 µg N cm[-2] per day). While the diazotrophic community was similar between the tissue and skeleton, RNA:DNA ratios indicate potential differences in relative diazotrophic activity between these compartments. In Pocillopora, DDN was found in endolithic, host, and symbiont compartments, while diazotrophic nifH sequences were only observed in the endolithic layer, suggesting a possible DDN exchange between the endolithic community and the overlying coral tissue. Our findings demonstrate that coral-associated diazotrophy is significant, even in nutrient-rich waters, and suggest that endolithic microbes are major contributors to coral nitrogen cycling on reefs.}, }
@article {pmid34257909, year = {2021}, author = {Demi, LM and Taylor, BW and Reading, BJ and Tordoff, MG and Dunn, RR}, title = {Understanding the evolution of nutritive taste in animals: Insights from biological stoichiometry and nutritional geometry.}, journal = {Ecology and evolution}, volume = {11}, number = {13}, pages = {8441-8455}, pmid = {34257909}, issn = {2045-7758}, abstract = {A major conceptual gap in taste biology is the lack of a general framework for understanding the evolution of different taste modalities among animal species. We turn to two complementary nutritional frameworks, biological stoichiometry theory and nutritional geometry, to develop hypotheses for the evolution of different taste modalities in animals. We describe how the attractive tastes of Na-, Ca-, P-, N-, and C-containing compounds are consistent with principles of both frameworks based on their shared focus on nutritional imbalances and consumer homeostasis. Specifically, we suggest that the evolution of multiple nutritive taste modalities can be predicted by identifying individual elements that are typically more concentrated in the tissues of animals than plants. Additionally, we discuss how consumer homeostasis can inform our understanding of why some taste compounds (i.e., Na, Ca, and P salts) can be either attractive or aversive depending on concentration. We also discuss how these complementary frameworks can help to explain the evolutionary history of different taste modalities and improve our understanding of the mechanisms that lead to loss of taste capabilities in some animal lineages. The ideas presented here will stimulate research that bridges the fields of evolutionary biology, sensory biology, and ecology.}, }
@article {pmid34256019, year = {2021}, author = {Gelabert, P and Sawyer, S and Bergström, A and Margaryan, A and Collin, TC and Meshveliani, T and Belfer-Cohen, A and Lordkipanidze, D and Jakeli, N and Matskevich, Z and Bar-Oz, G and Fernandes, DM and Cheronet, O and Özdoğan, KT and Oberreiter, V and Feeney, RNM and Stahlschmidt, MC and Skoglund, P and Pinhasi, R}, title = {Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment.}, journal = {Current biology : CB}, volume = {31}, number = {16}, pages = {3564-3574.e9}, pmid = {34256019}, issn = {1879-0445}, support = {852558/ERC_/European Research Council/International ; 217223/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; FC001595/MRC_/Medical Research Council/United Kingdom ; FC001595/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; FC001595/ARC_/Arthritis Research UK/United Kingdom ; FC001595/CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Animals ; *Bison/genetics ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; *Genome, Mitochondrial ; Georgia (Republic) ; Humans ; Phylogeny ; *Wolves/genetics ; }, abstract = {Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.}, }
@article {pmid34255084, year = {2022}, author = {Vankan, M and Ho, SYW and Duchêne, DA}, title = {Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.}, journal = {Systematic biology}, volume = {71}, number = {2}, pages = {490-500}, pmid = {34255084}, issn = {1076-836X}, mesh = {*Biological Evolution ; *Genome ; Genomics ; Models, Genetic ; Phylogeny ; }, abstract = {Phylogenetic analyses of genomic data provide a powerful means of reconstructing the evolutionary relationships among organisms, yet such analyses are often hindered by conflicting phylogenetic signals among loci. Identifying the signals that are most influential to species-tree estimation can help to inform the choice of data for phylogenomic analysis. We investigated this in an analysis of 30 phylogenomic data sets. For each data set, we examined the association between several branch-length characteristics of gene trees and the distance between these gene trees and the corresponding species trees. We found that the distance of each gene tree to the species tree inferred from the full data set was positively associated with variation in root-to-tip distances and negatively associated with mean branch support. However, no such associations were found for gene-tree length, a measure of the overall substitution rate at each locus. We further explored the usefulness of the best-performing branch-based characteristics for selecting loci for phylogenomic analyses. We found that loci that yield gene trees with high variation in root-to-tip distances have a disproportionately distant signal of tree topology compared with the complete data sets. These results suggest that rate variation across lineages should be taken into consideration when exploring and even selecting loci for phylogenomic analysis.[Branch support; data filtering; nucleotide substitution model; phylogenomics; substitution rate; summary coalescent methods.].}, }
@article {pmid34249034, year = {2021}, author = {Kaur, J and Sharma, J}, title = {Orchid Root Associated Bacteria: Linchpins or Accessories?.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {661966}, pmid = {34249034}, issn = {1664-462X}, abstract = {Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.}, }
@article {pmid34248863, year = {2021}, author = {Bednarz, VN and van de Water, JAJM and Grover, R and Maguer, JF and Fine, M and Ferrier-Pagès, C}, title = {Unravelling the Importance of Diazotrophy in Corals - Combined Assessment of Nitrogen Assimilation, Diazotrophic Community and Natural Stable Isotope Signatures.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {631244}, pmid = {34248863}, issn = {1664-302X}, abstract = {There is an increasing interest in understanding the structure and function of the microbiota associated with marine and terrestrial organisms, because it can play a major role in host nutrition and resistance to environmental stress. Reef-building corals live in association with diazotrophs, which are microbes able to fix dinitrogen. Corals are known to assimilate diazotrophically-derived nitrogen (DDN), but it is still not clear whether this nitrogen source is derived from coral-associated diazotrophs and whether it substantially contributes to the coral's nitrogen budget. In this study, we aimed to provide a better understanding of the importance of DDN for corals using a holistic approach by simultaneously assessing DDN assimilation rates (using [15]N2 tracer technique), the diazotrophic bacterial community (using nifH gene amplicon sequencing) and the natural δ[15]N signature in Stylophora pistillata corals from the Northern Red Sea along a depth gradient in winter and summer. Overall, our results show a discrepancy between the three parameters. DDN was assimilated by the coral holobiont during winter only, with an increased assimilation with depth. Assimilation rates were, however, not linked to the presence of coral-associated diazotrophs, suggesting that the presence of nifH genes does not necessarily imply functionality. It also suggests that DDN assimilation was independent from coral-associated diazotrophs and may instead result from nitrogen derived from planktonic diazotrophs. In addition, the δ[15]N signature presented negative values in almost all coral samples in both seasons, suggesting that nitrogen sources other than DDN contribute to the nitrogen budget of corals from this region. This study yields novel insight into the origin and importance of diazotrophy for scleractinian corals from the Northern Red Sea using multiple proxies.}, }
@article {pmid34237996, year = {2021}, author = {Paglia, L}, title = {From native core micriobiome to milk-oriented microbiome.}, journal = {European journal of paediatric dentistry}, volume = {22}, number = {2}, pages = {89}, doi = {10.23804/ejpd.2021.22.02.1}, pmid = {34237996}, issn = {2035-648X}, mesh = {Breast Feeding ; Child ; Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Milk, Human ; Mothers ; Pregnancy ; }, abstract = {The human microbiome is the full set of microorganisms (microbiota) present on and in our body. Its importance is such that the human being has been defined as a holobiont, that is, a superorganism made up of human eukaryotic cells and microbial cells. A balanced microbiota (eubiosis) is a prerequisite for health and well-being; on the contrary, an altered microbiota (dysbiosis) is the cause of pathological conditions. This concept is the cornerstone of the "microbiota revolution": Currently there is no disease that cannot be re- interpreted as a function of microbiome. While all human beings have similar DNA, it is the microbiome that make every person genetically unique; therefore the microbiome is the variable component of the genome which characterises each one of us. About one third of the microbiome is common to all individuals, while two thirds are specific to each subject and constitute a sort of fingerprint that forms and stabilises in the first 2-3 years of life. This timeframe is extremely important since it has been shown that the structure of the microbiome is already acquired in the embryonic-fetal period, it is completed within 3 years and lasts a lifetime. The native core microbiome is the first microbiota and characterises individuals for their whole life. It is affected by four main variables: The quality of family and social life of the mother-to-be, the intake of drugs during pregnancy, as well as the type of birth and breastfeeding. It is renowned that breast milk is a complex, unique and essential food for the growth of the child, but one of its functions - which is still under investigation today - is to feed and guide the formation of the microbiome of the newborn even after the introduction of solid foods, during the first 3 years of life. This function is carried out by the over one hundred different types of oligosaccharides that are present in breast milk, which is why these days we talk about the so-called MOM (milk-oriented microbiome). The correct formation of the microbiome affects the entire life of an individual. This is a more than valid reason to promote breastfeeding even after eruption of baby teeth and throughout the weaning period. The role of pediatric dentists, together with hygienists and pediatricians, is to spread and stress out the importance of oral hygiene so that breastfeeding can only bring benefits and not carious lesions!}, }
@article {pmid34237402, year = {2021}, author = {Thompson, HF and Gutierrez, T}, title = {Detection of hydrocarbon-degrading bacteria on deepwater corals of the northeast Atlantic using CARD-FISH.}, journal = {Journal of microbiological methods}, volume = {187}, number = {}, pages = {106277}, doi = {10.1016/j.mimet.2021.106277}, pmid = {34237402}, issn = {1872-8359}, mesh = {Animals ; Anthozoa/*microbiology ; Atlantic Ocean ; Biodegradation, Environmental ; Catalysis ; *Coral Reefs ; Hydrocarbons/*metabolism ; In Situ Hybridization, Fluorescence ; Marinobacter/*isolation &amp; purification/*metabolism ; Symbiosis ; }, abstract = {Recently, studies have begun to identify oil-degrading bacteria and host-taxon specific bacterial assemblages associated with the coral holobiont, including deep-sea cold-water corals, which are thought to provide metabolic functions and additional carbon sources to their coral hosts. Here, we describe the identification of Marinobacter on the soft tissue of Lophelia pertusa coral polyps by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). L. pertusa samples from three reef sites in the northeast Atlantic (Logachev, Mingulay and Pisces) were collected at depth by vacuum seal to eliminate contamination issues. After decalcification, histological processing and sagittal sectioning of the soft coral polyp tissues, the 16S rRNA-targeted oligonucleotide HRP-labelled probe Mrb-0625-a, and Cyanine 3 (Cy3)-labelled tyramides, were used to identify members of the hydrocarbon-degrading genus Marinobacter. Mrb-0625-a-hybridized bacterial cell signals were detected in different anatomical sites of all polyps collected from each of the three reef sites, suggesting a close, possibly intimate, association between them, but the purpose of which remains unknown. We posit that Marinobacter, and possibly other hydrocarbon-degrading bacteria associated with Lophelia, may confer the coral with the ability to cope with toxic levels of hydrocarbons in regions of natural oil seepage and where there is an active oil and gas industry presence.}, }
@article {pmid34226659, year = {2022}, author = {Glaze, TD and Erler, DV and Siljanen, HMP}, title = {Microbially facilitated nitrogen cycling in tropical corals.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {68-77}, pmid = {34226659}, issn = {1751-7370}, mesh = {*Ammonium Compounds ; Animals ; *Anthozoa ; Denitrification ; Nitrates ; Nitrification ; Nitrogen ; }, abstract = {Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This 'microbiome' possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.}, }
@article {pmid34220847, year = {2021}, author = {Schmittmann, L and Franzenburg, S and Pita, L}, title = {Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {689051}, pmid = {34220847}, issn = {1664-3224}, mesh = {Animals ; Gene Expression Regulation/drug effects ; Lipopolysaccharides/*pharmacology ; Porifera/*drug effects/genetics/immunology ; RNA-Seq ; Receptors, Pattern Recognition/*genetics ; }, abstract = {The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.}, }
@article {pmid34218251, year = {2022}, author = {Posadas, N and Baquiran, JIP and Nada, MAL and Kelly, M and Conaco, C}, title = {Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {58-67}, pmid = {34218251}, issn = {1751-7370}, mesh = {Animals ; Bacteria ; Immunity ; *Microbiota/genetics ; Oceans and Seas ; *Porifera/immunology/microbiology ; }, abstract = {The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment and the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the bacterial diversity and immune repertoire of the demosponge, Neopetrosia compacta, and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress based on climate scenarios predicted for 2100. Neopetrosia compacta harbors a diverse microbial community and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and immune response-related genes. Upon exposure to RCP 8.5 conditions, the microbiome composition and host transcriptome of N. compacta remained stable, which correlated with high survival (75%). In contrast, tissue necrosis and low survival (25%) of L. chagosensis was accompanied by microbial community shifts and downregulation of host immune-related pathways. Meta-analysis of microbiome diversity and immunological repertoire across poriferan classes further highlights the importance of host-microbe interactions in predicting the fate of sponges under future ocean conditions.}, }
@article {pmid34207399, year = {2021}, author = {Van Gerrewey, T and El-Nakhel, C and De Pascale, S and De Paepe, J and Clauwaert, P and Kerckhof, FM and Boon, N and Geelen, D}, title = {Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207399}, issn = {2076-2607}, support = {Not applicable//MELiSSA/ ; }, abstract = {Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3[-]/NH4[+] ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.}, }
@article {pmid34201731, year = {2021}, author = {Bona, E and Massa, N and Toumatia, O and Novello, G and Cesaro, P and Todeschini, V and Boatti, L and Mignone, F and Titouah, H and Zitouni, A and Lingua, G and Vuolo, F and Gamalero, E}, title = {Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34201731}, issn = {2076-2607}, abstract = {Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a "holobiont". In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.}, }
@article {pmid34201354, year = {2021}, author = {Fetsiukh, A and Conrad, J and Bergquist, J and Timmusk, S}, title = {Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils.}, journal = {International journal of molecular sciences}, volume = {22}, number = {12}, pages = {}, pmid = {34201354}, issn = {1422-0067}, support = {222-2014-1326//FORMAS/ ; 2017-5224//Swedish Research Council/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification/metabolism ; *Droughts ; Polysaccharides, Bacterial/*metabolism ; Rhizosphere ; Silicon Dioxide/*pharmacology ; Soil/*chemistry ; *Soil Microbiology ; Triticum/drug effects/*growth &amp; development/metabolism ; }, abstract = {In coming decades, drought is expected to expand globally owing to increased evaporation and reduced rainfall. Understanding, predicting, and controlling crop plants' rhizosphere has the potential to manipulate its responses to environmental stress. Our plant growth-promoting rhizobacteria (PGPR) are isolated from a natural laboratory, 'The Evolution Canyon', Israel, (EC), from the wild progenitors of cereals, where they have been co-habituating with their hosts for long periods of time. The study revealed that commercial TM50 silica particles (SN) triggered the PGPR production of exopolysaccharides (EPS) containing D-glucuronate (D-GA). The increased EPS content increased the PGPR water-holding capacity (WHC) and osmotic pressure of the biofilm matrix, which led to enhanced plant biomass in drought-stressed growth environments. Light- and cryo-electron- microscopic studies showed that, in the presence of silica (SN) particles, bacterial morphology is changed, indicating that SNs are associated with significant reprogramming in bacteria. The findings encourage the development of large-scale methods for isolate formulation with natural silicas that ensure higher WHC and hyperosmolarity under field conditions. Osmotic pressure involvement of holobiont cohabitation is also discussed.}, }
@article {pmid34200095, year = {2021}, author = {Mkaouar, H and Mariaule, V and Rhimi, S and Hernandez, J and Kriaa, A and Jablaoui, A and Akermi, N and Maguin, E and Lesner, A and Korkmaz, B and Rhimi, M}, title = {Gut Serpinome: Emerging Evidence in IBD.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34200095}, issn = {1422-0067}, support = {ANR-18-CE18-0019-03//Agence Nationale de la Recherche/ ; ANR-CE16-0018-01//Agence Nationale de la Recherche/ ; 41786NC//Campus France/ ; MICAfrica 952583//Horizon 2020/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*physiopathology ; Serine Proteases/*chemistry ; Serpins/*metabolism ; }, abstract = {Inflammatory bowel diseases (IBD) are incurable disorders whose prevalence and global socioeconomic impact are increasing. While the role of host genetics and immunity is well documented, that of gut microbiota dysbiosis is increasingly being studied. However, the molecular basis of the dialogue between the gut microbiota and the host remains poorly understood. Increased activity of serine proteases is demonstrated in IBD patients and may contribute to the onset and the maintenance of the disease. The intestinal proteolytic balance is the result of an equilibrium between the proteases and their corresponding inhibitors. Interestingly, the serine protease inhibitors (serpins) encoded by the host are well reported; in contrast, those from the gut microbiota remain poorly studied. In this review, we provide a concise analysis of the roles of serine protease in IBD physiopathology and we focus on the serpins from the gut microbiota (gut serpinome) and their relevance as a promising therapeutic approach.}, }
@article {pmid34192342, year = {2021}, author = {Salsbery, ME and DeLong, JP}, title = {Thermal adaptation in a holobiont accompanied by phenotypic changes in an endosymbiont.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {8}, pages = {2074-2084}, doi = {10.1111/evo.14301}, pmid = {34192342}, issn = {1558-5646}, mesh = {Acclimatization ; Adaptation, Physiological ; *Ciliophora ; *Paramecium ; Symbiosis ; Temperature ; }, abstract = {How and if organisms can adapt to changing temperatures has drastic consequences for the natural world. Thermal adaptation involves finding a match between temperatures permitting growth and the expected temperature distribution of the environment. However, if and how this match is achieved, and how tightly linked species change together, is poorly understood. Paramecium bursaria is a ciliate that has a tight physiological interaction with endosymbiotic green algae (zoochlorellae). We subjected a wild population of P. bursaria to a cold and warm climate (20 and 32℃) for ∼300 generations. We then measured the thermal performance curve (TPC) for intrinsic rate of growth (rmax) for these evolved lines across temperatures. We also evaluated number and size of the zoochlorellae populations within paramecia cells. TPCs for warm-adapted populations were shallower and broader than TPCs of cold-adapted populations, indicating that the warm populations adapted by moving along a thermal generalist/specialist trade off rather than right-shifting the TPC. Zoochlorellae populations within cold-adapted paramecia had fewer and larger zoochlorellae than hot-adapted paramecia, indicating phenotypic shifts in the endosymbiont accompany thermal adaptation in the host. Our results provide new and novel insight into how species involved in complex interactions will be affected by continuing increasing global temperatures.}, }
@article {pmid34185944, year = {2021}, author = {Mohanty, I and Nguyen, NA and Moore, SG and Biggs, JS and Gaul, DA and Garg, N and Agarwal, V}, title = {Enzymatic Synthesis Assisted Discovery of Proline-Rich Macrocyclic Peptides in Marine Sponges.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {22}, number = {16}, pages = {2614-2618}, pmid = {34185944}, issn = {1439-7633}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; R35 GM142882/GM/NIGMS NIH HHS/United States ; //Georgia Institute of Technology's Systems Mass Spectrometry Core Facility/ ; CHE-2004030//National Science Foundation/ ; }, mesh = {*Porifera/chemistry ; Animals ; *Proline/chemistry ; *Peptides, Cyclic/chemistry/chemical synthesis/biosynthesis ; }, abstract = {Proline-rich macrocyclic peptides (PRMPs) are natural products present in geographically and phylogenetically dispersed marine sponges. The large diversity and low abundance of PRMPs in sponge metabolomes precludes isolation and structure elucidation of each individual PRMP congener. Here, using standards developed via biomimetic enzymatic synthesis of PRMPs, a mass spectrometry-based workflow to sequence PRMPs was developed and validated to reveal that the diversity of PRMPs in marine sponges is much greater than that has been realized by natural product isolation-based strategies. Findings are placed in the context of diversity-oriented transamidative macrocyclization of peptide substrates in sponge holobionts.}, }
@article {pmid34183060, year = {2021}, author = {Ingham, AC and Kielsen, K and Mordhorst, H and Ifversen, M and Aarestrup, FM and Müller, KG and Pamp, SJ}, title = {Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {148}, pmid = {34183060}, issn = {2049-2618}, support = {643476//Horizon2020/ ; }, mesh = {Bacteria/genetics ; Child ; *Gastrointestinal Microbiome ; *Graft vs Host Disease ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients' microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT.<br><br>RESULTS: The bacterial diversity decreased in the gut, nose, and mouth during the first month and reconstituted again 1-3 months after allo-HSCT. The microbial community composition traversed three phases over 1 year. Distinct taxa discriminated the microbiota temporally at all three body sides, including Enterococcus spp., Lactobacillus spp., and Blautia spp. in the gut. Of note, certain microbial taxa appeared already changed in the patients prior to allo-HSCT as compared with healthy children. Acute GvHD occurring after allo-HSCT could be predicted from the microbiota composition at all three body sites prior to HSCT. The reconstitution of CD4[+] T cells, TH17, and B cells was associated with distinct taxa of the gut, oral, and nasal microbiota.<br><br>CONCLUSIONS: This study reveals for the first time bacteria in the mouth and nose that may predict aGvHD. Monitoring of the microbiota at different body sites in HSCT patients and particularly through involvement of samples prior to transplantation may be of prognostic value and could assist in guiding personalized treatment strategies. The identification of distinct bacteria that have a potential to predict post-transplant aGvHD might provide opportunities for an improved preventive clinical management, including a modulation of microbiomes. The host-microbiota associations shared between several body sites might also support an implementation of more feasible oral and nasal swab sampling-based analyses. Altogether, the findings suggest that the microbiota and host factors together could provide actionable information to guiding precision medicine. Video Abstract.}, }
@article {pmid34176179, year = {2021}, author = {Sánchez-Barreiro, F and Gopalakrishnan, S and Ramos-Madrigal, J and Westbury, MV and de Manuel, M and Margaryan, A and Ciucani, MM and Vieira, FG and Patramanis, Y and Kalthoff, DC and Timmons, Z and Sicheritz-Pontén, T and Dalén, L and Ryder, OA and Zhang, G and Marquès-Bonet, T and Moodley, Y and Gilbert, MTP}, title = {Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).}, journal = {Molecular ecology}, volume = {30}, number = {23}, pages = {6355-6369}, pmid = {34176179}, issn = {1365-294X}, support = {681396//H2020 European Research Council/ ; 7578//European Molecular Biology Organization/ ; }, mesh = {Animals ; *Anthropogenic Effects ; Genomics ; Inbreeding ; *Perissodactyla/genetics ; }, abstract = {Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.}, }
@article {pmid34176151, year = {2021}, author = {Capistrant-Fossa, KA and Morrison, HG and Engelen, AH and Quigley, CTC and Morozov, A and Serrão, EA and Brodie, J and Gachon, CMM and Badis, Y and Johnson, LE and Hoarau, G and Abreu, MH and Tester, PA and Stearns, LA and Brawley, SH}, title = {The microbiome of the habitat-forming brown alga Fucus vesiculosus (Phaeophyceae) has similar cross-Atlantic structure that reflects past and present drivers[1].}, journal = {Journal of phycology}, volume = {57}, number = {6}, pages = {1681-1698}, doi = {10.1111/jpy.13194}, pmid = {34176151}, issn = {1529-8817}, mesh = {*Fucus ; *Microbiota ; North Carolina ; Phylogeny ; Phylogeography ; }, abstract = {Latitudinal diversity gradients have provided many insights into species differentiation and community processes. In the well-studied intertidal zone, however, little is known about latitudinal diversity in microbiomes associated with habitat-forming hosts. We investigated microbiomes of Fucus vesiculosus because of deep understanding of this model system and its latitudinally large, cross-Atlantic range. Given multiple effects of photoperiod, we predicted that cross-Atlantic microbiomes of the Fucus microbiome would be similar at similar latitudes and correlate with environmental factors. We found that community structure and individual amplicon sequencing variants (ASVs) showed distinctive latitudinal distributions, but alpha diversity did not. Latitudinal differentiation was mostly driven by ASVs that were more abundant in cold temperate to subarctic (e.g., Granulosicoccus_t3260, Burkholderia/Caballeronia/Paraburkholderia_t8371) or warm temperate (Pleurocapsa_t10392) latitudes. Their latitudinal distributions correlated with different humidity, tidal heights, and air/sea temperatures, but rarely with irradiance or photoperiod. Many ASVs in potentially symbiotic genera displayed novel phylogenetic biodiversity with differential distributions among tissues and regions, including closely related ASVs with differing north-south distributions that correlated with Fucus phylogeography. An apparent southern range contraction of F. vesiculosus in the NW Atlantic on the North Carolina coast mimics that recently observed in the NE Atlantic. We suggest cross-Atlantic microbial structure of F. vesiculosus is related to a combination of past (glacial-cycle) and contemporary environmental drivers.}, }
@article {pmid34163371, year = {2021}, author = {Dellisanti, W and Chung, JTH and Chow, CFY and Wu, J and Wells, ML and Chan, LL}, title = {Experimental Techniques to Assess Coral Physiology in situ Under Global and Local Stressors: Current Approaches and Novel Insights.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {656562}, pmid = {34163371}, issn = {1664-042X}, abstract = {Coral reefs are declining worldwide due to global changes in the marine environment. The increasing frequency of massive bleaching events in the tropics is highlighting the need to better understand the stages of coral physiological responses to extreme conditions. Moreover, like many other coastal regions, coral reef ecosystems are facing additional localized anthropogenic stressors such as nutrient loading, increased turbidity, and coastal development. Different strategies have been developed to measure the health status of a damaged reef, ranging from the resolution of individual polyps to the entire coral community, but techniques for measuring coral physiology in situ are not yet widely implemented. For instance, while there are many studies of the coral holobiont response in single or limited-number multiple stressor experiments, they provide only partial insights into metabolic performance under more complex and temporally and spatially variable natural conditions. Here, we discuss the current status of coral reefs and their global and local stressors in the context of experimental techniques that measure core processes in coral metabolism (respiration, photosynthesis, and biocalcification) in situ, and their role in indicating the health status of colonies and communities. We highlight the need to improve the capability of in situ studies in order to better understand the resilience and stress response of corals under multiple global and local scale stressors.}, }
@article {pmid34159693, year = {2021}, author = {Campana, S and Busch, K and Hentschel, U and Muyzer, G and de Goeij, JM}, title = {DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM).}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4489-4504}, pmid = {34159693}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics ; DNA ; Isotopes ; *Microbiota ; *Porifera ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled ([12] C) and labelled ([13] C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.}, }
@article {pmid34156291, year = {2021}, author = {Sweet, M and Villela, H and Keller-Costa, T and Costa, R and Romano, S and Bourne, DG and Cárdenas, A and Huggett, MJ and Kerwin, AH and Kuek, F and Medina, M and Meyer, JL and Müller, M and Pollock, FJ and Rappé, MS and Sere, M and Sharp, KH and Voolstra, CR and Zaccardi, N and Ziegler, M and Peixoto, R}, title = {Insights into the Cultured Bacterial Fraction of Corals.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0124920}, pmid = {34156291}, issn = {2379-5077}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; UIDB/04565/2020//UNL | Faculdade de Ci&#xea;ncias e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; P20GM103430//Delaware IDeA Network of Biomedical Research Excellence (Delaware INBRE)/ ; Out of the Blue Box Reef Innovation Challenge People's Choice Award//Great Barrier Reef Foundation (GBRF)/ ; ANP 21005-4//Shell Brasil (Shell Brasil Ltda)/ ; }, abstract = {Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.}, }
@article {pmid34153755, year = {2021}, author = {Yu, X and Yu, K and Liao, Z and Chen, B and Deng, C and Yu, J and Yao, Q and Qin, Z and Liang, J}, title = {Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea.}, journal = {The Science of the total environment}, volume = {792}, number = {}, pages = {148438}, doi = {10.1016/j.scitotenv.2021.148438}, pmid = {34153755}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.}, }
@article {pmid34152600, year = {2021}, author = {Nguyen, KU and Zhang, R and Taniguchi, M and Lindsey, JS}, title = {Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts.}, journal = {Photochemistry and photobiology}, volume = {97}, number = {6}, pages = {1507-1515}, doi = {10.1111/php.13474}, pmid = {34152600}, issn = {1751-1097}, mesh = {*Chlorophyll/chemistry ; Chlorophyll A ; *Cyanobacteria/chemistry ; Fluorescence ; Spectrometry, Fluorescence ; }, abstract = {Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial-microbial holobiont (termed HT-58-2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a, complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH2 Cl2 /2-propanol, 1:1) of HT-58-2 cultures with NaBH4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17-dioxobacteriochlorins) exhibit a bathochromic shift (λabs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 13[1] -oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λem 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non-axenic cultures at microscale quantities (2 mL, 2 μm), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT-58-2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.}, }
@article {pmid34150209, year = {2021}, author = {Brahmi, C and Chapron, L and Le Moullac, G and Soyez, C and Beliaeff, B and Lazareth, CE and Gaertner-Mazouni, N and Vidal-Dupiol, J}, title = {Effects of elevated temperature and pCO2 on the respiration, biomineralization and photophysiology of the giant clam Tridacna maxima.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coab041}, pmid = {34150209}, issn = {2051-1434}, abstract = {Many reef organisms, such as the giant clams, are confronted with global change effects. Abnormally high seawater temperatures can lead to mass bleaching events and subsequent mortality, while ocean acidification may impact biomineralization processes. Despite its strong ecological and socio-economic importance, its responses to these threats still need to be explored. We investigated physiological responses of 4-year-old Tridacna maxima to realistic levels of temperature (+1.5°C) and partial pressure of carbon dioxide (pCO2) (+800 μatm of CO2) predicted for 2100 in French Polynesian lagoons during the warmer season. During a 65-day crossed-factorial experiment, individuals were exposed to two temperatures (29.2°C, 30.7°C) and two pCO2 (430 μatm, 1212 μatm) conditions. The impact of each environmental parameter and their potential synergetic effect were evaluated based on respiration, biomineralization and photophysiology. Kinetics of thermal and/or acidification stress were evaluated by performing measurements at different times of exposure (29, 41, 53, 65 days). At 30.7°C, the holobiont O2 production, symbiont photosynthetic yield and density were negatively impacted. High pCO2 had a significant negative effect on shell growth rate, symbiont photosynthetic yield and density. No significant differences of the shell microstructure were observed between control and experimental conditions in the first 29 days; however, modifications (i.e. less-cohesive lamellae) appeared from 41 days in all temperature and pCO2 conditions. No significant synergetic effect was found. Present thermal conditions (29.2°C) appeared to be sufficiently stressful to induce a host acclimatization response. All these observations indicate that temperature and pCO2 are both forcing variables affecting T. maxima's physiology and jeopardize its survival under environmental conditions predicted for the end of this century.}, }
@article {pmid34149752, year = {2021}, author = {Marín, O and González, B and Poupin, MJ}, title = {From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {650609}, pmid = {34149752}, issn = {1664-462X}, abstract = {Synthetic microbial communities (SynComs) are a useful tool for a more realistic understanding of the outcomes of multiple biotic interactions where microbes, plants, and the environment are players in time and space of a multidimensional and complex system. Toward a more in-depth overview of the knowledge that has been achieved using SynComs in the rhizosphere, a systematic review of the literature on SynComs was performed to identify the overall rationale, design criteria, experimental procedures, and outcomes of in vitro or in planta tests using this strategy. After an extensive bibliography search and a specific selection process, a total of 30 articles were chosen for further analysis, grouping them by their reported SynCom size. The reported SynComs were constituted with a highly variable number of members, ranging from 3 to 190 strains, with a total of 1,393 bacterial isolates, where the three most represented phyla were Proteobacteria, Actinobacteria, and Firmicutes. Only four articles did not reference experiments with SynCom on plants, as they considered only microbial in vitro studies, whereas the others chose different plant models and plant-growth systems; some of them are described and reviewed in this article. Besides, a discussion on different approaches (bottom-up and top-down) to study the microbiome role in the rhizosphere is provided, highlighting how SynComs are an effective system to connect and fill some knowledge gaps and to have a better understanding of the mechanisms governing these multiple interactions. Although the SynCom approach is already helpful and has a promising future, more systematic and standardized studies are needed to harness its full potential.}, }
@article {pmid34142885, year = {2021}, author = {Silva, CBP and Elias-Oliveira, J and McCarthy, CG and Wenceslau, CF and Carlos, D and Tostes, RC}, title = {Ethanol: striking the cardiovascular system by harming the gut microbiota.}, journal = {American journal of physiology. Heart and circulatory physiology}, volume = {321}, number = {2}, pages = {H275-H291}, pmid = {34142885}, issn = {1522-1539}, support = {K99 HL151889/HL/NHLBI NIH HHS/United States ; R00GM118885//Foundation for the National Institutes of Health (FNIH)/ ; R01 HL149762/HL/NHLBI NIH HHS/United States ; R01HL149762//Foundation for the National Institutes of Health (FNIH)/ ; R00 HL151889/HL/NHLBI NIH HHS/United States ; R00 GM118885/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol Drinking/immunology/*physiopathology ; Anti-Bacterial Agents/therapeutic use ; Anti-Infective Agents, Local ; Cardiovascular Diseases/immunology/*physiopathology/therapy ; Dysbiosis/immunology/*physiopathology/therapy ; Ethanol ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Prebiotics ; Probiotics/therapeutic use ; }, abstract = {Ethanol consumption represents a significant public health problem, and excessive ethanol intake is a risk factor for cardiovascular disease (CVD), one of the leading causes of death and disability worldwide. The mechanisms underlying the effects of ethanol on the cardiovascular system are complex and not fully comprehended. The gut microbiota and their metabolites are indispensable symbionts essential for health and homeostasis and therefore, have emerged as potential contributors to ethanol-induced cardiovascular system dysfunction. By mechanisms that are not completely understood, the gut microbiota modulates the immune system and activates several signaling pathways that stimulate inflammatory responses, which in turn, contribute to the development and progression of CVD. This review summarizes preclinical and clinical evidence on the effects of ethanol in the gut microbiota and discusses the mechanisms by which ethanol-induced gut dysbiosis leads to the activation of the immune system and cardiovascular dysfunction. The cross talk between ethanol consumption and the gut microbiota and its implications are detailed. In summary, an imbalance in the symbiotic relationship between the host and the commensal microbiota in a holobiont, as seen with ethanol consumption, may contribute to CVD. Therefore, manipulating the gut microbiota, by using antibiotics, probiotics, prebiotics, and fecal microbiota transplantation might prove a valuable opportunity to prevent/mitigate the deleterious effects of ethanol and improve cardiovascular health and risk prevention.}, }
@article {pmid34139059, year = {2021}, author = {Rolli, E and Vergani, L and Ghitti, E and Patania, G and Mapelli, F and Borin, S}, title = {'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {5690-5703}, pmid = {34139059}, issn = {1462-2920}, mesh = {Biodegradation, Environmental ; Environmental Pollution ; *Microbiota ; *Polychlorinated Biphenyls/analysis/metabolism ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the 'cry-for-help' hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto-extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by-products with a higher toxicity. We propose that the 'cry-for-help' mechanism could drive the exudation-mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.}, }
@article {pmid34136011, year = {2021}, author = {Vallet, M and Kaftan, F and Grabe, V and Ghaderiardakani, F and Fenizia, S and Svatoš, A and Pohnert, G and Wichard, T}, title = {A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry.}, journal = {Beilstein journal of organic chemistry}, volume = {17}, number = {}, pages = {1313-1322}, pmid = {34136011}, issn = {1860-5397}, abstract = {Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.}, }
@article {pmid34128329, year = {2021}, author = {Zhou, K and Qian, PY and Zhang, T and Xu, Y and Zhang, R}, title = {Unique phage-bacterium interplay in sponge holobionts from the southern Okinawa Trough hydrothermal vent.}, journal = {Environmental microbiology reports}, volume = {13}, number = {5}, pages = {675-683}, pmid = {34128329}, issn = {1758-2229}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics/metabolism ; *Hydrothermal Vents/microbiology ; Phylogeny ; *Porifera ; }, abstract = {Deep-sea hydrothermal vents harbour diverse and abundant animals and their symbiotic microorganisms, which together comprise holobionts. The interplay between bacterial members of holobionts and their viruses (phages) is important for maintaining these symbiotic systems; however, phage-bacterium interactions in deep-sea vent holobionts are not well understood. Marine sponges serve as good models for such studies and are used to unveil phage-bacterium interplay via metagenomic analysis. In three demosponges from deep-sea hydrothermal vent fields in the southern Okinawa Trough, the genomes of a diverse array of symbiotic bacteria, including 10 bacterial phyla, were found to lack intact prophages. Genes related to diverse anti-viral defence systems, for example, the restriction-modification and toxin-antitoxin systems, were abundant in the bacterial communities. We also detected phage genes that could complement or compensate host bacterial metabolism, indicating beneficial roles of phage infection. Our findings provide insight into phage-bacterium interplay in sponges from deep-sea hydrothermal vents.}, }
@article {pmid34113972, year = {2021}, author = {Sugiyama, A}, title = {Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {85}, number = {9}, pages = {1919-1931}, doi = {10.1093/bbb/zbab106}, pmid = {34113972}, issn = {1347-6947}, support = {JPMJCR17O2//JST/ ; //CREST/ ; 18H02313//JSPS/ ; //Kyoto University/ ; }, mesh = {*Agriculture ; Flavonoids/*analysis ; Microbiota ; Plant Roots/*chemistry ; *Rhizosphere ; Saponins/*analysis ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.}, }
@article {pmid34109033, year = {2021}, author = {Tilstra, A and Roth, F and El-Khaled, YC and Pogoreutz, C and Rädecker, N and Voolstra, CR and Wild, C}, title = {Relative abundance of nitrogen cycling microbes in coral holobionts reflects environmental nitrate availability.}, journal = {Royal Society open science}, volume = {8}, number = {6}, pages = {201835}, pmid = {34109033}, issn = {2054-5703}, abstract = {Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral-Symbiodiniaceae symbiosis.}, }
@article {pmid34089786, year = {2021}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Sangsrakru, D and Kongkachana, W and Sonthirod, C and Naktang, C and Jomchai, N and U-Thoomporn, S and Yeemin, T and Pengsakun, S and Sutthacheep, M and Tangphatsornruang, S}, title = {Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2717-2729}, doi = {10.1016/j.ygeno.2021.06.001}, pmid = {34089786}, issn = {1089-8646}, mesh = {Animals ; *Anthozoa/genetics ; Bacteria/genetics ; *Dinoflagellida/genetics ; Genes, rRNA ; RNA, Ribosomal, 16S/genetics ; Thailand ; }, abstract = {Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.}, }
@article {pmid34083731, year = {2021}, author = {Kullapanich, C and Jandang, S and Palasuk, M and Viyakarn, V and Chavanich, S and Somboonna, N}, title = {First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {11762}, pmid = {34083731}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; *Bacteria/classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/growth &amp; development/*microbiology ; Life Cycle Stages ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Symbiosis ; }, abstract = {A symbiosis of bacterial community (sometimes called microbiota) play essential roles in developmental life cycle and health of coral, starting since a larva. For examples, coral bacterial holobionts function nitrogen fixation, carbon supply, sulfur cycling and antibiotic production. Yet, a study of the dynamic of bacteria associated coral larvae development is complicated owning to a vast diversity and culturable difficulty of bacteria; hence this type of study remains unexplored for Acropora humilis larvae in Thai sea. This study represented the first to utilize 16S rRNA gene sequencing to describe the timely bacterial compositions during successfully cultured and reared A. humilis larval transformation in aquaculture (gametes were collected from Sattahip Bay, Chonburi province, Thailand), from gamete spawning (0 h) and fertilization stage (1 h), to embryonic cleavage (8 h), round cell development (28, 39 and 41 h), and planula formation (48 h). The sequencing results as estimated by Good's coverage at genus level covered 99.65 ± 0.24% of total bacteria. While core phyla of bacteria were observed (Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes), changes in bacterial population structures and differential predominant core bacterial orders were denoted for each larval developmental stage, from fertilization to embryonic cleavage and subsequently from the embryonic cleavage to round cell development (P = 0.007). For instances, Pseudoalteromonas and Oceanospirillales were found prevalent at 8 h, and Rhizobiales were at 48 h. The bacterial population structures from the round cell stage, particularly at 41 h, showed gradual drift towards those of the planula formation stage, suggesting microbial selection. Overall, this study provides preliminary insights into the dynamics of bacterial community and their potentially functional association (estimated from the bacterial compositions) during the developmental embryonic A. humilis in a cultivation system in Southeast Asia region.}, }
@article {pmid34078452, year = {2021}, author = {Röthig, T and Puntin, G and Wong, JCY and Burian, A and McLeod, W and Baker, DM}, title = {Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {127}, pmid = {34078452}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; *Cnidaria ; *Dinoflagellida ; Eutrophication ; Nitrogen ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana.<br><br>METHODS: Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate ([13]C) and nitrate ([15]N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae.<br><br>RESULTS: C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae.<br><br>CONCLUSION: Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.}, }
@article {pmid34078289, year = {2021}, author = {Moitinho-Silva, L and Wegener, M and May, S and Schrinner, F and Akhtar, A and Boysen, TJ and Schaeffer, E and Hansen, C and Schmidt, T and Rühlemann, MC and Hübenthal, M and Rausch, P and Kondakci, MT and Maetzler, W and Weidinger, S and Laudes, M and Süß, P and Schulte, D and Junker, R and Sommer, F and Weisser, B and Bang, C and Franke, A}, title = {Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {162}, pmid = {34078289}, issn = {1471-2180}, support = {EXC2167//Deutsche Forschungsgemeinschaft/ ; FOR5042//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Diet ; *Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements.<br><br>RESULTS: Different biometric responses between endurance and strength activities were identified, such as a significant increase of lymphocytes and decrease of mean corpuscular haemoglobin concentration (MCHC) only within the strength intervention group. In the endurance group, we observed a significant reduction in hip circumference and an increase in physical working capacity (PWC). Though a large variation of microbiota changes were observed between individuals of the same group, we did not find specific collective alterations in the endurance nor the strength groups, arguing for microbiome variations specific to individuals, and therefore, were not captured in our analysis.<br><br>CONCLUSIONS: We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology.<br><br>TRIAL REGISTRATION: DRKS, DRKS00015873 .&#xa0;Registered 12 December 2018; Retrospectively registered.}, }
@article {pmid34072177, year = {2021}, author = {Liu, Y and Palaniveloo, K and Alias, SA and Sathiya Seelan, JS}, title = {Species Diversity and Secondary Metabolites of Sarcophyton-Associated Marine Fungi.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {11}, pages = {}, pmid = {34072177}, issn = {1420-3049}, mesh = {Alkaloids/*chemistry ; Alternaria ; Amino Acids/chemistry ; Animals ; Anthozoa/metabolism/*microbiology ; Anthraquinones/metabolism ; Biodiversity ; Biological Assay ; Biological Products/chemistry/*metabolism ; Fungi/*metabolism ; Inhibitory Concentration 50 ; Ketones/metabolism ; Microbiota ; Symbiosis ; }, abstract = {Soft corals are widely distributed across the globe, especially in the Indo-Pacific region, with Sarcophyton being one of the most abundant genera. To date, there have been 50 species of identified Sarcophyton. These soft corals host a diverse range of marine fungi, which produce chemically diverse, bioactive secondary metabolites as part of their symbiotic nature with the soft coral hosts. The most prolific groups of compounds are terpenoids and indole alkaloids. Annually, there are more bio-active compounds being isolated and characterised. Thus, the importance of the metabolite compilation is very much important for future reference. This paper compiles the diversity of Sarcophyton species and metabolites produced by their associated marine fungi, as well as the bioactivity of these identified compounds. A total of 88 metabolites of structural diversity are highlighted, indicating the huge potential these symbiotic relationships hold for future research.}, }
@article {pmid34067328, year = {2021}, author = {Bourgin, M and Kriaa, A and Mkaouar, H and Mariaule, V and Jablaoui, A and Maguin, E and Rhimi, M}, title = {Bile Salt Hydrolases: At the Crossroads of Microbiota and Human Health.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34067328}, issn = {2076-2607}, support = {PhD fellowship-BM//MICA Department - INRAE/ ; PhD fellowship-BM//ONIRIS/ ; MICAfrica - 952583//Horizon 2020/ ; }, abstract = {The gut microbiota has been increasingly linked to metabolic health and disease over the last few decades. Several factors have been suggested to be involved in lipid metabolism and metabolic responses. One mediator that has gained great interest as a clinically important enzyme is bile salt hydrolase (BSH). BSH enzymes are widely distributed in human gastrointestinal microbial communities and are believed to play key roles in both microbial and host physiology. In this review, we discuss the current evidence related to the role of BSHs in health and provide useful insights that may pave the way for new therapeutic targets in human diseases.}, }
@article {pmid34066959, year = {2021}, author = {Miller, WB and Enguita, FJ and Leitão, AL}, title = {Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution.}, journal = {Cells}, volume = {10}, number = {5}, pages = {}, pmid = {34066959}, issn = {2073-4409}, mesh = {Animals ; *Biological Evolution ; *Cell Engineering ; Cognition/*physiology ; *Gene Editing ; *Homeostasis ; Humans ; *Selection, Genetic ; }, abstract = {Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.}, }
@article {pmid34065848, year = {2021}, author = {Lyu, D and Msimbira, LA and Nazari, M and Antar, M and Pagé, A and Shah, A and Monjezi, N and Zajonc, J and Tanney, CAS and Backer, R and Smith, DL}, title = {The Coevolution of Plants and Microbes Underpins Sustainable Agriculture.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34065848}, issn = {2076-2607}, support = {RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.}, }
@article {pmid34058984, year = {2021}, author = {Medina Munoz, M and Brenner, C and Richmond, D and Spencer, N and Rio, RVM}, title = {The holobiont transcriptome of teneral tsetse fly species of varying vector competence.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {400}, pmid = {34058984}, issn = {1471-2164}, support = {R01 AI118789/AI/NIAID NIH HHS/United States ; R01AI118789//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Animals ; Enterobacteriaceae/genetics ; Humans ; Transcriptome ; *Tsetse Flies/genetics ; Wigglesworthia/genetics ; }, abstract = {BACKGROUND: Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment and development, yet our understanding of why remains fragmentary. The tsetse gut microbiome is dominated by two Gammaproteobacteria, an essential and ancient mutualist Wigglesworthia glossinidia and a commensal Sodalis glossinidius. Here, we characterize and compare the metatranscriptome of teneral Glossina morsitans to that of G. brevipalpis and describe unique immunological, physiological, and metabolic landscapes that may impact vector competence differences between these two species.<br><br>RESULTS: An active expression profile was observed for Wigglesworthia immediately following host adult metamorphosis. Specifically, 'translation, ribosomal structure and biogenesis' followed by 'coenzyme transport and metabolism' were the most enriched clusters of orthologous genes (COGs), highlighting the importance of nutrient transport and metabolism even following host species diversification. Despite the significantly smaller Wigglesworthia genome more differentially expressed genes (DEGs) were identified between interspecific isolates (n&#xa0;=&#x2009;326, ~&#x2009;55% of protein coding genes) than between the corresponding Sodalis isolates (n&#xa0;=&#x2009;235, ~&#x2009;5% of protein coding genes) likely reflecting distinctions in host co-evolution and adaptation. DEGs between Sodalis isolates included genes involved in chitin degradation that may contribute towards trypanosome susceptibility by compromising the immunological protection provided by the peritrophic matrix. Lastly, G. brevipalpis tenerals demonstrate a more immunologically robust background with significant upregulation of IMD and melanization pathways.<br><br>CONCLUSIONS: These transcriptomic differences may collectively contribute to vector competence differences between tsetse species and offers translational relevance towards the design of novel vector control strategies.}, }
@article {pmid34048702, year = {2021}, author = {Traylor-Knowles, N}, title = {Unlocking the single-cell mysteries of a reef-building coral.}, journal = {Cell}, volume = {184}, number = {11}, pages = {2802-2804}, doi = {10.1016/j.cell.2021.05.007}, pmid = {34048702}, issn = {1097-4172}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; Ecosystem ; }, abstract = {Coral reefs are one of the most important ecosystems in the world but least understood from a cellular level. In this issue of Cell, Levy et al. unravel the single-cell gene expression of the coral holobiont and open the doors to better understand the novel diversity of cell types.}, }
@article {pmid34026358, year = {2021}, author = {Calvert, MD and Madden, AA and Nichols, LM and Haddad, NM and Lahne, J and Dunn, RR and McKenney, EA}, title = {A review of sourdough starters: ecology, practices, and sensory quality with applications for baking and recommendations for future research.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11389}, pmid = {34026358}, issn = {2167-8359}, abstract = {The practice of sourdough bread-making is an ancient science that involves the development, maintenance, and use of a diverse and complex starter culture. The sourdough starter culture comes in many different forms and is used in bread-making at both artisanal and commercial scales, in countries all over the world. While there is ample scientific research related to sourdough, there is no standardized approach to using sourdough starters in science or the bread industry; and there are few recommendations on future directions for sourdough research. Our review highlights what is currently known about the microbial ecosystem of sourdough (including microbial succession within the starter culture), methods of maintaining sourdough (analogous to land management) on the path to bread production, and factors that influence the sensory qualities of the final baked product. We present new hypotheses for the successful management of sourdough starters and propose future directions for sourdough research and application to better support and engage the sourdough baking community.}, }
@article {pmid34025695, year = {2021}, author = {Li, T and Wu, S and Yang, W and Selosse, MA and Gao, J}, title = {How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {647114}, pmid = {34025695}, issn = {1664-462X}, abstract = {Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.}, }
@article {pmid34025595, year = {2021}, author = {Manriquez, B and Muller, D and Prigent-Combaret, C}, title = {Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {619122}, pmid = {34025595}, issn = {1664-302X}, abstract = {In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.}, }
@article {pmid34020587, year = {2021}, author = {Maire, J and Blackall, LL and van Oppen, MJH}, title = {Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {152}, pmid = {34020587}, issn = {1471-2180}, mesh = {Animal Structures/microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Coral Reefs ; DNA, Bacterial/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sea Anemones/*microbiology/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Coral reefs are among the most diverse and productive ecosystems on Earth. This success relies on the coral's association with a wide range of microorganisms, including dinoflagellates of the family Symbiodiniaceae that provide coral hosts with most of their organic carbon requirements. While bacterial associates have long been overlooked, research on these microorganisms is gaining traction, and deciphering bacterial identity and function is greatly enhancing our understanding of cnidarian biology. Here, we investigated bacterial communities in defensive tissues (acontia) of the coral model, the sea anemone Exaiptasia diaphana. Acontia are internal filaments that are ejected upon detection of an external threat and release toxins to repel predators.<br><br>RESULTS: Using culturing techniques and 16S rRNA gene metabarcoding we identified bacterial communities associated with acontia of four Great Barrier Reef-sourced E. diaphana genotypes. We show that bacterial communities are similar across genotypes, and dominated by Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, and Saprospiraceae. By analyzing abundant amplicon sequence variants (ASVs) from metabarcoding data from acontia and comparing these to data from whole anemones, we identified five potentially important bacterial genera of the acontia microbiome: Vibrio, Sulfitobacter, Marivita, Alteromonas, and Lewinella. The role of these bacteria within the acontia remains uninvestigated but could entail assistance in defense processes such as toxin production.<br><br>CONCLUSIONS: This study provides insight into potential bacterial involvement in cnidarian defense tissues and highlights the need to study bacterial communities in individual compartments within a holobiont.}, }
@article {pmid34014937, year = {2021}, author = {Tibatá, VM and Sanchez, A and Palmer-Young, E and Junca, H and Solarte, VM and Madella, S and Ariza, F and Figueroa, J and Corona, M}, title = {Africanized honey bees in Colombia exhibit high prevalence but low level of infestation of Varroa mites and low prevalence of pathogenic viruses.}, journal = {PloS one}, volume = {16}, number = {5}, pages = {e0244906}, pmid = {34014937}, issn = {1932-6203}, mesh = {Animals ; Bees/*microbiology/virology ; Colombia ; Insect Viruses/*pathogenicity ; Varroidae/*pathogenicity ; }, abstract = {The global spread of the ectoparasitic mite Varroa destructor has promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees (AHBs), which are considered more resistant to Varroa compared to European honey bees. However, the relationship between Varroa levels and the spread of honey bee viruses in AHBs remains unknown. In this study, we determined Varroa prevalence and infestation levels as well as the prevalence of seven major honey bee viruses in AHBs from three regions of Colombia. We found that although Varroa exhibited high prevalence (92%), its infestation levels were low (4.5%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all colonies were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4%, ABPV 10.56%). Our findings indicate that AHBs possess a natural resistance to Varroa that does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.}, }
@article {pmid34011286, year = {2021}, author = {Zhang, Y and Yang, Q and Ling, J and Long, L and Huang, H and Yin, J and Wu, M and Tang, X and Lin, X and Zhang, Y and Dong, J}, title = {Correction to: Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {150}, pmid = {34011286}, issn = {1471-2180}, }
@article {pmid33996285, year = {2021}, author = {Karimi, E and Geslain, E and Belcour, A and Frioux, C and Aïte, M and Siegel, A and Corre, E and Dittami, SM}, title = {Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e11344}, pmid = {33996285}, issn = {2167-8359}, abstract = {Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.}, }
@article {pmid33991262, year = {2021}, author = {Zhang, Y and Yang, Q and Zhang, Y and Ahmad, M and Ling, J and Dong, J and Wang, Y}, title = {The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {5}, pages = {986-995}, pmid = {33991262}, issn = {1573-3017}, support = {41676107//National Natural Science Foundation of China/ ; XDA13020300//Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Archaea ; Biodiversity ; Coral Reefs ; Fungi ; }, abstract = {Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.}, }
@article {pmid33990868, year = {2021}, author = {Aguirre-von-Wobeser, E}, title = {Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria.}, journal = {Current microbiology}, volume = {78}, number = {7}, pages = {2623-2630}, pmid = {33990868}, issn = {1432-0991}, support = {CB-2014-01-242956//SEP/CONACyT/ ; }, mesh = {*Alphaproteobacteria ; *Microbiota ; *Persea ; Photosynthesis ; *Photosynthetic Reaction Center Complex Proteins ; Plant Bark ; }, abstract = {The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.}, }
@article {pmid33990786, year = {2021}, author = {Nagpal, J and Cryan, JF}, title = {Host genetics, the microbiome &amp; behaviour-a 'Holobiont' perspective.}, journal = {Cell research}, volume = {31}, number = {8}, pages = {832-833}, pmid = {33990786}, issn = {1748-7838}, support = {SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; GOIPD/2019/714//Irish Research Council (An Chomhairle um Thaighde in &#xc9;irinn)/ ; }, mesh = {*Microbiota/genetics ; Symbiosis/genetics ; }, }
@article {pmid33990699, year = {2021}, author = {Rasmussen, JA and Villumsen, KR and Duchêne, DA and Puetz, LC and Delmont, TO and Sveier, H and Jørgensen, LVG and Præbel, K and Martin, MD and Bojesen, AM and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts.}, journal = {Communications biology}, volume = {4}, number = {1}, pages = {579}, pmid = {33990699}, issn = {2399-3642}, mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; *Metagenome ; Mycoplasma/*genetics ; Phylogeny ; Salmonidae/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.}, }
@article {pmid33957989, year = {2021}, author = {Doering, T and Wall, M and Putchim, L and Rattanawongwan, T and Schroeder, R and Hentschel, U and Roik, A}, title = {Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {102}, pmid = {33957989}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Thermotolerance ; }, abstract = {BACKGROUND: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding.<br><br>RESULTS: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 &#xb0;C). One hundred twelve (Pocillopora sp.) and&#xa0;sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few&#xa0;bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context.<br><br>CONCLUSIONS: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.}, }
@article {pmid33957417, year = {2021}, author = {Rinkevich, B}, title = {Augmenting coral adaptation to climate change via coral gardening (the nursery phase).}, journal = {Journal of environmental management}, volume = {291}, number = {}, pages = {112727}, doi = {10.1016/j.jenvman.2021.112727}, pmid = {33957417}, issn = {1095-8630}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa ; Climate Change ; Conservation of Natural Resources ; Coral Reefs ; Ecosystem ; Gardening ; }, abstract = {Unceasing climate change and anthropogenic impacts on coral reefs worldwide lead the needs for augmenting adaptive potential of corals. Currently, the most successful approach for restoring degraded reefs is 'coral gardening', where corals are farmed in underwater nurseries, then outplanted to damaged reefs. Dealing with enhanced coral adaptation, the 'coral gardening' approach is conceptually structured here within a hierarchical list of five encircling tiers that include all restoration activities, focusing on the nursery phase. Each tier encompasses all the activities performed in the levels below it hierarchically. The first is the 'coral mariculture' tier, followed by the 'ecological engineering' tier. The third is the adaptation-based reef restoration (ABRR) tier, preceding the fourth ('ecosystem seascape') and the fifth ('ecosystem services') tiers. The ABRR tier is further conceptualized and its constituent five classes (phenotypic plasticity, assisted migration, epigenetics, coral chimerism, holobiont modification) are detailed. It is concluded that the nursery phase of the 'gardening' tenet may further serve as a platform to enhance the adaptation capacities of corals to climate change through the five ABBR classes. Employing the 'gardening' tiers in reef restoration without considering ABRR will scarcely be able to meet global targets for healthy reef ecosystems in the future.}, }
@article {pmid33953396, year = {2021}, author = {Kim, B and Kanai, MI and Oh, Y and Kyung, M and Kim, EK and Jang, IH and Lee, JH and Kim, SG and Suh, GSB and Lee, WJ}, title = {Response of the microbiome-gut-brain axis in Drosophila to amino acid deficit.}, journal = {Nature}, volume = {593}, number = {7860}, pages = {570-574}, pmid = {33953396}, issn = {1476-4687}, support = {R01 DK116294/DK/NIDDK NIH HHS/United States ; R01 DK106636/DK/NIDDK NIH HHS/United States ; }, mesh = {Amino Acids, Essential/*administration &amp; dosage/deficiency ; Animal Nutritional Physiological Phenomena ; Animals ; Animals, Genetically Modified ; Appetite ; *Brain-Gut Axis ; Drosophila/*physiology ; Enterocytes ; Female ; *Food Preferences ; *Gastrointestinal Microbiome ; Germ-Free Life ; Hunger ; Leucine ; Symbiosis ; }, abstract = {A balanced intake of macronutrients-protein, carbohydrate and fat-is essential for the well-being of organisms. An adequate calorific intake but with insufficient protein consumption can lead to several ailments, including kwashiorkor[1]. Taste receptors (T1R1-T1R3)[2] can detect amino acids in the environment, and cellular sensors (Gcn2 and Tor)[3] monitor the levels of amino acids in the cell. When deprived of dietary protein, animals select a food source that contains a greater proportion of protein or essential amino acids (EAAs)[4]. This suggests that food selection is geared towards achieving the target amount of a particular macronutrient with assistance of the EAA-specific hunger-driven response, which is poorly understood. Here we show in Drosophila that a microbiome-gut-brain axis detects a deficit of EAAs and stimulates a compensatory appetite for EAAs. We found that the neuropeptide CNMamide (CNMa)[5] was highly induced in enterocytes of the anterior midgut during protein deprivation. Silencing of the CNMa-CNMa receptor axis blocked the EAA-specific hunger-driven response in deprived flies. Furthermore, gnotobiotic flies bearing an EAA-producing symbiotic microbiome exhibited a reduced appetite for EAAs. By contrast, gnotobiotic flies with a mutant microbiome that did not produce leucine or other EAAs showed higher expression of CNMa and a greater compensatory appetite for EAAs. We propose that gut enterocytes sense the levels of diet- and microbiome-derived EAAs and communicate the EAA-deprived condition to the brain through CNMa.}, }
@article {pmid33948583, year = {2021}, author = {Bellone, C and Lüscher, C}, title = {Bugs R Us: Restoring sociability with microbiota in autism.}, journal = {Cell reports. Medicine}, volume = {2}, number = {4}, pages = {100256}, pmid = {33948583}, issn = {2666-3791}, mesh = {Animals ; *Autistic Disorder ; Bacteria ; Disease Models, Animal ; Membrane Proteins ; Mice ; Mice, Knockout ; *Microbiota ; Nerve Tissue Proteins ; }, abstract = {In a recent publication in Cell, Buffington et al. provide a fascinating example of hologenomic behavioral regulation in an autism mouse model.[1] The authors report that gut bacteria from wild-type mice rescue the social deficit of Cntnap2 knockout mice.}, }
@article {pmid33947806, year = {2021}, author = {Swain, TD and Lax, S and Gilbert, J and Backman, V and Marcelino, LA}, title = {A Phylogeny-Informed Analysis of the Global Coral-Symbiodiniaceae Interaction Network Reveals that Traits Correlated with Thermal Bleaching Are Specific to Symbiont Transmission Mode.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947806}, issn = {2379-5077}, abstract = {The complex network of associations between corals and their dinoflagellates (family Symbiodiniaceae) are the basis of coral reef ecosystems but are sensitive to increasing global temperatures. Coral-symbiont interactions are restricted by ecological and evolutionary determinants that constrain partner choice and influence holobiont response to environmental stress; however, little is known about how these processes shape thermal resilience of the holobiont. Here, we built a network of global coral-Symbiodiniaceae associations, mapped species traits (e.g., symbiont transmission mode and biogeography) and phylogenetic relationships of both partners onto the network, and assigned thermotolerance to both host and symbiont nodes. Using network analysis and phylogenetic comparative methods, we determined the contribution of species traits to thermal resilience of the holobiont, while accounting for evolutionary patterns among species. We found that the network shows nonrandom interactions among species, which are shaped by evolutionary history, symbiont transmission mode (horizontally transmitted [HT] or vertically transmitted [VT] corals) and biogeography. Coral phylogeny, but not Symbiodiniaceae phylogeny, symbiont transmission mode, or biogeography, was a good predictor of thermal resilience. Closely related corals have similar Symbiodiniaceae interaction patterns and bleaching susceptibilities. Nevertheless, the association patterns that explain increased host thermal resilience are not generalizable across the entire network but are instead unique to HT and VT corals. Under nonstress conditions, thermally resilient VT coral species associate with thermotolerant phylotypes and limit their number of unique symbionts and overall symbiont thermotolerance diversity, while thermally resilient HT coral species associate with a few host-specific symbiont phylotypes.IMPORTANCE Recent advances have revealed a complex network of interactions between coral and Symbiodiniaceae. Specifically, nonrandom association patterns, which are determined in part by restrictions imposed by symbiont transmission mode, increase the sensitivity of the overall network to thermal stress. However, little is known about the extent to which coral-Symbiodiniaceae network resistance to thermal stress is shaped by host and symbiont species phylogenetic relationships and host and symbiont species traits, such as symbiont transmission mode. We built a frequency-weighted global coral-Symbiodiniaceae network and used network analysis and phylogenetic comparative methods to show that evolutionary relatedness, but not transmission mode, predicts thermal resilience of the coral-Symbiodiniaceae holobiont. Consequently, thermal stress events could result in nonrandom pruning of susceptible lineages and loss of taxonomic diversity with catastrophic effects on community resilience to future events. Our results show that inclusion of the contribution of evolutionary and ecological processes will further our understanding of the fate of coral assemblages under climate change.}, }
@article {pmid33946450, year = {2021}, author = {Embacher, J and Neuhauser, S and Zeilinger, S and Kirchmair, M}, title = {Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {5}, pages = {}, pmid = {33946450}, issn = {2309-608X}, support = {Y 801/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.}, }
@article {pmid33941698, year = {2021}, author = {Savary, R and Barshis, DJ and Voolstra, CR and Cárdenas, A and Evensen, NR and Banc-Prandi, G and Fine, M and Meibom, A}, title = {Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {19}, pages = {}, pmid = {33941698}, issn = {1091-6490}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/classification/*genetics/microbiology ; Bacteria/classification/genetics ; *Coral Reefs ; Heat-Shock Response/*genetics ; Hot Temperature ; Indian Ocean ; Microbiota/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; RNA-Seq/methods ; Symbiosis/genetics ; Time Factors ; Transcriptome/*genetics ; }, abstract = {Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (>94%) and algal (>71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean.}, }
@article {pmid33930136, year = {2021}, author = {Zilber-Rosenberg, I and Rosenberg, E}, title = {Microbial-driven genetic variation in holobionts.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {6}, pages = {}, doi = {10.1093/femsre/fuab022}, pmid = {33930136}, issn = {1574-6976}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; Humans ; *Microbiota/genetics ; *Symbiosis/genetics ; }, abstract = {Genetic variation in holobionts (host and microbiome), occurring in both host and microbiome genomes, can be observed from two perspectives: observable variations and processes that bring about the variation. Observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotes. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa and a more diverse non-core, enabling considerable genetic variation. Thus, the human gut microbiome, for example, contains 1000 times more unique genes than are present in the human genome. Microbial-driven genetic variation processes in holobionts include: (1) acquisition of novel microbes from the environment, (2) amplification/reduction of certain microbes in the microbiome, (3) horizontal gene transfer between microbes and between microbes and host and (4) mutation, which plays a role in optimizing interactions between microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, a greater chance of vertical transmission and a greater effect of microbiome on evolution than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.}, }
@article {pmid33923980, year = {2021}, author = {Gasulla, F and Del Campo, EM and Casano, LM and Guéra, A}, title = {Advances in Understanding of Desiccation Tolerance of Lichens and Lichen-Forming Algae.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {4}, pages = {}, pmid = {33923980}, issn = {2223-7747}, support = {CGL2016-80259-P//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; }, abstract = {Lichens are symbiotic associations (holobionts) established between fungi (mycobionts) and certain groups of cyanobacteria or unicellular green algae (photobionts). This symbiotic association has been essential in the colonization of terrestrial dry habitats. Lichens possess key mechanisms involved in desiccation tolerance (DT) that are constitutively present such as high amounts of polyols, LEA proteins, HSPs, a powerful antioxidant system, thylakoidal oligogalactolipids, etc. This strategy allows them to be always ready to survive drastic changes in their water content. However, several studies indicate that at least some protective mechanisms require a minimal time to be induced, such as the induction of the antioxidant system, the activation of non-photochemical quenching including the de-epoxidation of violaxanthin to zeaxanthin, lipid membrane remodeling, changes in the proportions of polyols, ultrastructural changes, marked polysaccharide remodeling of the cell wall, etc. Although DT in lichens is achieved mainly through constitutive mechanisms, the induction of protection mechanisms might allow them to face desiccation stress in a better condition. The proportion and relevance of constitutive and inducible DT mechanisms seem to be related to the ecology at which lichens are adapted to.}, }
@article {pmid33914388, year = {2021}, author = {Wong, KH and Goodbody-Gringley, G and de Putron, SJ and Becker, DM and Chequer, A and Putnam, HM}, title = {Brooded coral offspring physiology depends on the combined effects of parental press and pulse thermal history.}, journal = {Global change biology}, volume = {27}, number = {13}, pages = {3179-3195}, doi = {10.1111/gcb.15629}, pmid = {33914388}, issn = {1365-2486}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Chlorophyll A ; Coral Reefs ; Hot Temperature ; }, abstract = {Reef-building corals respond to the temporal integration of both pulse events (i.e., heat waves) and press thermal history (i.e., local environment) via physiological changes, with ecological consequences. We used a "press-pulse-press" experimental framework to expose the brooding coral Porites astreoides to various thermal histories to understand the physiological response of temporal dynamics within and across generations. We collected adult colonies from two reefs (outer Rim reef and inner Patch reef) in Bermuda with naturally contrasting thermal regimes as our initial "press" scenario, followed by a 21-day ex situ "pulse" thermal stress of 30.4°C during larval brooding, and a "press" year-long adult reciprocal transplant between the original sites. Higher endosymbiont density and holobiont protein was found in corals originating from the lower thermal variability site (Rim) compared to the higher thermal variability site (Patch). The thermal pulse event drove significant declines in photosynthesis, endosymbiont density, and chlorophyll a, with bleaching phenotype convergence for adults from both histories. Following the reciprocal transplant, photosynthesis was higher in previously heated corals, indicating recovery from the thermal pulse. The effect of origin (initial press) modulated the response to transplant site for endosymbiont density and chlorophyll a, suggesting contrasting acclimation strategies. Higher respiration and photosynthetic rates were found in corals originating from the Rim site, indicating greater energy available for reproduction, supported by larger larvae released from Rim corals post-transplantation. Notably, parental exposure to the pulse thermal event resulted in increased offspring plasticity when parents were transplanted to foreign sites, highlighting the legacy of the pulse event and the importance of the environment during recovery in contributing to cross-generational or developmental plasticity. Together, these findings provide novel insight into the role of historical disturbance events in driving differential outcomes within and across generations, which is of critical importance in forecasting reef futures.}, }
@article {pmid33912198, year = {2020}, author = {Harman, G and Khadka, R and Doni, F and Uphoff, N}, title = {Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {610065}, pmid = {33912198}, issn = {1664-462X}, abstract = {Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.}, }
@article {pmid33912144, year = {2021}, author = {Wolter, LA and Mitulla, M and Kalem, J and Daniel, R and Simon, M and Wietz, M}, title = {CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {628055}, pmid = {33912144}, issn = {1664-302X}, abstract = {Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62-1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62-1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain "polysaccharide niches." Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.}, }
@article {pmid33911273, year = {2021}, author = {Rhie, A and McCarthy, SA and Fedrigo, O and Damas, J and Formenti, G and Koren, S and Uliano-Silva, M and Chow, W and Fungtammasan, A and Kim, J and Lee, C and Ko, BJ and Chaisson, M and Gedman, GL and Cantin, LJ and Thibaud-Nissen, F and Haggerty, L and Bista, I and Smith, M and Haase, B and Mountcastle, J and Winkler, S and Paez, S and Howard, J and Vernes, SC and Lama, TM and Grutzner, F and Warren, WC and Balakrishnan, CN and Burt, D and George, JM and Biegler, MT and Iorns, D and Digby, A and Eason, D and Robertson, B and Edwards, T and Wilkinson, M and Turner, G and Meyer, A and Kautt, AF and Franchini, P and Detrich, HW and Svardal, H and Wagner, M and Naylor, GJP and Pippel, M and Malinsky, M and Mooney, M and Simbirsky, M and Hannigan, BT and Pesout, T and Houck, M and Misuraca, A and Kingan, SB and Hall, R and Kronenberg, Z and Sović, I and Dunn, C and Ning, Z and Hastie, A and Lee, J and Selvaraj, S and Green, RE and Putnam, NH and Gut, I and Ghurye, J and Garrison, E and Sims, Y and Collins, J and Pelan, S and Torrance, J and Tracey, A and Wood, J and Dagnew, RE and Guan, D and London, SE and Clayton, DF and Mello, CV and Friedrich, SR and Lovell, PV and Osipova, E and Al-Ajli, FO and Secomandi, S and Kim, H and Theofanopoulou, C and Hiller, M and Zhou, Y and Harris, RS and Makova, KD and Medvedev, P and Hoffman, J and Masterson, P and Clark, K and Martin, F and Howe, K and Flicek, P and Walenz, BP and Kwak, W and Clawson, H and Diekhans, M and Nassar, L and Paten, B and Kraus, RHS and Crawford, AJ and Gilbert, MTP and Zhang, G and Venkatesh, B and Murphy, RW and Koepfli, KP and Shapiro, B and Johnson, WE and Di Palma, F and Marques-Bonet, T and Teeling, EC and Warnow, T and Graves, JM and Ryder, OA and Haussler, D and O'Brien, SJ and Korlach, J and Lewin, HA and Howe, K and Myers, EW and Durbin, R and Phillippy, AM and Jarvis, ED}, title = {Towards complete and error-free genome assemblies of all vertebrate species.}, journal = {Nature}, volume = {592}, number = {7856}, pages = {737-746}, pmid = {33911273}, issn = {1476-4687}, support = {U41 HG002371/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; MR/T021985/1/MRC_/Medical Research Council/United Kingdom ; R01 HG010485/HG/NHGRI NIH HHS/United States ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; 207492/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; R01 GM130691/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R21 DC014432/DC/NIDCD NIH HHS/United States ; R44 HG008118/HG/NHGRI NIH HHS/United States ; }, mesh = {Animals ; Birds ; Gene Library ; *Genome ; Genome Size ; Genome, Mitochondrial ; Genomics/*methods ; Haplotypes ; High-Throughput Nucleotide Sequencing ; Molecular Sequence Annotation ; Sequence Alignment ; Sequence Analysis, DNA ; Sex Chromosomes/genetics ; Vertebrates/*genetics ; }, abstract = {High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species[1-4]. To address this issue, the international Genome 10K (G10K) consortium[5,6] has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.}, }
@article {pmid33910503, year = {2021}, author = {Zhang, Y and Yang, Q and Ling, J and Long, L and Huang, H and Yin, J and Wu, M and Tang, X and Lin, X and Zhang, Y and Dong, J}, title = {Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {130}, pmid = {33910503}, issn = {1471-2180}, mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions/*physiology ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond.<br><br>RESULTS: High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community &#x3b1;-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure.<br><br>CONCLUSIONS: Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.}, }
@article {pmid33905604, year = {2021}, author = {Mayer, T and Mari, A and Almario, J and Murillo-Roos, M and Syed M Abdullah, H and Dombrowski, N and Hacquard, S and Kemen, EM and Agler, MT}, title = {Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing.}, journal = {Molecular ecology resources}, volume = {21}, number = {6}, pages = {1952-1965}, doi = {10.1111/1755-0998.13408}, pmid = {33905604}, issn = {1755-0998}, support = {//Deutsche Forschungsgemeinschaft/ ; 390713860//Germany's Excellence Strategy/ ; //International Leibniz Research School/ ; //Max-Planck Gesellschaft/ ; //University of T&#xfc;bingen/ ; //European Research Council (ERC)/ ; ERC-2018-COG 820124//DeCoCt research progra/ ; }, mesh = {Bacteria/classification ; Fungi/classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Oomycetes/classification ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce "blocking oligos", a low-cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A. thaliana-specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots (Bromus erectus, Plantago lanceolata, Lotus corniculatus, Amaranth sp., Arabidopsis thaliana). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant-derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A. thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package.}, }
@article {pmid33898524, year = {2021}, author = {Mach, N and Moroldo, M and Rau, A and Lecardonnel, J and Le Moyec, L and Robert, C and Barrey, E}, title = {Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {656204}, pmid = {33898524}, issn = {2296-889X}, abstract = {Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPARγ, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.}, }
@article {pmid33897663, year = {2021}, author = {Berg, G and Kusstatscher, P and Abdelfattah, A and Cernava, T and Smalla, K}, title = {Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {650610}, pmid = {33897663}, issn = {1664-302X}, abstract = {Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.}, }
@article {pmid33897642, year = {2021}, author = {Costa, RM and Cárdenas, A and Loussert-Fonta, C and Toullec, G and Meibom, A and Voolstra, CR}, title = {Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {637834}, pmid = {33897642}, issn = {1664-302X}, abstract = {Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼10[4] and ∼10[5] bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.}, }
@article {pmid33896632, year = {2021}, author = {Saborío-Montero, A and López-García, A and Gutiérrez-Rivas, M and Atxaerandio, R and Goiri, I and García-Rodriguez, A and Jiménez-Montero, JA and González, C and Tamames, J and Puente-Sánchez, F and Varona, L and Serrano, M and Ovilo, C and González-Recio, O}, title = {A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding.}, journal = {Journal of dairy science}, volume = {104}, number = {7}, pages = {8135-8151}, doi = {10.3168/jds.2020-20005}, pmid = {33896632}, issn = {1525-3198}, mesh = {Animals ; Cattle/genetics ; Female ; Fermentation ; *Methane/metabolism ; *Microbiota/genetics ; Rumen/metabolism ; Selective Breeding ; Spain ; }, abstract = {The rumen is a complex microbial system of substantial importance in terms of greenhouse gas emissions and feed efficiency. This study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome toward reduced methane emissions. We analyzed nanopore long reads from the rumen metagenome of 437 Holstein cows from 14 commercial herds in 4 northern regions in Spain. After filtering, data were treated as compositional. The large complexity of the rumen microbiota was aggregated, through principal component analysis (PCA), into few principal components (PC) that were used as proxies of the core metagenome. The PCA allowed us to condense the huge and fuzzy taxonomical and functional information from the metagenome into a few PC. Bivariate animal models were applied using these PC and methane production as phenotypes. The variability condensed in these PC is controlled by the cow genome, with heritability estimates for the first PC of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being >0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (≥0.70), with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. Enteric methane production was positively associated with relative abundance of eukaryotes (protozoa and fungi) through the first component of the PCA at phylum, class, order, family, and genus. Nanopore long reads allowed the characterization of the core rumen metagenome using whole-metagenome sequencing, and the purposed aggregated variables could be used in animal breeding programs to reduce methane emissions in future generations.}, }
@article {pmid33879261, year = {2021}, author = {Bozzi, D and Rasmussen, JA and Carøe, C and Sveier, H and Nordøy, K and Gilbert, MTP and Limborg, MT}, title = {Salmon gut microbiota correlates with disease infection status: potential for monitoring health in farmed animals.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {30}, pmid = {33879261}, issn = {2524-4671}, support = {FoodTrancriptomics - 6150-00033B//Innovationsfonden (DK)/ ; CEH - DNRF143//Statens Jordbrugs- og Veterin&#xe6;rvidenskabelige Forskningsr&#xe5;d (DK)/ ; HappyFish - (#8022-00005A)//Danmarks Frie Forskningsfond/ ; HoloFood - 817729//Horizon 2020/ ; }, abstract = {BACKGROUND: Infectious diseases cause significant production losses in aquaculture every year. Since the gut microbiota plays an essential role in regulating the host immune system, health and physiology, altered gut microbiota compositions are often associated with a diseased status. However, few studies have examined the association between disease severity and degree of gut dysbiosis, especially when the gut is not the site of the primary infection. Moreover, there is a lack of knowledge on whether bath treatment with formalin, a disinfectant commonly used in aquaculture to treat external infections, might affect the gut microbiome as a consequence of formalin ingestion. Here we investigate, through 16S rRNA gene metabarcoding, changes in the distal gut microbiota composition of a captive-reared cohort of 80 Atlantic salmon (Salmo salar L.), in consequence of an external bacterial skin infection due to a natural outbreak and subsequent formalin treatment.<br><br>RESULTS: We identified Tenacibaculum dicentrarchi as the causative disease pathogen and we show that the distal gut of diseased salmon presented a different composition from that of healthy individuals. A new, yet undescribed, Mycoplasma genus characterized the gut of healthy salmon, while in the sick fish we observed an increase in terms of relative abundance of Aliivibrio sp., a strain regarded as opportunistic. We also noticed a positive correlation between fish weight and Mycoplasma sp. relative abundance, potentially indicating a beneficial effect for its host. Moreover, we observed that the gut microbiota of fish treated with formalin was more similar to those of sick fish than healthy ones.<br><br>CONCLUSIONS: We conclude that external Tenacibaculum infections have the potential of indirectly affecting the host gut microbiota. As such, treatment optimization procedures should account for that. Formalin treatment is not an optimal solution from a holistic perspective, since we observe an altered gut microbiota in the treated fish. We suggest its coupling with a probiotic treatment aimed at re-establishing a healthy community. Lastly, we have observed a positive correlation of Mycoplasma sp. with salmon health and weight, therefore we encourage further investigations towards its potential utilization as a biomarker for monitoring health in salmon and potentially other farmed fish species.}, }
@article {pmid33845886, year = {2021}, author = {Cambon-Bonavita, MA and Aubé, J and Cueff-Gauchard, V and Reveillaud, J}, title = {Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {87}, pmid = {33845886}, issn = {2049-2618}, mesh = {Animals ; *Decapoda ; *Hydrothermal Vents ; Phylogeny ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations.<br><br>RESULTS: Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences.<br><br>CONCLUSION: These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.}, }
@article {pmid33841191, year = {2021}, author = {Aldana, M and Robeva, R}, title = {New Challenges in Systems Biology: Understanding the Holobiont.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {662878}, pmid = {33841191}, issn = {1664-042X}, }
@article {pmid33833260, year = {2021}, author = {Li, S and Roger, LM and Kumar, L and Lewinski, NA and Klein-Seetharaman, J and Gagnon, A and Putnam, HM and Yang, J}, title = {Digital image processing to detect subtle motion in stony coral.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7722}, pmid = {33833260}, issn = {2045-2322}, abstract = {Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community.}, }
@article {pmid33829521, year = {2021}, author = {Catania, F and Baedke, J and Fábregas-Tejeda, A and Nieves Delgado, A and Vitali, V and Long, LAN}, title = {Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {6}, pages = {e2100049}, doi = {10.1002/bies.202100049}, pmid = {33829521}, issn = {1521-1878}, mesh = {Climate Change ; Diet ; Dysbiosis ; Humans ; *Life History Traits ; *Microbiota ; }, abstract = {Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet-driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet-driven microbiome changes lead to dysbiosis, they can also shape life-history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome-host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra-holobiont stress response, which encourages the holobiont to re-establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change-related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life-history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate-related dietary challenges for policy and health interventions.}, }
@article {pmid33824199, year = {2021}, author = {Cross, KL and Leigh, BA and Hatmaker, EA and Mikaelyan, A and Miller, AK and Bordenstein, SR}, title = {Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33824199}, issn = {2379-5077}, abstract = {Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species? Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown.IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.}, }
@article {pmid33805166, year = {2021}, author = {Lyu, D and Zajonc, J and Pagé, A and Tanney, CAS and Shah, A and Monjezi, N and Msimbira, LA and Antar, M and Nazari, M and Backer, R and Smith, DL}, title = {Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33805166}, issn = {2076-2607}, support = {G250030 AAFC BioFuelNet//Agriculture and Agri-Food Canada/ ; RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.}, }
@article {pmid33803291, year = {2021}, author = {Cuffaro, B and Assohoun, ALW and Boutillier, D and Peucelle, V and Desramaut, J and Boudebbouze, S and Croyal, M and Waligora-Dupriet, AJ and Rhimi, M and Grangette, C and Maguin, E}, title = {Identification of New Potential Biotherapeutics from Human Gut Microbiota-Derived Bacteria.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33803291}, issn = {2076-2607}, abstract = {The role of the gut microbiota in health and disease is well recognized and the microbiota dysbiosis observed in many chronic diseases became a new therapeutic target. The challenge is to get a better insight into the functionality of commensal bacteria and to use this knowledge to select live biotherapeutics as new preventive or therapeutic products. In this study, we set up a screening approach to evaluate the functional capacities of a set of 21 strains isolated from the gut microbiota of neonates and adults. For this purpose, we selected key biological processes involved in the microbiome-host symbiosis and known to impact the host physiology i.e., the production of short-chain fatty acids and the ability to strengthen an epithelial barrier (Caco-2), to induce the release of the anti-inflammatory IL-10 cytokine after co-culture with human immune cells (PBMC) or to increase GLP-1 production from STC-1 endocrine cell line. This strategy highlighted fifteen strains exhibiting beneficial activities among which seven strains combined several of them. Interestingly, this work revealed for the first time a high prevalence of potential health-promoting functions among intestinal commensal strains and identified several appealing novel candidates for the management of chronic diseases, notably obesity and inflammatory bowel diseases.}, }
@article {pmid33802197, year = {2021}, author = {Mariaule, V and Kriaa, A and Soussou, S and Rhimi, S and Boudaya, H and Hernandez, J and Maguin, E and Lesner, A and Rhimi, M}, title = {Digestive Inflammation: Role of Proteolytic Dysregulation.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33802197}, issn = {1422-0067}, support = {Titan-ANR number ANR-18-CE18-0019-03//Agence Nationale de la Recherche/ ; SerpinGuTarget ANR-CE16-0018-01//Agence Nationale de la Recherche/ ; CMCU-PHC Utique (No. 19G0819)-Campus France (41786NC)//Campus France/ ; Twinning European project MICAfrica 952583//Horizon 2020/ ; }, mesh = {Animals ; Humans ; Inflammation/enzymology/pathology ; Inflammatory Bowel Diseases/*enzymology/pathology ; Matrix Metalloproteinases/*metabolism ; *Proteolysis ; Serine Proteases/*metabolism ; }, abstract = {Dysregulation of the proteolytic balance is often associated with diseases. Serine proteases and matrix metalloproteases are involved in a multitude of biological processes and notably in the inflammatory response. Within the framework of digestive inflammation, several studies have stressed the role of serine proteases and matrix metalloproteases (MMPs) as key actors in its pathogenesis and pointed to the unbalance between these proteases and their respective inhibitors. Substantial efforts have been made in developing new inhibitors, some of which have reached clinical trial phases, notwithstanding that unwanted side effects remain a major issue. However, studies on the proteolytic imbalance and inhibitors conception are directed toward host serine/MMPs proteases revealing a hitherto overlooked factor, the potential contribution of their bacterial counterpart. In this review, we highlight the role of proteolytic imbalance in human digestive inflammation focusing on serine proteases and MMPs and their respective inhibitors considering both host and bacterial origin.}, }
@article {pmid33798277, year = {2021}, author = {Mitchison-Field, LMY and Gladfelter, AS}, title = {Culturing and Multiplexed Time-Lapse Imaging of Fungal Isolates from Marine and Coastal Environments.}, journal = {Current protocols}, volume = {1}, number = {4}, pages = {e94}, doi = {10.1002/cpz1.94}, pmid = {33798277}, issn = {2691-1299}, support = {2016022//NSF MCB/ ; GBMF9343//NSF MCB/ ; }, mesh = {Animals ; *Biodiversity ; Culture Media ; *Fungi ; Seawater ; Time-Lapse Imaging ; }, abstract = {Fungi play a crucial role in biogeochemical cycling and shaping biological communities at macro- and microcosmic scales. However, fungi have been largely overlooked in studies of marine ecology and microbiology. Here we present protocols for preparing culture media, collecting and culturing fungi from several types of marine environments and animal hosts, and preparing microscopy slides for long-term time lapse imaging of fungal isolates. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Solid media preparation Alternate Protocol 1: Liquid media preparation Basic Protocol 2: Sample collection and plating from ocean water Alternate Protocol 2: Sample collection and plating from coastal sediment Alternate Protocol 3: Sample collection and plating from animal holobionts Support Protocol 1: Making frozen stocks Support Protocol 2: Streaking cultures from frozen stocks Basic Protocol 3: Slide preparation and assembly for imaging © 2021 by John Wiley &amp; Sons, Inc.}, }
@article {pmid33785073, year = {2021}, author = {Bo, TB and Kohl, KD}, title = {Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {26}, pmid = {33785073}, issn = {2524-4671}, abstract = {Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.}, }
@article {pmid33774874, year = {2021}, author = {Chen, H and Wang, M and Li, M and Lian, C and Zhou, L and Zhang, X and Zhang, H and Zhong, Z and Wang, H and Cao, L and Li, C}, title = {A glimpse of deep-sea adaptation in chemosynthetic holobionts: Depressurization causes DNA fragmentation and cell death of methanotrophic endosymbionts rather than their deep-sea Bathymodiolinae host.}, journal = {Molecular ecology}, volume = {30}, number = {10}, pages = {2298-2312}, doi = {10.1111/mec.15904}, pmid = {33774874}, issn = {1365-294X}, mesh = {Acclimatization ; Animals ; Cell Death ; DNA Fragmentation ; *Hydrothermal Vents ; *Mytilidae ; Phylogeny ; Symbiosis/genetics ; }, abstract = {Bathymodiolinae mussels are typical species in deep-sea cold seeps and hydrothermal vents and an ideal model for investigating chemosynthetic symbiosis and the influence of high hydrostatic pressure on deep-sea organisms. Herein, the potential influence of depressurization on DNA fragmentation and cell death in Bathymodiolinae hosts and their methanotrophic symbionts were surveyed using isobaric and unpressurized samples. As a hallmark of cell death, massive DNA fragmentation was observed in methanotrophic symbionts from unpressurized Bathymodiolinae while several endonucleases and restriction enzymes were upregulated. Additionally, genes involved in DNA repair, glucose/methane metabolism as well as two-component regulatory system were also differentially expressed in depressurized symbionts. DNA fragmentation and programmed cell death, however, were rarely detected in the host bacteriocytes owing to the orchestrated upregulation of inhibitor of apoptosis genes and downregulation of caspase genes. Meanwhile, diverse host immune recognition receptors were promoted during depressurization, probably enabling the regain of symbionts. When the holobionts were subjected to a prolonged acclimation at atmospheric pressure, alternations in both the DNA fragmentation and the expression atlas of aforesaid genes were continuously observed in symbionts, demonstrating the persistent influence of depressurization. Contrarily, the host cells demonstrated certain tolerance against depressurization stress as expression level of some immune-related genes returned to the basal level in isobaric samples. Altogether, the present study illustrates the distinct stress responses of Bathymodiolinae hosts and their methanotrophic symbionts against depressurization, which could provide further insight into the deep-sea adaptation of Bathymodiolinae holobionts while highlighting the necessity of using isobaric sampling methods in deep-sea research.}, }
@article {pmid33767748, year = {2021}, author = {Zhu, L and Zhang, Z and Chen, H and Lamer, JT and Wang, J and Wei, W and Fu, L and Tang, M and Wang, C and Lu, G}, title = {Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective.}, journal = {Evolutionary applications}, volume = {14}, number = {3}, pages = {735-745}, pmid = {33767748}, issn = {1752-4571}, abstract = {Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.}, }
@article {pmid33766108, year = {2021}, author = {Keller-Costa, T and Lago-Lestón, A and Saraiva, JP and Toscan, R and Silva, SG and Gonçalves, J and Cox, CJ and Kyrpides, N and Nunes da Rocha, U and Costa, R}, title = {Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {72}, pmid = {33766108}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Dysbiosis ; *Host-Pathogen Interactions ; Metagenome/*genetics ; *Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella.<br><br>RESULTS: Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system.<br><br>CONCLUSIONS: This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.}, }
@article {pmid33758981, year = {2022}, author = {Campos, AB and Cavalcante, LC and de Azevedo, AR and Loiola, M and Silva, AET and Ara, A and Meirelles, PM}, title = {CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {252-255}, pmid = {33758981}, issn = {1432-184X}, support = {11268//Minist&#xe9;rio da Ci&#xea;ncia, Tecnologia, Inova&#xe7;&#xf5;es e Comunica&#xe7;&#xf5;es/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.301758/2018-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; }, abstract = {Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.}, }
@article {pmid33754443, year = {2021}, author = {Baum, L and Nguyen, MTHD and Jia, Y and Biazik, J and Thomas, T}, title = {Characterization of a novel roseophage and the morphological and transcriptional response of the sponge symbiont Ruegeria AU67 to infection.}, journal = {Environmental microbiology}, volume = {23}, number = {5}, pages = {2532-2549}, doi = {10.1111/1462-2920.15474}, pmid = {33754443}, issn = {1462-2920}, mesh = {Animals ; *Bacteriophages/genetics ; Porifera/*microbiology ; *Rhodobacteraceae/virology ; *Siphoviridae ; }, abstract = {Sponges have recently been recognized to contain complex communities of bacteriophages; however, little is known about how they interact with their bacterial hosts. Here, we isolated a novel phage, called Ruegeria phage Tedan, and characterized its impact on the bacterial sponge symbiont Ruegeria AU67 on a morphological and molecular level. Phage Tedan was structurally, genomically and phylogenetically characterized to be affiliated with the genus Xiamenvirus of the family Siphoviridae. Through microscopic observations and transcriptomic analysis, we show that phage Tedan upon infection induces a process leading to metabolic and morphological changes in its host. These changes would render Ruegeria AU67 better adapted to inhabit the sponge holobiont due to an improved utilization of ecologically relevant energy and carbon sources as well as a potential impediment of phagocytosis by the sponge through cellular enlargement. An increased survival or better growth of the bacterium in the sponge environment will likely benefit the phage reproduction. Our results point towards the possibility that phages from host-associated environments require, and have thus evolved, different strategies to interact with their host when compared to those phages from free-living or planktonic environments.}, }
@article {pmid33749821, year = {2021}, author = {Lemay, MA and Davis, KM and Martone, PT and Parfrey, LW}, title = {Kelp-associated Microbiota are Structured by Host Anatomy[1].}, journal = {Journal of phycology}, volume = {57}, number = {4}, pages = {1119-1130}, doi = {10.1111/jpy.13169}, pmid = {33749821}, issn = {1529-8817}, mesh = {Bacteria/genetics ; *Kelp ; *Laminaria ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Seaweed-associated microbiota are essential for the health and resilience of nearshore ecosystems, marine biogeochemical cycling, and host health. Yet much remains unknown about the ecology of seaweed-microbe symbioses. In this study, we quantified fine-scale patterns of microbial community structure across distinct anatomical regions of the kelp Laminaria setchellii. These anatomical regions represent a gradient of tissue ages: perennial holdfasts can be several years old, whereas stipe epicortex and blades are younger annual structures. Within blades, new growth occurs at the base, while the blade tips may be several months old and undergoing senescence. We hypothesized that microbial communities will differ across anatomical regions (holdfast, stipe, blade base, and blade tip), such that younger tissues will harbor fewer microbes that are more consistent across replicate individuals. Our data support this hypothesis, with the composition of bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities showing significant differences across the four anatomical regions, with the surfaces of older tissues (holdfast and blade tips) harboring significantly greater microbial richness compared to the younger tissues of the meristematic region. Additional samples collected from the surfaces of new L. setchellii recruits (<1y old) also showed differences in microbial community structure across anatomical regions, which demonstrates that these microbial differences are established early. We also observed this pattern in two additional algal species, suggesting that microbial community structure across host anatomy may be a common feature of the seaweed microbiome.}, }
@article {pmid33732246, year = {2021}, author = {Fiuza, BSD and Fonseca, HF and Meirelles, PM and Marques, CR and da Silva, TM and Figueiredo, CA}, title = {Understanding Asthma and Allergies by the Lens of Biodiversity and Epigenetic Changes.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {623737}, pmid = {33732246}, issn = {1664-3224}, mesh = {Animals ; Asthma/*genetics/*immunology/metabolism ; Bacteria/immunology ; Chromatin Assembly and Disassembly ; DNA Methylation ; Environmental Exposure/adverse effects ; *Epigenesis, Genetic ; Genetic Predisposition to Disease ; Helminths/immunology ; Host-Pathogen Interactions ; Humans ; Hygiene Hypothesis ; Hypersensitivity/*genetics/*immunology/metabolism ; *Immunogenetic Phenomena ; Microbiota/*immunology ; Risk Assessment ; Risk Factors ; Viruses/immunology ; }, abstract = {Exposure to different organisms (bacteria, mold, virus, protozoan, helminths, among others) can induce epigenetic changes affecting the modulation of immune responses and consequently increasing the susceptibility to inflammatory diseases. Epigenomic regulatory features are highly affected during embryonic development and are responsible for the expression or repression of different genes associated with cell development and targeting/conducting immune responses. The well-known, "window of opportunity" that includes maternal and post-natal environmental exposures, which include maternal infections, microbiota, diet, drugs, and pollutant exposures are of fundamental importance to immune modulation and these events are almost always accompanied by epigenetic changes. Recently, it has been shown that these alterations could be involved in both risk and protection of allergic diseases through mechanisms, such as DNA methylation and histone modifications, which can enhance Th2 responses and maintain memory Th2 cells or decrease Treg cells differentiation. In addition, epigenetic changes may differ according to the microbial agent involved and may even influence different asthma or allergy phenotypes. In this review, we discuss how exposure to different organisms, including bacteria, viruses, and helminths can lead to epigenetic modulations and how this correlates with allergic diseases considering different genetic backgrounds of several ancestral populations.}, }
@article {pmid33731352, year = {2021}, author = {Liu, C and Gao, J and Cui, X and Li, Z and Chen, L and Yuan, Y and Zhang, Y and Mei, L and Zhao, L and Cai, D and Hu, M and Zhou, B and Li, Z and Qin, T and Si, H and Li, G and Lin, Z and Xu, Y and Zhu, C and Yin, Y and Zhang, C and Xu, W and Li, Q and Wang, K and Gilbert, MTP and Heller, R and Wang, W and Huang, J and Qiu, Q}, title = {A towering genome: Experimentally validated adaptations to high blood pressure and extreme stature in the giraffe.}, journal = {Science advances}, volume = {7}, number = {12}, pages = {}, pmid = {33731352}, issn = {2375-2548}, mesh = {Acclimatization ; Adaptation, Physiological ; Animals ; Genome ; *Giraffes/genetics ; *Hypertension/genetics ; Mice ; }, abstract = {The suite of adaptations associated with the extreme stature of the giraffe has long interested biologists and physiologists. By generating a high-quality chromosome-level giraffe genome and a comprehensive comparison with other ruminant genomes, we identified a robust catalog of giraffe-specific mutations. These are primarily related to cardiovascular, bone growth, vision, hearing, and circadian functions. Among them, the giraffe FGFRL1 gene is an outlier with seven unique amino acid substitutions not found in any other ruminant. Gene-edited mice with the giraffe-type FGFRL1 show exceptional hypertension resistance and higher bone mineral density, both of which are tightly connected with giraffe adaptations to high stature. Our results facilitate a deeper understanding of the molecular mechanism underpinning distinct giraffe traits, and may provide insights into the study of hypertension in humans.}, }
@article {pmid33727403, year = {2021}, author = {Mohanty, I and Tapadar, S and Moore, SG and Biggs, JS and Freeman, CJ and Gaul, DA and Garg, N and Agarwal, V}, title = {Presence of Bromotyrosine Alkaloids in Marine Sponges Is Independent of Metabolomic and Microbiome Architectures.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33727403}, issn = {2379-5077}, support = {K99 ES026620/ES/NIEHS NIH HHS/United States ; R00 ES026620/ES/NIEHS NIH HHS/United States ; }, abstract = {Marine sponge holobionts are prolific sources of natural products. One of the most geographically widespread classes of sponge-derived natural products is the bromotyrosine alkaloids. A distinguishing feature of bromotyrosine alkaloids is that they are present in phylogenetically disparate sponges. In this study, using sponge specimens collected from Guam, the Solomon Islands, the Florida Keys, and Puerto Rico, we queried whether the presence of bromotyrosine alkaloids potentiates metabolomic and microbiome conservation among geographically distant and phylogenetically different marine sponges. A multi-omic characterization of sponge holobionts revealed vastly different metabolomic and microbiome architectures among different bromotyrosine alkaloid-harboring sponges. However, we find statistically significant correlations between the microbiomes and metabolomes, signifying that the microbiome plays an important role in shaping the overall metabolome, even in low-microbial-abundance sponges. Molecules mined from the polar metabolomes of these sponges revealed conservation of biosynthetic logic between bromotyrosine alkaloids and brominated pyrrole-imidazole alkaloids, another class of marine sponge-derived natural products. In light of prior findings postulating the sponge host itself to be the biosynthetic source of bromotyrosine alkaloids, our data now set the stage for investigating the causal relationships that dictate the microbiome-metabolome interconnectedness for marine sponges in which the microbiome may not contribute to natural product biogenesis.IMPORTANCE Our work demonstrates that phylogenetically and geographically distant sponges with very different microbiomes can harbor natural product chemical classes that are united in their core chemical structures and biosynthetic logic. Furthermore, we show that independent of geographical dispersion, natural product chemistry, and microbial abundance, overall sponge metabolomes tightly correlate with their microbiomes.}, }
@article {pmid33715441, year = {2021}, author = {Cornwell, BH and Hernández, L}, title = {Genetic structure in the endosymbiont Breviolum 'muscatinei' is correlated with geographical location, environment and host species.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1946}, pages = {20202896}, pmid = {33715441}, issn = {1471-2954}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Ecosystem ; Genetic Structures ; *Sea Anemones ; Symbiosis ; }, abstract = {Corals and cnidarians form symbioses with dinoflagellates across a wide range of habitats from the tropics to temperate zones. Notably, these partnerships create the foundation of coral reef ecosystems and are at risk of breaking down due to climate change. This symbiosis couples the fitness of the partners, where adaptations in one species can benefit the holobiont. However, the scales over which each partner can match their current-and future-environment are largely unknown. We investigated population genetic patterns of temperate anemones (Anthopleura spp.) and their endosymbiont Breviolum 'muscatinei', across an extensive geographical range to identify the spatial scales over which local adaptation is possible. Similar to previously published results, two solitary host species exhibited isolation by distance across hundreds of kilometres. However, symbionts exhibited genetic structure across multiple spatial scales, from geographical location to depth in the intertidal zone, and host species, suggesting that symbiont populations are more likely than their hosts to adaptively mitigate the impact of increasing temperatures.}, }
@article {pmid33705715, year = {2021}, author = {Kirch, M and Romundset, A and Gilbert, MTP and Jones, FC and Foote, AD}, title = {Ancient and modern stickleback genomes reveal the demographic constraints on adaptation.}, journal = {Current biology : CB}, volume = {31}, number = {9}, pages = {2027-2036.e8}, doi = {10.1016/j.cub.2021.02.027}, pmid = {33705715}, issn = {1879-0445}, mesh = {Alleles ; Animals ; Demography ; Genomics ; Humans ; Infant, Newborn ; Lakes ; Paleontology ; *Smegmamorpha/genetics ; }, abstract = {Adaptation is typically studied by comparing modern populations with contrasting environments. Individuals persisting in the ancestral habitat are typically used to represent the ancestral founding population; however, it has been questioned whether these individuals are good proxies for the actual ancestors.[1] To address this, we applied a paleogenomics approach[2] to directly access the ancestral genepool: partially sequencing the genomes of two 11- to 13,000-year-old stickleback recovered from the transitionary layer between marine and freshwater sediments of two Norwegian isolation lakes[3] and comparing them with 30 modern stickleback genomes from the same lakes and adjacent marine fjord, in addition to a global dataset of 20 genomes.[4] The ancient stickleback shared genome-wide ancestry with the modern fjord population, whereas modern lake populations have lost substantial ancestral variation following founder effects, and subsequent drift and selection. Freshwater-adaptive alleles found in one ancient stickleback genome have not risen to high frequency in the present-day population from the same lake. Comparison to the global dataset suggested incomplete adaptation to freshwater in our modern lake populations. Our findings reveal the impact of population bottlenecks in constraining adaptation due to reduced efficacy of selection on standing variation present in founder populations.}, }
@article {pmid33705688, year = {2021}, author = {Buffington, SA and Dooling, SW and Sgritta, M and Noecker, C and Murillo, OD and Felice, DF and Turnbaugh, PJ and Costa-Mattioli, M}, title = {Dissecting the contribution of host genetics and the microbiome in complex behaviors.}, journal = {Cell}, volume = {184}, number = {7}, pages = {1740-1756.e16}, pmid = {33705688}, issn = {1097-4172}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biopterins/analogs &amp; derivatives/metabolism ; Disease Models, Animal ; Excitatory Postsynaptic Potentials ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Limosilactobacillus reuteri/metabolism/physiology ; *Locomotion ; Membrane Proteins/deficiency/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nerve Tissue Proteins/deficiency/genetics ; Neurodevelopmental Disorders/genetics/microbiology/pathology/therapy ; Principal Component Analysis ; Psychomotor Agitation/pathology ; *Social Behavior ; Synaptic Transmission ; }, abstract = {The core symptoms of many neurological disorders have traditionally been thought to be caused by genetic variants affecting brain development and function. However, the gut microbiome, another important source of variation, can also influence specific behaviors. Thus, it is critical to unravel the contributions of host genetic variation, the microbiome, and their interactions to complex behaviors. Unexpectedly, we discovered that different maladaptive behaviors are interdependently regulated by the microbiome and host genes in the Cntnap2[-/-] model for neurodevelopmental disorders. The hyperactivity phenotype of Cntnap2[-/-] mice is caused by host genetics, whereas the social-behavior phenotype is mediated by the gut microbiome. Interestingly, specific microbial intervention selectively rescued the social deficits in Cntnap2[-/-] mice through upregulation of metabolites in the tetrahydrobiopterin synthesis pathway. Our findings that behavioral abnormalities could have distinct origins (host genetic versus microbial) may change the way we think about neurological disorders and how to treat them.}, }
@article {pmid33691030, year = {2021}, author = {Cowen, LJ and Klein-Seetharaman, J and Putnam, H}, title = {Bioinformatics of corals: Investigating heterogeneous omics data from coral holobionts for insight into reef health and resillience.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {26}, number = {}, pages = {336-340}, pmid = {33691030}, issn = {2335-6936}, mesh = {Animals ; *Anthozoa/genetics ; Computational Biology ; Coral Reefs ; *Microbiota ; }, abstract = {Coral reefs are home to over 2 million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic and other -omics data from different species of reef building corals, the uni-cellular dinoagellates, plus the coral microbiome (where corals have possibly the most complex microbiome yet discovered, consisting of over 20,000 different species), is becoming increasingly available for corals. This new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. This paper summarizes the content of the Bioinformatics of Corals workshop, that is being held as part of PSB 2021. It is particularly relevant for this workshop to occur at PSB, given the abundance of and reliance on coral reefs in Hawaii and the conference's traditional association with the region.}, }
@article {pmid33687778, year = {2021}, author = {Borrero de Acuña, JM and Bernal, P}, title = {Plant holobiont interactions mediated by the type VI secretion system and the membrane vesicles: promising tools for a greener agriculture.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {1830-1836}, doi = {10.1111/1462-2920.15457}, pmid = {33687778}, issn = {1462-2920}, mesh = {Agriculture ; Crops, Agricultural ; *Microbiota ; Plant Development ; Plant Roots ; Soil Microbiology ; *Type VI Secretion Systems ; }, abstract = {A deeper understanding of the complex relationship between plants and their microbiota is allowing researchers to appreciate a plethora of possibilities to improve crops using chemical-free alternatives based on beneficial microorganisms. An increase in crop yield from the promotion of plant growth or even simultaneous protection of the plants from the attack of phytopathogens can be achieved in the presence of different plant-associated microorganisms known as plant-growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCAs), respectively. Thus, the study of the great diversity of plant-microbe and microbe-microbe interactions is an attention-grabbing topic covering studies of interactions since the plant seed and through all developmental stages, from root to shoot. The intricate communication systems that plant holobionts co-evolved has resulted in many different strategies and interplays between these organisms shaping the bacterial communities and the plant fitness simultaneously. Herein, we emphasize two understudied delivery systems existing in plant-associated bacteria: the type VI secretion system (T6SS) and the membrane vesicles with a huge potential to boost a highly demanded and necessary green agriculture.}, }
@article {pmid33675372, year = {2021}, author = {Varasteh, T and Tschoeke, D and Garcia, G and Lima, AS and Moreira, APB and Thompson, C and Thompson, F}, title = {Insights into the genomic repertoire of Aquimarina litoralis CCMR20, a symbiont of coral Mussismilia braziliensis.}, journal = {Archives of microbiology}, volume = {203}, number = {5}, pages = {2743-2746}, pmid = {33675372}, issn = {1432-072X}, mesh = {Animals ; Anthozoa/*microbiology ; Brazil ; Coral Reefs ; Flavobacteriaceae/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Symbiosis/*genetics ; }, abstract = {Aquimarina litoralis CCMR20 originated from the coral Mussismilia braziliensis (Sebastião Gomes Reef, Brazil, summer 2010). To gain new insights into the genomic repertoire associated with symbioses, we obtained the genome sequence of this strains using Illumina sequencing. CCMR20 has a genome size of 6.3 Mb, 32.6%GC, and 5513 genes (37 tRNA and 4 rRNA). A more fine-grained examination of the gene repertoire of CCMR20 disclosed genes engaged with symbiosis (heterotrophic carbon metabolism, CAZymes, B-vitamins group, carotenoid pigment and antioxidant molecules production). Genomic evidence further expand the possible relevance of this symbiont in the health of Mussismilia holobiont.Whole Genome Shotgun project has been deposited at DDBJ/ENA/GeneBank under the accession number WEKL00000000.}, }
@article {pmid33671759, year = {2021}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Musella, M and Quero, GM and Prada, F and Mancuso, A and Seyfarth, AM and Turroni, S and Candela, M and Biagi, E}, title = {Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33671759}, issn = {2076-2607}, support = {818290//Horizon 2020/ ; }, abstract = {Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.}, }
@article {pmid33669823, year = {2021}, author = {Saati-Santamaría, Z and Rivas, R and Kolařik, M and García-Fraile, P}, title = {A New Perspective of Pseudomonas-Host Interactions: Distribution and Potential Ecological Functions of the Genus Pseudomonas within the Bark Beetle Holobiont.}, journal = {Biology}, volume = {10}, number = {2}, pages = {}, pmid = {33669823}, issn = {2079-7737}, support = {19-09072S//Grantov&#xe1; agentura &#x10c;esk&#xe9; republiky (GA&#x10c;R)/ ; CLU-2018-04//Excellence Unit of the Spanish-Portuguese Institute for Agricultural Research (CIALE)/ ; }, abstract = {Symbiosis between microbes and insects has been raised as a promising area for understanding biological implications of microbe-host interactions. Among them, the association between fungi and bark beetles has been generally recognized as essential for the bark beetle ecology. However, many works investigating bark beetle bacterial communities and their functions usually meet in a common finding: Pseudomonas is a broadly represented genus within this holobiont and it may provide beneficial roles to its host. Thus, we aimed to review available research on this microbe-host interaction and point out the probable relevance of Pseudomonas strains for these insects, in order to guide future research toward a deeper analysis of the importance of these bacteria for the beetle's life cycle.}, }
@article {pmid33665032, year = {2021}, author = {Dittami, SM and Arboleda, E and Auguet, JC and Bigalke, A and Briand, E and Cárdenas, P and Cardini, U and Decelle, J and Engelen, AH and Eveillard, D and Gachon, CMM and Griffiths, SM and Harder, T and Kayal, E and Kazamia, E and Lallier, FH and Medina, M and Marzinelli, EM and Morganti, TM and Núñez Pons, L and Prado, S and Pintado, J and Saha, M and Selosse, MA and Skillings, D and Stock, W and Sunagawa, S and Toulza, E and Vorobev, A and Leblanc, C and Not, F}, title = {A community perspective on the concept of marine holobionts: current status, challenges, and future directions.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10911}, pmid = {33665032}, issn = {2167-8359}, support = {U17 CE002001/CE/NCIPC CDC HHS/United States ; }, abstract = {Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.}, }
@article {pmid33660094, year = {2021}, author = {Onyango, CA and Glassom, D and MacDonald, A}, title = {De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress.}, journal = {Molecular biology reports}, volume = {48}, number = {3}, pages = {2083-2092}, pmid = {33660094}, issn = {1573-4978}, mesh = {Animals ; Anthozoa/*genetics/*physiology ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Heat-Shock Response/*genetics ; Molecular Sequence Annotation ; Principal Component Analysis ; *Sequence Analysis, RNA ; Transcriptome/*genetics ; }, abstract = {Rising seawater temperatures cause coral bleaching. The molecular responses of the coral holobiont under stress conditions, determine the success of the symbiosis. Anomastraea irregularis is a hard coral commonly found in the harsh intertidal zones of the south coast of KwaZulu-Natal (KZN), South Africa, where it thrives at the very margins of hard coral distribution in the Western Indian Ocean. To identify the possible molecular and cellular mechanisms underlying its resilience to heat stress, experimental and control nubbins were exposed to temperatures of 29 and 19 °C respectively for 24 h. The transcriptome was assembled de novo from 42.8 million quality controlled 63 bp paired-end short sequence reads obtained via RNA sequencing (RNA-seq). The assembly yielded 333,057 contigs (> 500 bp = 55,626, Largest = 6341 bp N50 = 747 bp). 1362 (1.23%) of the transcripts were significantly differentially expressed between heat stressed and control samples. Log fold change magnitudes among individual genes ranged from - 4.6 to 7.2. Overall, the heat stress response in the A. irregularis constituted a protective response involving up regulation of apoptosis and SUMOylation. Gene ontology (GO) analyses revealed that heat stress in the coral affected the metabolism, protein synthesis, photosynthesis, transport and cytoskeleton. This is the first study to produce a reference transcriptome of this coral species and analyze its response to heat stress. The assembled transcriptome also presents a valuable resource for further transcriptomic and genomic studies.}, }
@article {pmid33652230, year = {2021}, author = {Koonin, EV and Dolja, VV and Krupovic, M}, title = {The healthy human virome: from virus-host symbiosis to disease.}, journal = {Current opinion in virology}, volume = {47}, number = {}, pages = {86-94}, doi = {10.1016/j.coviro.2021.02.002}, pmid = {33652230}, issn = {1879-6265}, mesh = {Bacteriophages/classification/pathogenicity/physiology ; *Host-Pathogen Interactions ; Humans ; *Symbiosis ; Virome/*physiology ; Virus Physiological Phenomena ; Virus Replication ; Viruses/classification/pathogenicity ; }, abstract = {Viruses are ubiquitous, essential components of any ecosystem, and of multicellular organism holobionts. Numerous viruses cause acute infection, killing the host or being cleared by immune system. In many other cases, viruses coexist with the host as symbionts, either temporarily or for the duration of the host's life. Apparently, virus-host relationships span the entire range from aggressive parasitism to mutualism. Here we attempt to delineate the healthy human virome, that is, the entirety of viruses that are present in a healthy human body. The bulk of the healthy virome consists of bacteriophages infecting bacteria in the intestine and other locations. However, a variety of viruses, such as anelloviruses and herpesviruses, and the numerous endogenous retroviruses, persist by replicating in human cells, and these are our primary focus. Crucially, the boundary between symbiotic and pathogenic viruses is fluid such that members of the healthy virome can become pathogens under changing conditions.}, }
@article {pmid33651189, year = {2021}, author = {Yang, X and Xiang, R and Iqbal, NM and Duan, YH and Zhang, XA and Wang, L and Yu, LZ and Li, JZ and Sun, MF and Yang, Q and Zheng, CT and Liao, SQ}, title = {Marinobacter shengliensis subsp. alexandrii Subsp. Nov., Isolated from Cultivable Phycosphere Microbiota of Highly Toxic Dinoflagellate Alexandrium catenella LZT09 and Description of Marinobacter shengliensis Subsp. shengliensis Subsp. Nov.}, journal = {Current microbiology}, volume = {78}, number = {4}, pages = {1648-1655}, pmid = {33651189}, issn = {1432-0991}, support = {41876114//NSFC/ ; 31872460//NSFC/ ; R2020YJ-LJ001//Special Fund for Scientific Innovation Strategy-construction of High Level Academy of Agriculture Science/ ; R2018QD-091//Special Fund for Scientific Innovation Strategy-construction of High Level Academy of Agriculture Science/ ; R2018QD-092//Special Fund for Scientific Innovation Strategy-construction of High Level Academy of Agriculture Science/ ; 201723//Presidential&#xa0;Foundation&#xa0;of&#xa0;GAAS/ ; 201918//Presidential&#xa0;Foundation&#xa0;of&#xa0;GAAS/ ; 201804010338//Guangzhou Municipal Science and Technology Bureau/ ; 201623TD//Discipline Team Building Projects of GAAS in the 13th Five-Year Period/ ; }, mesh = {Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Dinoflagellida/genetics ; Fatty Acids/analysis ; Marinobacter ; *Microbiota ; Nucleic Acid Hybridization ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Phycosphere hosts the boundary of unique holobionts harboring dynamic algae-bacteria interactions. During our investigating the microbial consortia composition of phycosphere microbiota (PM) derived from diverse harmful algal blooms (HAB) dinoflagellates, a novel rod-shaped, motile and faint yellow-pigmented bacterium, designated as strain LZ-6[ T], was isolated from HAB Alexandrium catenella LZT09 which produces high levels paralytic shellfish poisoning toxins. Phylogenetic analysis based on 16S rRNA gene and two housekeeping genes, rpoA and pheS sequences showed that the novel isolate shared the highest gene similarity with Marinobacter shengliensis CGMCC 1.12758[ T] (99.6%) with the similarity values of 99.6%, 99.9% and 98.5%, respectively. Further phylogenomic calculations of average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strains LZ-6[ T] and the type strain of M. shengliensis were 95.9%, 96.4% and 68.5%, respectively. However, combined phenotypic and chemotaxonomic characterizations revealed that the new isolate was obviously different from the type strain of M. shengliensis. The obtained taxonomic evidences supported that strain LZ-6[ T] represents a novel subspecies of M. shengliensis, for which the name is proposed, Marinobacter shengliensis subsp. alexandrii subsp. nov. with the type strain LZ-6[ T] (= CCTCC AB 2018388T[T] = KCTC 72197[ T]). This proposal automatically creates Marinobacter shengliensis subsp. shengliensis for which the type strain is SL013A34A2[T] (= LMG 27740[ T] = CGMCC 1.12758[ T]).}, }
@article {pmid33643235, year = {2021}, author = {Storo, R and Easson, C and Shivji, M and Lopez, JV}, title = {Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {605285}, pmid = {33643235}, issn = {1664-302X}, abstract = {Profiles of symbiotic microbial communities ("microbiomes") can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes of lemon and Caribbean reef sharks. Lemon shark teeth communities (n = 11) contained a high abundance of both Vibrio (10.8 ± 26.0%) and Corynebacterium (1.6 ± 5.1%), genera that can include human pathogenic taxa. The Vibrio (2.8 ± 6.34%) and Kordia (3.1 ± 6.0%) genera and Salmonella enterica (2.6 ± 6.4%) were the most abundant members of nurse shark teeth microbial communities. The Vibrio genus was highly represented in the sandbar shark (54.0 ± 46.0%) and tiger shark (5.8 ± 12.3%) teeth microbiomes. The prevalence of genera containing potential human pathogens could be informative in shark bite treatment protocols and future research to confirm or deny human pathogenicity. We conclude that South Florida sharks host species specific microbiomes that are distinct from their surrounding environment and vary due to differences in microbial community composition among shark species and diversity and composition among anatomical locations. Additionally, when considering the confounding effects of both species and location, microbial community diversity and composition varies.}, }
@article {pmid33624265, year = {2021}, author = {Choi, K and Khan, R and Lee, SW}, title = {Dissection of plant microbiota and plant-microbiome interactions.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {281-291}, pmid = {33624265}, issn = {1976-3794}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Microbial Interactions ; *Microbiota ; Plant Physiological Phenomena ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.}, }
@article {pmid33608555, year = {2021}, author = {Lan, Y and Sun, J and Chen, C and Sun, Y and Zhou, Y and Yang, Y and Zhang, W and Li, R and Zhou, K and Wong, WC and Kwan, YH and Cheng, A and Bougouffa, S and Van Dover, CL and Qiu, JW and Qian, PY}, title = {Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1165}, pmid = {33608555}, issn = {2041-1723}, mesh = {Animals ; Bacteria/*genetics/metabolism ; Gammaproteobacteria/genetics/metabolism ; Gene Expression ; Genome, Bacterial ; Genomics ; Hydrothermal Vents/*microbiology ; Phylogeny ; Snails/*genetics/metabolism/*microbiology ; Sulfur/metabolism ; Symbiosis/*genetics/physiology ; Transcriptome ; }, abstract = {Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host-symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.}, }
@article {pmid33604175, year = {2021}, author = {Nguyen, M and Wemheuer, B and Laffy, PW and Webster, NS and Thomas, T}, title = {Taxonomic, functional and expression analysis of viral communities associated with marine sponges.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10715}, pmid = {33604175}, issn = {2167-8359}, abstract = {Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of 'virus-laden' seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.}, }
@article {pmid33603147, year = {2021}, author = {Jahn, MT and Lachnit, T and Markert, SM and Stigloher, C and Pita, L and Ribes, M and Dutilh, BE and Hentschel, U}, title = {Lifestyle of sponge symbiont phages by host prediction and correlative microscopy.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {2001-2011}, pmid = {33603147}, issn = {1751-7370}, mesh = {Animals ; *Bacteriophages/genetics ; Life Style ; *Microbiota ; Microscopy ; *Porifera ; Symbiosis ; }, abstract = {Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.}, }
@article {pmid33602493, year = {2021}, author = {McFall-Ngai, M and Bosch, TCG}, title = {Animal development in the microbial world: The power of experimental model systems.}, journal = {Current topics in developmental biology}, volume = {141}, number = {}, pages = {371-397}, pmid = {33602493}, issn = {1557-8933}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; R01 AI050661/AI/NIAID NIH HHS/United States ; R01 GM135254/GM/NIGMS NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, mesh = {Aliivibrio fischeri ; Animals ; Decapodiformes/*embryology/*microbiology/physiology ; Embryo, Nonmammalian/microbiology ; Gene Expression Regulation ; Hydra/metabolism/*microbiology ; Light ; *Microbiota ; Symbiosis ; Wnt Signaling Pathway ; }, abstract = {The development of powerful model systems has been a critical strategy for understanding the mechanisms underlying the progression of an animal through its ontogeny. Here we provide two examples that allow deep and mechanistic insight into the development of specific animal systems. Species of the cnidarian genus Hydra have provided excellent models for studying host-microbe interactions and how metaorganisms function in vivo. Studies of the Hawaiian bobtail squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri have been used for over 30 years to understand the impact of a broad array of levels, from ecology to genomics, on the development and persistence of symbiosis. These examples provide an integrated perspective of how developmental processes work and evolve within the context of a microbial world, a new view that opens vast horizons for developmental biology research. The Hydra and the squid systems also lend an example of how profound insights can be discovered by taking advantage of the "experiments" that evolution had done in shaping conserved developmental processes.}, }
@article {pmid33593943, year = {2021}, author = {Andersen, SB and Schluter, J}, title = {A metagenomics approach to investigate microbiome sociobiology.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {10}, pages = {}, pmid = {33593943}, issn = {1091-6490}, mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Sociobiology ; }, }
@article {pmid33583434, year = {2021}, author = {Hudspith, M and Rix, L and Achlatis, M and Bougoure, J and Guagliardo, P and Clode, PL and Webster, NS and Muyzer, G and Pernice, M and de Goeij, JM}, title = {Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {44}, pmid = {33583434}, issn = {2049-2618}, mesh = {Animals ; Carbon/metabolism ; Microbiota/*physiology ; Nitrogen/metabolism ; Nutrients/*metabolism ; Porifera/*metabolism/*microbiology ; *Symbiosis ; }, abstract = {BACKGROUND: Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of [13]C- and [15]N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.<br><br>RESULTS: The two sponge species showed significant enrichment of DOM- and POM-derived [13]C and [15]N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.<br><br>CONCLUSIONS: Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.}, }
@article {pmid33576852, year = {2021}, author = {Zhou, G and Tong, H and Cai, L and Huang, H}, title = {Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {572-580}, pmid = {33576852}, issn = {1432-184X}, support = {41876192//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; Oceans and Seas ; Seawater ; }, abstract = {Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.}, }
@article {pmid33548192, year = {2021}, author = {Iha, C and Dougan, KE and Varela, JA and Avila, V and Jackson, CJ and Bogaert, KA and Chen, Y and Judd, LM and Wick, R and Holt, KE and Pasella, MM and Ricci, F and Repetti, SI and Medina, M and Marcelino, VR and Chan, CX and Verbruggen, H}, title = {Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.}, journal = {Current biology : CB}, volume = {31}, number = {7}, pages = {1393-1402.e5}, doi = {10.1016/j.cub.2021.01.018}, pmid = {33548192}, issn = {1879-0445}, mesh = {Adaptation, Biological/*genetics ; Animals ; *Anthozoa ; Chlorophyta/*genetics ; *Genomics ; *Symbiosis ; }, abstract = {The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.}, }
@article {pmid33546771, year = {2021}, author = {Piccinni, MZ and Watts, JEM and Fourny, M and Guille, M and Robson, SC}, title = {The skin microbiome of Xenopus laevis and the effects of husbandry conditions.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {17}, pmid = {33546771}, issn = {2524-4671}, support = {NC/P001009/1/NC3RS_/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom ; 212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1//Biotechnology and Biological Sciences Research Council (GB)/ ; E3//Research England/ ; }, abstract = {BACKGROUND: Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a "low microbial load" or "clean" state, where embryos are surface sterilized before entering the housing system; instead of the conventional, "standard" conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, "clean" and "standard" husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies.<br><br>RESULTS: We found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity.<br><br>CONCLUSIONS: Our findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.}, }
@article {pmid33542710, year = {2020}, author = {Marzocchi, U and Bonaglia, S and Zaiko, A and Quero, GM and Vybernaite-Lubiene, I and Politi, T and Samuiloviene, A and Zilius, M and Bartoli, M and Cardini, U}, title = {Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {610269}, pmid = {33542710}, issn = {1664-302X}, abstract = {Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.}, }
@article {pmid33537923, year = {2021}, author = {Overby, HB and Ferguson, JF}, title = {Gut Microbiota-Derived Short-Chain Fatty Acids Facilitate Microbiota:Host Cross talk and Modulate Obesity and Hypertension.}, journal = {Current hypertension reports}, volume = {23}, number = {2}, pages = {8}, pmid = {33537923}, issn = {1534-3111}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK117144/DK/NIDDK NIH HHS/United States ; R01 HL142856/HL/NHLBI NIH HHS/United States ; R01DK117144/NH/NIH HHS/United States ; }, mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; *Hypertension ; *Microbiota ; Obesity ; }, abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize the evidence supporting a role of short-chain fatty acids (SCFAs) as messengers facilitating cross talk between the host and gut microbiota and discuss the effects of altered SCFA signaling in obesity and hypertension.<br><br>RECENT FINDINGS: Recent evidence suggests there to be a significant contribution of gut microbiota-derived SCFAs to microbe:host communication and host metabolism. SCFA production within the intestine modulates intestinal pH, microbial composition, and intestinal barrier integrity. SCFA signaling through host receptors, such as PPAR&#x3b3; and GPCRs, modulates host health and disease physiology. Alterations in SCFA signaling and downstream effects on inflammation are implicated in the development of obesity and hypertension. SCFAs are crucial components of the holobiont relationship; in the proper environment, they support normal gut, immune, and metabolic function. Dysregulation of microbial SCFA signaling affects downstream host metabolism, with implications in obesity and hypertension.}, }
@article {pmid33536938, year = {2020}, author = {Wang, J and Chen, J and Wang, S and Li, F and Fu, C and Wang, Y}, title = {Monoclonal Culture and Characterization of Symbiodiniaceae C1 Strain From the Scleractinian Coral Galaxea fascicularis.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {621111}, pmid = {33536938}, issn = {1664-042X}, abstract = {The symbiosis between cnidarian hosts and photosynthetic dinoflagellates of the family Symbiodiniaceae (i.e., zooxanthellae) provides the energy foundation of coral reef ecosystems in oligotrophic waters. The structure of symbiont biota and the dominant species of algal symbiont partly shape the environmental adaptability of coral symbiotes. In this study, the algal symbiont cells were isolated from the tentacles of Galaxea fascicularis, a hermatypic coral with obvious differentiation in heat resistance, and were cultured in vitro with an improved L1 medium. An algal monoclonal cell line was established using separated algal culture drops and soft agar plating method, and named by GF19C1 as it was identified as Cladocopium sp. C1 (Symbiodiniaceae) based on its ITS1, ITS2, and the non-coding region of the plastid psbA minicircle (psbA [ncr]) sequences. Most GF19C1 cells were at the coccoid stage of the gymnodinioid, their markedly thickened (ca. two times) cell wall suggests that they developed into vegetative cysts and have sexual and asexual reproductive potential. The average diameter of GF19C1 cells decreased significantly, probably due to the increasing mitotic rate. The chloroplasts volume density of GF19C1 was significantly lower than that of their symbiotic congeners, while the surface area density of thylakoids relative to volumes of chloroplasts was not significantly changed. The volume fraction of vacuoles increased by nearly fivefold, but there was no significant change in mitochondria and accumulation bodies. Light-temperature orthogonal experiments showed that, GF19C1 growth preferred the temperature 25 ± 1°C (at which it is maintained post-isolation) rather than 28 ± 1°C under the light intensity of 42 ± 2 or 62 ± 2 μmol photons m[-2] s[-1], indicating an inertia for temperature adaptation. The optimum salinity for GF19C1 growth ranged between 28-32 ppt. The monoclonal culture techniques established in this study were critical to clarify the physiological and ecological characteristics of various algal symbiont species, and will be instrumental to further reveal the roles of algal symbionts in the adaptive differentiation of coral-zooxanthellae holobionts in future studies.}, }
@article {pmid33528835, year = {2021}, author = {Molins, A and Moya, P and Muggia, L and Barreno, E}, title = {Thallus Growth Stage and Geographic Origin Shape Microalgal Diversity in Ramalina farinacea Lichen Holobionts.}, journal = {Journal of phycology}, volume = {57}, number = {3}, pages = {975-987}, doi = {10.1111/jpy.13140}, pmid = {33528835}, issn = {1529-8817}, mesh = {*Ascomycota ; *Chlorophyta/genetics ; *Lichens ; *Microalgae ; Symbiosis ; }, abstract = {Lichen symbioses are microecosystems hosting many other living organisms besides the two major lichen symbionts (i.e., lichenized fungi [the mycobiont] and green microalgae or cyanobacteria [the photobiont]). Recent investigations evidenced that other fungi, non-photosynthetic bacteria, and microalgae co-inhabit within the lichen thalli, but their diversity and their roles are still underinvestigated. Here we present an ad hoc stratified sampling design and in-depth Illumina paired-end metabarcoding approach to explore microalgal diversity in lichen thalli of the model species Ramalina farinacea from different ecologies. Lichen thalli were surveyed according to three different sizes, and different thallus parts were considered for molecular, bioinformatics, and community diversity analyses. The results revealed that microalgal diversity strongly depends on the growth stage of the thalli, the geographic area, and the habitat type. The results also show that microalgal diversity does not vary along the thallus branches (lacinias)-that is, it does not correlate with the apical growth and founder effects-and that there is no balanced co-presence of two main photobionts as previously established in R. farinacea. The sampling design performed here minimizes bias in the assessment of photobiont diversity in lichens and is proposed to be reliable and applicable to further study microalgal diversity in lichen symbioses.}, }
@article {pmid33523848, year = {2021}, author = {Williams, A and Chiles, EN and Conetta, D and Pathmanathan, JS and Cleves, PA and Putnam, HM and Su, X and Bhattacharya, D}, title = {Metabolomic shifts associated with heat stress in coral holobionts.}, journal = {Science advances}, volume = {7}, number = {1}, pages = {}, pmid = {33523848}, issn = {2375-2548}, support = {P30 CA072720/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida/physiology ; Dipeptides ; Heat-Shock Response ; *Sea Anemones ; Symbiosis ; }, abstract = {Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is "coral bleaching," usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral.}, }
@article {pmid33519751, year = {2020}, author = {Alibrandi, P and Schnell, S and Perotto, S and Cardinale, M}, title = {Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {604964}, pmid = {33519751}, issn = {1664-302X}, abstract = {The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.}, }
@article {pmid33504360, year = {2021}, author = {Wicaksono, WA and Kusstatscher, P and Erschen, S and Reisenhofer-Graber, T and Grube, M and Cernava, T and Berg, G}, title = {Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {29}, pmid = {33504360}, issn = {2049-2618}, support = {P 29285/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Anti-Infective Agents/*pharmacology ; Ascomycota/*drug effects/*genetics ; Colistin/pharmacology ; Drug Resistance, Microbial/*drug effects/*genetics ; Glycine/analogs &amp; derivatives/pharmacology ; Microbiota/*drug effects/*genetics ; Pyrazines/pharmacology ; RNA, Ribosomal, 16S/genetics ; Tetracycline/pharmacology ; Glyphosate ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.<br><br>RESULTS: The&#xa0;analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria&#xa0;as well as other diverse and abundant&#xa0;bacterial communities (up to 10[8] 16S rRNA gene copies ng[-1] DNA) dominated by Alphaproteobacteria and Bacteroidetes.&#xa0;Moreover, the natural resistome of this&#xa0;meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different&#xa0;concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure&#xa0;and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the&#xa0;clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials.&#xa0;Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes&#xa0;suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders,&#xa0;Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.<br><br>CONCLUSIONS: Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.}, }
@article {pmid33500473, year = {2021}, author = {Sivaguru, M and Todorov, LG and Miller, CAH and Fouke, CE and Munro, CMO and Fouke, KW and Fouke, KE and Baughman, ME and Fouke, BW}, title = {Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2230}, pmid = {33500473}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/physiology ; Climate Change ; Dinoflagellida/physiology ; Female ; Magnetic Resonance Angiography ; Male ; Photosynthesis/physiology ; Sleep Wake Disorders/*physiopathology ; }, abstract = {The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.}, }
@article {pmid33500354, year = {2021}, author = {Rädecker, N and Pogoreutz, C and Gegner, HM and Cárdenas, A and Roth, F and Bougoure, J and Guagliardo, P and Wild, C and Pernice, M and Raina, JB and Meibom, A and Voolstra, CR}, title = {Heat stress destabilizes symbiotic nutrient cycling in corals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {5}, pages = {}, pmid = {33500354}, issn = {1091-6490}, mesh = {Amino Acids/metabolism ; Ammonium Compounds/metabolism ; Animals ; Anthozoa/genetics/*physiology ; Carbon/metabolism ; Gene Expression Regulation ; Heat-Shock Response/*physiology ; Models, Biological ; Nitrogen/metabolism ; *Nutrients ; Oxidative Stress ; Photosynthesis ; Symbiosis/*physiology ; }, abstract = {Recurrent mass bleaching events are pushing coral reefs worldwide to the brink of ecological collapse. While the symptoms and consequences of this breakdown of the coral-algal symbiosis have been extensively characterized, our understanding of the underlying causes remains incomplete. Here, we investigated the nutrient fluxes and the physiological as well as molecular responses of the widespread coral Stylophora pistillata to heat stress prior to the onset of bleaching to identify processes involved in the breakdown of the coral-algal symbiosis. We show that altered nutrient cycling during heat stress is a primary driver of the functional breakdown of the symbiosis. Heat stress increased the metabolic energy demand of the coral host, which was compensated by the catabolic degradation of amino acids. The resulting shift from net uptake to release of ammonium by the coral holobiont subsequently promoted the growth of algal symbionts and retention of photosynthates. Together, these processes form a feedback loop that will gradually lead to the decoupling of carbon translocation from the symbiont to the host. Energy limitation and altered symbiotic nutrient cycling are thus key factors in the early heat stress response, directly contributing to the breakdown of the coral-algal symbiosis. Interpreting the stability of the coral holobiont in light of its metabolic interactions provides a missing link in our understanding of the environmental drivers of bleaching and may ultimately help uncover fundamental processes underpinning the functioning of endosymbioses in general.}, }
@article {pmid33499978, year = {2020}, author = {Zanotti, AA and Gregoracci, GB and Capel, KCC and Kitahara, MV}, title = {Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {29}, pmid = {33499978}, issn = {2524-4671}, support = {2014/01332-0//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 301436/2018-5//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {BACKGROUND: Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts' fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with sun-coral larvae and adult colonies from a locality displaying a high invasion development.<br><br>RESULTS: The usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis' microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species.<br><br>CONCLUSION: Although diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.}, }
@article {pmid33489789, year = {2021}, author = {Macchi, M and Festa, S and Nieto, E and Irazoqui, JM and Vega-Vela, NE and Junca, H and Valacco, MP and Amadio, AF and Morelli, IS and Coppotelli, BM}, title = {Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {29}, number = {}, pages = {e00588}, pmid = {33489789}, issn = {2215-017X}, abstract = {Two synthetic bacterial consortia (SC) composed of bacterial strains Sphingobium sp. (AM), Klebsiella aerogenes (B), Pseudomonas sp. (Bc-h and T), Burkholderia sp. (Bk) and Inquilinus limosus (Inq) isolated from a natural phenanthrene (PHN)-degrading consortium (CON) were developed and evaluated as an alternative approach to PHN biodegradation in bioremediation processes. A metabolic network showing the potential role of strains was reconstructed by in silico study of the six genomes and classification of dioxygenase enzymes using RHObase and AromaDeg databases. Network analysis suggested that AM and Bk were responsible for PHN initial attack, while Inq, B, T and Bc-h would degrade PHN metabolites. The predicted roles were further confirmed by physiological, RT-qPCR and metaproteomic assays. SC-1 with AM as the sole PHN degrader was the most efficient. The ecological roles inferred in this study can be applied to optimize the design of bacterial consortia and tackle the biodegradation of complex environmental pollutants.}, }
@article {pmid33488540, year = {2020}, author = {Freitas-Silva, J and de Oliveira, BFR and Vigoder, FM and Muricy, G and Dobson, ADW and Laport, MS}, title = {Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha).}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {592735}, pmid = {33488540}, issn = {1664-302X}, abstract = {Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.}, }
@article {pmid33484584, year = {2021}, author = {Eckert, EM and Anicic, N and Fontaneto, D}, title = {Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment.}, journal = {Molecular ecology}, volume = {30}, number = {6}, pages = {1545-1558}, doi = {10.1111/mec.15815}, pmid = {33484584}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Fresh Water ; *Microbiota/genetics ; Zooplankton/genetics ; }, abstract = {The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co-evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species-specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of "core" microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co-evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host-microbiome association to originate and persist.}, }
@article {pmid33479490, year = {2021}, author = {Bonthond, G and Bayer, T and Krueger-Hadfield, SA and Stärck, N and Wang, G and Nakaoka, M and Künzel, S and Weinberger, F}, title = {The role of host promiscuity in the invasion process of a seaweed holobiont.}, journal = {The ISME journal}, volume = {15}, number = {6}, pages = {1668-1679}, pmid = {33479490}, issn = {1751-7370}, mesh = {Humans ; Introduced Species ; *Microbiota ; *Rhodophyta ; *Seaweed ; }, abstract = {Invasive species are co-introduced with microbiota from their native range and also interact with microbiota found in the novel environment to which they are introduced. Host flexibility toward microbiota, or host promiscuity, is an important trait underlying terrestrial plant invasions. To test whether host promiscuity may be important in macroalgal invasions, we experimentally simulated an invasion in a common garden setting, using the widespread invasive macroalga Agarophyton vermiculophyllum as a model invasive seaweed holobiont. After disturbing the microbiota of individuals from native and non-native populations with antibiotics, we monitored the microbial succession trajectories in the presence of a new source of microbes. Microbial communities were strongly impacted by the treatment and changed compositionally and in terms of diversity but recovered functionally by the end of the experiment in most respects. Beta-diversity in disturbed holobionts strongly decreased, indicating that different populations configure more similar -or more common- microbial communities when exposed to the same conditions. This decline in beta-diversity occurred not only more rapidly, but was also more pronounced in non-native populations, while individuals from native populations retained communities more similar to those observed in the field. This study demonstrates that microbial communities of non-native A. vermiculophyllum are more flexibly adjusted to the environment and suggests that an intraspecific increase in host promiscuity has promoted the invasion process of A. vermiculophyllum. This phenomenon may be important among invasive macroalgal holobionts in general.}, }
@article {pmid33466994, year = {2021}, author = {Ferrier-Pagès, C and Martinez, S and Grover, R and Cybulski, J and Shemesh, E and Tchernov, D}, title = {Tracing the Trophic Plasticity of the Coral-Dinoflagellate Symbiosis Using Amino Acid Compound-Specific Stable Isotope Analysis.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33466994}, issn = {2076-2607}, abstract = {The association between corals and photosynthetic dinoflagellates is one of the most well-known nutritional symbioses, but nowadays it is threatened by global changes. Nutritional exchanges are critical to understanding the performance of this symbiosis under stress conditions. Here, compound-specific δ[15]N and δ[13]C values of amino acids (δ[15]NAA and δ[13]CAA) were assessed in autotrophic, mixotrophic and heterotrophic holobionts as diagnostic tools to follow nutritional interactions between the partners. Contrary to what was expected, heterotrophy was mainly traced through the δ[15]N of the symbiont's amino acids (AAs), suggesting that symbionts directly profit from host heterotrophy. The trophic index (TP) ranged from 1.1 to 2.3 from autotrophic to heterotrophic symbionts. In addition, changes in TP across conditions were more significant in the symbionts than in the host. The similar δ[13]C-AAs signatures of host and symbionts further suggests that symbiont-derived photosynthates are the main source of carbon for AAs synthesis. Symbionts, therefore, appear to be a key component in the AAs biosynthetic pathways, and might, via this obligatory function, play an essential role in the capacity of corals to withstand environmental stress. These novel findings highlight important aspects of the nutritional exchanges in the coral-dinoflagellates symbiosis. In addition, they feature δ[15]NAA as a useful tool for studies regarding the nutritional exchanges within the coral-symbiodiniaceae symbiosis.}, }
@article {pmid33462310, year = {2021}, author = {Carradec, Q and Poulain, J and Boissin, E and Hume, BCC and Voolstra, CR and Ziegler, M and Engelen, S and Cruaud, C and Planes, S and Wincker, P}, title = {Author Correction: A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2076}, doi = {10.1038/s41598-021-81544-6}, pmid = {33462310}, issn = {2045-2322}, }
@article {pmid33444387, year = {2021}, author = {Egfjord, AF and Margaryan, A and Fischer, A and Sjögren, KG and Price, TD and Johannsen, NN and Nielsen, PO and Sørensen, L and Willerslev, E and Iversen, R and Sikora, M and Kristiansen, K and Allentoft, ME}, title = {Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark.}, journal = {PloS one}, volume = {16}, number = {1}, pages = {e0244872}, pmid = {33444387}, issn = {1932-6203}, mesh = {*Archaeology ; DNA, Ancient ; Denmark ; Female ; *Genomics ; Haplotypes ; History, Ancient ; Human Migration ; Humans ; Male ; Sex Determination Analysis ; Skeleton/*metabolism ; }, abstract = {The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500-2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.}, }
@article {pmid33440837, year = {2021}, author = {Bredon, M and Depuydt, E and Brisson, L and Moulin, L and Charles, C and Haenn, S and Moumen, B and Bouchon, D}, title = {Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33440837}, issn = {2076-2607}, support = {BiodivUP//State-Region Planning Contracts (CPER), European Regional Development Fund (FEDER)/ ; }, abstract = {The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host's diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the "eco-holobiont" conceptualization of macroorganisms.}, }
@article {pmid33436514, year = {2021}, author = {Fagorzi, C and Bacci, G and Huang, R and Cangioli, L and Checcucci, A and Fini, M and Perrin, E and Natali, C and diCenzo, GC and Mengoni, A}, title = {Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436514}, issn = {2379-5077}, abstract = {Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.}, }
@article {pmid33435275, year = {2021}, author = {Mannaa, M and Seo, YS}, title = {Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33435275}, issn = {2223-7747}, abstract = {Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes-differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions-are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant's biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen-one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen-one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.}, }
@article {pmid33434804, year = {2021}, author = {Zhang, Y and Yang, Q and Zhang, Y and Ahmad, M and Ling, J and Tang, X and Dong, J}, title = {Shifts in abundance and network complexity of coral bacteria in response to elevated ammonium stress.}, journal = {The Science of the total environment}, volume = {768}, number = {}, pages = {144631}, doi = {10.1016/j.scitotenv.2020.144631}, pmid = {33434804}, issn = {1879-1026}, mesh = {*Ammonium Compounds ; Animals ; *Anthozoa ; Bacteria/genetics ; Chlorophyll A ; Coral Reefs ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral bacteria are highly dynamic and acutely affected by host health and environmental conditions. However, there is limited knowledge of how the dynamics of coral-associated bacterial communities and interactions among bacterial members change in response to dissolved inorganic nutrient stressors. Here, we used high-throughput sequencing of the 16S rRNA gene to examine dynamic changes in coral-associated bacterial communities under elevated ammonium stress. Short-term exposure to high levels of ammonium does not significantly harm coral holobiont. Physiological parameters such as carbohydrate, chlorophyll a, and lipid content of coral holobiont were not affected. After three weeks of elevated ammonium stress, however, the coral-associated bacterial community changed significantly. The abundance of certain bacterial populations increased significantly, with enrichment of pathogenic and opportunistic bacteria and a decrease in defensive and core bacteria. Keystone bacterial species in the co-occurrence network changed considerably. Under elevated ammonium stress, the abundance of keystone species associated with corals was lower and the complexity of keystone bacterial relationships decreased significantly. Our results indicate that bacteria respond to elevated ammonium stress through changes in abundance and co-occurrence among bacterial members. This precedes visual symptoms of changes in coral physiological conditions and could be used as an early warning indicator of elevated ammonium stress in coastal coral reef management.}, }
@article {pmid33417693, year = {2021}, author = {Bonacolta, AM and Connelly, MT and Rosales, SM and Del Campo, J and Traylor-Knowles, N}, title = {The starlet sea anemone, Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum.}, journal = {FEMS microbiology letters}, volume = {368}, number = {3}, pages = {}, doi = {10.1093/femsle/fnab002}, pmid = {33417693}, issn = {1574-6968}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Host Microbial Interactions/*physiology ; Microbiota/genetics ; Phylogeny ; Sea Anemones/*microbiology ; Spirochaetales/*genetics ; }, abstract = {Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.}, }
@article {pmid33409285, year = {2020}, author = {Martinez, S and Kolodny, Y and Shemesh, E and Scucchia, F and Nevo, R and Levin-Zaidman, S and Paltiel, Y and Keren, N and Tchernov, D and Mass, T}, title = {Energy Sources of the Depth-Generalist Mixotrophic Coral Stylophora pistillata.}, journal = {Frontiers in Marine Science}, volume = {7}, number = {}, pages = {988}, pmid = {33409285}, issn = {2296-7745}, support = {755876/ERC_/European Research Council/International ; }, abstract = {Energy sources of corals, ultimately sunlight and plankton availability, change dramatically from shallow to mesophotic (30-150 m) reefs. Depth-generalist corals, those that occupy both of these two distinct ecosystems, are adapted to cope with such extremely diverse conditions. In this study, we investigated the trophic strategy of the depth-generalist hermatypic coral Stylophora pistillata and the ability of mesophotic colonies to adapt to shallow reefs. We compared symbiont genera composition, photosynthetic traits and the holobiont trophic position and carbon sources, calculated from amino acids compound-specific stable isotope analysis (AA-CSIA), of shallow, mesophotic and translocated corals. This species harbors different Symbiodiniaceae genera at the two depths: Cladocopium goreaui (dominant in mesophotic colonies) and Symbiodinium microadriaticum (dominant in shallow colonies) with a limited change after transplantation. This allowed us to determine which traits stem from hosting different symbiont species compositions across the depth gradient. Calculation of holobiont trophic position based on amino acid δ[15]N revealed that heterotrophy represents the same portion of the total energy budget in both depths, in contrast to the dogma that predation is higher in corals growing in low light conditions. Photosynthesis is the major carbon source to corals growing at both depths, but the photosynthetic rate is higher in the shallow reef corals, implicating both higher energy consumption and higher predation rate in the shallow habitat. In the corals transplanted from deep to shallow reef, we observed extensive photo-acclimation by the Symbiodiniaceae cells, including substantial cellular morphological modifications, increased cellular chlorophyll a, lower antennae to photosystems ratios and carbon signature similar to the local shallow colonies. In contrast, non-photochemical quenching remains low and does not increase to cope with the high light regime of the shallow reef. Furthermore, host acclimation is much slower in these deep-to-shallow transplanted corals as evident from the lower trophic position and tissue density compared to the shallow-water corals, even after long-term transplantation (18 months). Our results suggest that while mesophotic reefs could serve as a potential refuge for shallow corals, the transition is complex, as even after a year and a half the acclimation is only partial.}, }
@article {pmid33392741, year = {2021}, author = {Taulé, C and Vaz-Jauri, P and Battistoni, F}, title = {Insights into the early stages of plant-endophytic bacteria interaction.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {37}, number = {1}, pages = {13}, pmid = {33392741}, issn = {1573-0972}, mesh = {Bacteria ; *Bacterial Physiological Phenomena ; Endophytes/*physiology ; Host Microbial Interactions/*physiology ; Microbiota ; Plant Development ; Plant Roots/microbiology ; Plants/*microbiology ; Seeds/growth &amp; development/microbiology ; Soil ; Soil Microbiology ; }, abstract = {The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.}, }
@article {pmid33389691, year = {2022}, author = {Miquel, PA and Hwang, SY}, title = {On biological individuation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {141}, number = {2}, pages = {203-211}, pmid = {33389691}, issn = {1611-7530}, mesh = {Computer Simulation ; *Earth, Planet ; *Individuation ; Kinetics ; }, abstract = {In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R1) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change as the fact that their structure is the recursive result of their operations (R2). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R1R2) operators are applied to themselves, so that RN = (R1R2)N. We suggest that under specific thermodynamic (open systems out of equilibrium) and chemical conditions (autocatalysis, kinetic dynamic stability), this mapping can go up to a limit characterized by a fixed-point equation: [Formula: see text]. In this equation, ([Formula: see text]) symbolizes a regime of permanent resonance characterizing the biosphere, as open from inside, by the recursive differential relation between the biosphere and all its holobionts. As such the biosphere is closed on itself as a pure differential entity. ([Formula: see text]) symbolizes the regime of permanent change characterizing the emergence of evolution in the biosphere. As such the biosphere is closed on itself, by the principle of descent with modifications, and by the fact that every holobiont evolves in a niche, while evolving with it.}, }
@article {pmid33364590, year = {2021}, author = {Niemann, J and Gopalakrishnan, S and Yamaguchi, N and Ramos-Madrigal, J and Wales, N and Gilbert, MTP and Sinding, MS}, title = {Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū.}, journal = {iScience}, volume = {24}, number = {1}, pages = {101904}, pmid = {33364590}, issn = {2589-0042}, abstract = {The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding.}, }
@article {pmid33342999, year = {2021}, author = {Babbin, AR and Tamasi, T and Dumit, D and Weber, L and Rodríguez, MVI and Schwartz, SL and Armenteros, M and Wankel, SD and Apprill, A}, title = {Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1222-1235}, pmid = {33342999}, issn = {1751-7370}, mesh = {Anaerobiosis ; Animals ; *Anthozoa ; Coral Reefs ; *Microbiota ; Nitrogen ; }, abstract = {Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use [15]N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm[-2] d[-1]. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.}, }
@article {pmid33327517, year = {2020}, author = {Menaa, F and Wijesinghe, PAUI and Thiripuranathar, G and Uzair, B and Iqbal, H and Khan, BA and Menaa, B}, title = {Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions.}, journal = {Marine drugs}, volume = {18}, number = {12}, pages = {}, pmid = {33327517}, issn = {1660-3397}, mesh = {Animals ; *Ecology ; Humans ; *Industry ; *Microbiota ; Seaweed/*chemistry ; }, abstract = {Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)-microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.}, }
@article {pmid33326321, year = {2021}, author = {Lim, SY and You, H and Lee, J and Lee, J and Lee, Y and Lee, KA and Kim, B and Lee, JH and Jeong, J and Jang, S and Kim, B and Choi, H and Hwang, G and Choi, MS and Yoon, SE and Kwon, JY and Lee, WJ and Kim, YJ and Suh, GSB}, title = {Identification and characterization of GAL4 drivers that mark distinct cell types and regions in the Drosophila adult gut.}, journal = {Journal of neurogenetics}, volume = {35}, number = {1}, pages = {33-44}, doi = {10.1080/01677063.2020.1853722}, pmid = {33326321}, issn = {1563-5260}, mesh = {Animals ; Brain-Gut Axis/physiology ; Drosophila Proteins/*genetics/metabolism ; Drosophila melanogaster ; Enteric Nervous System/*metabolism ; Gastrointestinal Tract/*metabolism ; *Gene Expression Regulation, Developmental ; Neurons/*metabolism ; Transcription Factors/*genetics/metabolism ; }, abstract = {The gastrointestinal tract in the adult Drosophila serves as a model system for exploring the mechanisms underlying digestion, absorption and excretion, stem cell plasticity, and inter-organ communication, particularly through the gut-brain axis. It is also useful for studying the cellular and adaptive responses to dietary changes, alterations in microbiota and immunity, and systematic and endocrine signals. Despite the various cell types and distinct regions in the gastrointestinal tract, few tools are available to target and manipulate the activity of each cell type and region, and their gene expression. Here, we report 353 GAL4 lines and several split-GAL4 lines that are expressed in enteric neurons (ENs), progenitors (ISCs and EBs), enterocytes (ECs), enteroendocrine cells (EEs), or/and other cell types that are yet to be identified in distinct regions of the gut. We had initially collected approximately 600 GAL4 lines that may be expressed in the gut based on RNA sequencing data, and then crossed them to UAS-GFP to perform immunohistochemistry to identify those that are expressed selectively in the gut. The cell types and regional expression patterns that are associated with the entire set of GAL4 drivers and split-GAL4 combinations are annotated online at http://kdrc.kr/index.php (K-Gut Project). This GAL4 resource can be used to target specific populations of distinct cell types in the fly gut, and therefore, should permit a more precise investigation of gut cells that regulate important biological processes.}, }
@article {pmid33324385, year = {2020}, author = {Mironov, T and Sabaneyeva, E}, title = {A Robust Symbiotic Relationship Between the Ciliate Paramecium multimicronucleatum and the Bacterium Ca. Trichorickettsia Mobilis.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {603335}, pmid = {33324385}, issn = {1664-302X}, abstract = {Close reciprocal interactions in symbiotic systems have suggested the holobiont concept, in which the host and its microbiota are considered as a single entity. Ciliates are known for their ability to form symbiotic associations with prokaryotes. Relationships between the partners in such systems vary from mutualism to parasitism and differ significantly in their robustness. We assessed the viability of the ciliate Paramecium multimicronucleatum and its ability to maintain its intranuclear endosymbiont Ca. Trichorickettsia mobilis (Rickettsiaceae) after treatment with antibiotics characterized by different mode of action, such as ampicillin, streptomycin, chloramphenicol, tetracycline. The presence of endosymbionts in the host cell was determined by means of living cell observations made using differential interference contrast or fluorescence in situ hybridization with the species-specific oligonucleotide probe (FISH). Administration of antibiotics traditionally used in treatments of rickettsioses, tetracycline and chloramphenicol, depending on the concentration used and the ciliate strain treated, either caused death of both, infected and control cells, or did not affect the ability of the host to maintain the intranuclear endosymbiont. The surviving cells always manifested motile bacteria in the macronucleus. Streptomycin treatment never led to the loss of endosymbionts in any of the four infected strains, and nearly all ciliates remained viable. Ampicillin treatment never caused host cell death, but resulted in formation of filamentous and immobile oval bacterial forms. Under repeated ampicillin treatments, a part of endosymbionts was registered in the host cytoplasm, as evidenced both by FISH and transmission electron microscopy. Endosymbionts located in the host cytoplasm were enclosed in vacuoles, apparently, corresponding to autophagosomes. Nevertheless, the bacteria seemed to persist in this compartment and might cause relapse of the infection. Although the antibiotic sensitivity profile of Trichorickettsia seems to resemble that of other representatives of Rickettsiaceae, causative agents of severe diseases in humans, neither of the antibiotic treatments used in this study resulted in an aposymbiotic cell line, apparently, due to the protists' sensitivity to tetracyclines, the drugs of preference in rickettsiosis treatment. The observed robustness of this symbiotic system makes it a good model for further elaboration of the holobiont concept.}, }
@article {pmid33323078, year = {2020}, author = {Lyndby, NH and Rädecker, N and Bessette, S and Søgaard Jensen, LH and Escrig, S and Trampe, E and Kühl, M and Meibom, A}, title = {Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea-Symbiodiniaceae symbiosis.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1941}, pages = {20202393}, pmid = {33323078}, issn = {1471-2954}, mesh = {Ammonium Compounds ; Animals ; Anthozoa ; Dinoflagellida/*physiology ; Ecosystem ; Nitrogen/metabolism ; Nutrients ; Photosynthesis ; Scyphozoa/*physiology ; Symbiosis/*physiology ; }, abstract = {The upside-down jellyfish Cassiopea engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. By contrast to most other symbiotic cnidarians, algal endosymbionts in Cassiopea are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in Cassiopea remains unknown. By combining isotopic labelling experiments with correlated scanning electron microscopy, and Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging, we quantified the anabolic assimilation of inorganic carbon and nitrogen at the subcellular level in juvenile Cassiopea medusae bell tissue. Amoebocytes were clustered near the sub-umbrella epidermis and facilitated efficient assimilation of inorganic nutrients. Photosynthetically fixed carbon was efficiently translocated between endosymbionts, amoebocytes and host epidermis at rates similar to or exceeding those observed in corals. The Cassiopea holobionts efficiently assimilated ammonium, while no nitrate assimilation was detected, possibly reflecting adaptation to highly dynamic environmental conditions of their natural habitat. The motile amoebocytes allow Cassiopea medusae to distribute their endosymbiont population to optimize access to light and nutrients, and transport nutrition between tissue areas. Amoebocytes thus play a vital role for the assimilation and translocation of nutrients in Cassiopea, providing an interesting new model for studies of metabolic interactions in photosymbiotic marine organisms.}, }
@article {pmid33322780, year = {2020}, author = {Oliveira, BFR and Lopes, IR and Canellas, ALB and Muricy, G and Dobson, ADW and Laport, MS}, title = {Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33322780}, issn = {2076-2607}, abstract = {Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.}, }
@article {pmid33322411, year = {2020}, author = {Bombin, A and Cunneely, O and Eickman, K and Bombin, S and Ruesy, A and Su, M and Myers, A and Cowan, R and Reed, L}, title = {Influence of Lab Adapted Natural Diet and Microbiota on Life History and Metabolic Phenotype of Drosophila melanogaster.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33322411}, issn = {2076-2607}, support = {R01 GM098856/GM/NIGMS NIH HHS/United States ; }, abstract = {Symbiotic microbiota can help its host to overcome nutritional challenges, which is consistent with a holobiont theory of evolution. Our project investigated the effects produced by the microbiota community, acquired from the environment and horizontal transfer, on metabolic traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster, from ten wild-derived genetic lines on naturally fermented peaches, preserving genuine microbial conditions. Larvae raised on the natural and standard lab diets were significantly different in every tested phenotype. Frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development. On the peach diet, the presence of parental microbiota increased the weight and development rate. Larvae raised on each tested diet formed microbial communities distinct from each other. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.}, }
@article {pmid33321044, year = {2021}, author = {Peixoto, RS and Sweet, M and Villela, HDM and Cardoso, P and Thomas, T and Voolstra, CR and Høj, L and Bourne, DG}, title = {Coral Probiotics: Premise, Promise, Prospects.}, journal = {Annual review of animal biosciences}, volume = {9}, number = {}, pages = {265-288}, doi = {10.1146/annurev-animal-090120-115444}, pmid = {33321044}, issn = {2165-8110}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida ; Microbiota ; *Probiotics ; Symbiosis ; }, abstract = {The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.}, }
@article {pmid33316514, year = {2021}, author = {Valdespino-Castillo, PM and Bautista-García, A and Favoretto, F and Merino-Ibarra, M and Alcántara-Hernández, RJ and Pi-Puig, T and Castillo, FS and Espinosa-Matías, S and Holman, HY and Blanco-Jarvio, A}, title = {Interplay of microbial communities with mineral environments in coralline algae.}, journal = {The Science of the total environment}, volume = {757}, number = {}, pages = {143877}, doi = {10.1016/j.scitotenv.2020.143877}, pmid = {33316514}, issn = {1879-1026}, mesh = {Biodiversity ; Humans ; *Microbiota ; Minerals ; *Rhodophyta ; Temperature ; }, abstract = {Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO2 world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.}, }
@article {pmid33316299, year = {2021}, author = {Sukhoverkhov, AV and Gontier, N}, title = {Non-genetic inheritance: Evolution above the organismal level.}, journal = {Bio Systems}, volume = {200}, number = {}, pages = {104325}, doi = {10.1016/j.biosystems.2020.104325}, pmid = {33316299}, issn = {1872-8324}, mesh = {Adaptation, Physiological/*physiology ; Animals ; *Biological Evolution ; Humans ; Inheritance Patterns/*physiology ; *Models, Theoretical ; Phenotype ; *Social Behavior ; }, abstract = {The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less on community system traits (synergetic/organizational traits) that characterize transgenerational biological, ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of interacting populations, and for which the individual members can belong to the same or to different species. Examples of communities include biofilms, ant colonies, symbiotic associations resulting in holobiont formation, and human societies. The proposed model of evolution at the level of communities revises classic theorizing on the major transitions in evolution by analyzing the interplay between community/social traits and individual traits, and how this brings forth ideas of top-down regulations of bottom-up evolutionary processes (collaboration of downward and upward causation). The work demonstrates that such interplay also includes reticulate interactions and reticulate causation. In this regard, we exemplify how community systems provide various non-genetic 'scaffoldings', 'constraints', and 'affordances' for individual and sociocultural evolutionary development. Such research complements prevailing models that focus on the vertical transmission of heritable information, from parent to offspring, with research that instead focusses on horizontal, oblique and even reverse information transmission, going from offspring to parent. We call this reversed information transfer the 'offspring effect' to contrast it from the 'parental effect'. We argue that the proposed approach to inheritance is effective for modelling cumulative and distributed developmental process and for explaining the biological origins and evolution of language.}, }
@article {pmid33309942, year = {2021}, author = {Wang, X and Feng, H and Wang, Y and Wang, M and Xie, X and Chang, H and Wang, L and Qu, J and Sun, K and He, W and Wang, C and Dai, C and Chu, Z and Tian, C and Yu, N and Zhang, X and Liu, H and Wang, E}, title = {Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis.}, journal = {Molecular plant}, volume = {14}, number = {3}, pages = {503-516}, doi = {10.1016/j.molp.2020.12.002}, pmid = {33309942}, issn = {1752-9867}, mesh = {Microbiota/physiology ; Mycorrhizae/*physiology ; RNA, Ribosomal, 16S/genetics ; Rhizobium/physiology ; Rhizosphere ; Symbiosis/genetics/physiology ; }, abstract = {Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.}, }
@article {pmid33281689, year = {2020}, author = {Robinson, JM and Cameron, R}, title = {The Holobiont Blindspot: Relating Host-Microbiome Interactions to Cognitive Biases and the Concept of the "Umwelt".}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {591071}, pmid = {33281689}, issn = {1664-1078}, abstract = {Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we discuss the host's microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host-microbiome (collectively termed a "holobiont") interactions in a given behavior, may underpin a potentially important cognitive bias - which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking - that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited.}, }
@article {pmid33274469, year = {2021}, author = {Sharifi, R and Ryu, CM}, title = {Social networking in crop plants: Wired and wireless cross-plant communications.}, journal = {Plant, cell &amp; environment}, volume = {44}, number = {4}, pages = {1095-1110}, pmid = {33274469}, issn = {1365-3040}, mesh = {Communication ; Crops, Agricultural/*physiology ; Ecology ; Plant Defense Against Herbivory ; Plant Immunity ; *Plant Physiological Phenomena ; Plants/metabolism ; }, abstract = {The plant-associated microbial community (microbiome) has an important role in plant-plant communications. Plants decipher their complex habitat situations by sensing the environmental stimuli and molecular patterns and associated with microbes, herbivores and dangers. Perception of these cues generates inter/intracellular signals that induce modifications of plant metabolism and physiology. Signals can also be transferred between plants via different mechanisms, which we classify as wired- and wireless communications. Wired communications involve direct signal transfers between plants mediated by mycorrhizal hyphae and parasitic plant stems. Wireless communications involve plant volatile emissions and root exudates elicited by microbes/insects, which enable inter-plant signalling without physical contact. These producer-plant signals induce microbiome adaptation in receiver plants via facilitative or competitive mechanisms. Receiver plants eavesdrop to anticipate responses to improve fitness against stresses. An emerging body of information in plant-plant communication can be leveraged to improve integrated crop management under field conditions.}, }
@article {pmid33265911, year = {2020}, author = {Saha, M and Dove, S and Weinberger, F}, title = {Chemically Mediated Microbial "Gardening" Capacity of a Seaweed Holobiont Is Dynamic.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33265911}, issn = {2076-2607}, support = {CP1215//DFG Excellence Cluster Future Ocean/ ; }, abstract = {Terrestrial plants are known to "garden" the microbiota of their rhizosphere via released metabolites (that can attract beneficial microbes and deter pathogenic microbes). Such a "gardening" capacity is also known to be dynamic in plants. Although microbial "gardening" has been recently demonstrated for seaweeds, we do not know whether this capacity is a dynamic property in any aquatic flora like in terrestrial plants. Here, we tested the dynamic microbial "gardening" capacity of seaweeds using the model invasive red seaweed Agarophyton vermiculophyllum. Following an initial extraction of surface-associated metabolites (immediately after field collection), we conducted a long-term mesocosm experiment for 5 months to test the effect of two different salinities (low = 8.5 and medium = 16.5) on the microbial "gardening" capacity of the alga over time. We tested "gardening" capacity of A. vermiculophyllum originating from two different salinity levels (after 5 months treatments) in settlement assays against three disease causing pathogenic bacteria and seven protective bacteria. We also compared the capacity of the alga with field-collected samples. Abiotic factors like low salinity significantly increased the capacity of the alga to deter colonization by pathogenic bacteria while medium salinity significantly decreased the capacity of the alga over time when compared to field-collected samples. However, capacity to attract beneficial bacteria significantly decreased at both tested salinity levels when compared to field-collected samples. Dynamic microbial "gardening" capacity of a seaweed to attract beneficial bacteria and deter pathogenic bacteria is demonstrated for the first time. Such a dynamic capacity as found in the current study could also be applicable to other aquatic host-microbe interactions. Our results may provide an attractive direction of research towards manipulation of salinity and other abiotic factors leading to better defended A. vermiculophyllum towards pathogenic bacteria thereby enhancing sustained production of healthy A. vermiculophyllum in farms.}, }
@article {pmid33263887, year = {2020}, author = {Ye, S and Siemann, E}, title = {Endosymbiont-Mediated Adaptive Responses to Stress in Holobionts.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {559-580}, pmid = {33263887}, issn = {0080-1844}, mesh = {Adaptation, Biological ; Animals ; Aquatic Organisms/*microbiology ; Bacteria ; Climate Change ; Ecosystem ; *Host Microbial Interactions ; Insecta/*microbiology ; Plants/*microbiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.}, }
@article {pmid33263873, year = {2020}, author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M}, title = {Phenotype Heritability in Holobionts: An Evolutionary Model.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {199-223}, pmid = {33263873}, issn = {0080-1844}, mesh = {*Biological Evolution ; Genome ; Genomics ; *Host Microbial Interactions ; *Inheritance Patterns ; *Microbiota/genetics ; *Phenotype ; }, abstract = {Many complex diseases are expressed with high incidence only in certain populations. Genealogy studies determine that these diseases are inherited with a high probability. However, genetic studies have been unable to identify the genomic signatures responsible for such heritability, as identifying the genetic variants that make a population prone to a given disease is not enough to explain its high occurrence within the population. This gap is known as the missing heritability problem. We know that the microbiota plays a very important role in determining many important phenotypic characteristics of its host, in particular the complex diseases for which the missing heritability occurs. Therefore, when computing the heritability of a phenotype, it is important to consider not only the genetic variation in the host but also in its microbiota. Here we test this hypothesis by studying an evolutionary model based on gene regulatory networks. Our results show that the holobiont (the host plus its microbiota) is capable of generating a much larger variability than the host alone, greatly reducing the missing heritability of the phenotype. This result strongly suggests that a considerably large part of the missing heritability can be attributed to the microbiome.}, }
@article {pmid33262788, year = {2020}, author = {Lahue, C and Madden, AA and Dunn, RR and Smukowski Heil, C}, title = {History and Domestication of Saccharomyces cerevisiae in Bread Baking.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {584718}, pmid = {33262788}, issn = {1664-8021}, abstract = {The yeast Saccharomyces cerevisiae has been instrumental in the fermentation of foods and beverages for millennia. In addition to fermentations like wine, beer, cider, sake, and bread, S. cerevisiae has been isolated from environments ranging from soil and trees, to human clinical isolates. Each of these environments has unique selection pressures that S. cerevisiae must adapt to. Bread dough, for example, requires S. cerevisiae to efficiently utilize the complex sugar maltose; tolerate osmotic stress due to the semi-solid state of dough, high salt, and high sugar content of some doughs; withstand various processing conditions, including freezing and drying; and produce desirable aromas and flavors. In this review, we explore the history of bread that gave rise to modern commercial baking yeast, and the genetic and genomic changes that accompanied this. We illustrate the genetic and phenotypic variation that has been documented in baking strains and wild strains, and how this variation might be used for baking strain improvement. While we continue to improve our understanding of how baking strains have adapted to bread dough, we conclude by highlighting some of the remaining open questions in the field.}, }
@article {pmid33249664, year = {2021}, author = {Porro, B and Zamoum, T and Mallien, C and Hume, BCC and Voolstra, CR and Röttinger, E and Furla, P and Forcioli, D}, title = {Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis (Cnidaria, Anthozoa) species complex.}, journal = {Molecular ecology}, volume = {30}, number = {2}, pages = {391-405}, doi = {10.1111/mec.15755}, pmid = {33249664}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; *Dinoflagellida ; Mediterranean Sea ; *Sea Anemones/genetics ; Symbiosis/genetics ; }, abstract = {All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the adult stage. The Mediterranean snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down symbionts from one generation to the next by vertical transmission, but the capacity for such horizontal acquisition is still unexplored. To unravel the flexibility of the association between the different host lineages identified in A. viridis and its Symbiodiniaceae, we genotyped both the animal hosts and their symbiont communities in members of host clones in five different locations in the North Western Mediterranean Sea. The composition of within-host-symbiont populations was more dependent on the geographical origin of the hosts than their membership to a given lineage or even to a given clone. Additionally, similarities in host-symbiont communities were greater among genets (i.e. among different clones) than among ramets (i.e. among members of the same given clonal genotype). Taken together, our results demonstrate that A. viridis may form associations with a range of symbiotic dinoflagellates and suggest a capacity for horizontal acquisition. A mixed-mode transmission strategy in A. viridis, as we posit here, may help explain the large phenotypic plasticity that characterizes this anemone.}, }
@article {pmid33246955, year = {2020}, author = {Cooke, I and Ying, H and Forêt, S and Bongaerts, P and Strugnell, JM and Simakov, O and Zhang, J and Field, MA and Rodriguez-Lanetty, M and Bell, SC and Bourne, DG and van Oppen, MJ and Ragan, MA and Miller, DJ}, title = {Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.}, journal = {Science advances}, volume = {6}, number = {48}, pages = {}, pmid = {33246955}, issn = {2375-2548}, abstract = {Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.}, }
@article {pmid33243513, year = {2021}, author = {Calegario, G and Freitas, L and Appolinario, LR and Venas, T and Arruda, T and Otsuki, K and Masi, B and Omachi, C and Moreira, AP and Soares, AC and Rezende, CE and Garcia, G and Tschoeke, D and Thompson, C and Thompson, FL}, title = {Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef.}, journal = {The Science of the total environment}, volume = {760}, number = {}, pages = {143411}, doi = {10.1016/j.scitotenv.2020.143411}, pmid = {33243513}, issn = {1879-1026}, mesh = {Coral Reefs ; Metagenome ; *Microbiota ; Photosynthesis ; *Rhodophyta ; Seawater ; }, abstract = {The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km[2] off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δ[13]C) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m[-2] day[-1]. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.}, }
@article {pmid33240603, year = {2020}, author = {Aichelman, HE and Barshis, DJ}, title = {Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10201}, pmid = {33240603}, issn = {2167-8359}, abstract = {Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions.}, }
@article {pmid33225561, year = {2021}, author = {Garcias-Bonet, N and Eguíluz, VM and Díaz-Rúa, R and Duarte, CM}, title = {Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {2021-2034}, doi = {10.1111/1462-2920.15334}, pmid = {33225561}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Bacteroidetes ; Firmicutes ; Indian Ocean ; *Microbiota ; }, abstract = {The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.}, }
@article {pmid33222325, year = {2021}, author = {Grottoli, AG and Toonen, RJ and van Woesik, R and Vega Thurber, R and Warner, ME and McLachlan, RH and Price, JT and Bahr, KD and Baums, IB and Castillo, KD and Coffroth, MA and Cunning, R and Dobson, KL and Donahue, MJ and Hench, JL and Iglesias-Prieto, R and Kemp, DW and Kenkel, CD and Kline, DI and Kuffner, IB and Matthews, JL and Mayfield, AB and Padilla-Gamiño, JL and Palumbi, S and Voolstra, CR and Weis, VM and Wu, HC}, title = {Increasing comparability among coral bleaching experiments.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {31}, number = {4}, pages = {e02262}, pmid = {33222325}, issn = {1939-5582}, support = {NSF-1838667//National Science Foundation/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Temperature ; }, abstract = {Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide.}, }
@article {pmid33220182, year = {2021}, author = {Song, H and Hewitt, OH and Degnan, SM}, title = {Arginine Biosynthesis by a Bacterial Symbiont Enables Nitric Oxide Production and Facilitates Larval Settlement in the Marine-Sponge Host.}, journal = {Current biology : CB}, volume = {31}, number = {2}, pages = {433-437.e3}, doi = {10.1016/j.cub.2020.10.051}, pmid = {33220182}, issn = {1879-0445}, mesh = {Animals ; Aquatic Organisms/*growth &amp; development/metabolism/microbiology ; Arginine/biosynthesis ; Bacteria/*metabolism ; Citrulline/metabolism ; Larva/*growth &amp; development/metabolism/microbiology ; Metamorphosis, Biological ; Nitric Oxide/biosynthesis ; Porifera/*growth &amp; development/metabolism/microbiology ; Seawater/chemistry ; Symbiosis/*physiology ; }, abstract = {Larval settlement and metamorphosis are regulated by nitric oxide (NO) signaling in a wide diversity of marine invertebrates.[1-10] It is thus surprising that, in most invertebrates, the substrate for NO synthesis-arginine-cannot be biosynthesized but instead must be exogenously sourced.[11] In the sponge Amphimedon queenslandica, vertically inherited proteobacterial symbionts in the larva are able to biosynthesize arginine.[12][,][13] Here, we test the hypothesis that symbionts provide arginine to the sponge host so that nitric oxide synthase expressed in the larva can produce NO, which regulates metamorphosis,[8] and the byproduct citrulline (Figure 1). First, we find support for an arginine-citrulline biosynthetic loop in this sponge larval holobiont by using stable isotope tracing. In symbionts, incorporated [13]C-citrulline decreases as [13]C-arginine increases, consistent with the use of exogenous citrulline for arginine synthesis. In contrast, [13]C-citrulline accumulates in larvae as [13]C-arginine decreases, demonstrating the uptake of exogenous arginine and its conversion to NO and citrulline. Second, we show that, although Amphimedon larvae can derive arginine directly from seawater, normal settlement and metamorphosis can occur in artificial sea water lacking arginine. Together, these results support holobiont complementation of the arginine-citrulline loop and NO biosynthesis in Amphimedon larvae, suggesting a critical role for bacterial symbionts in the development of this marine sponge. Given that NO regulates settlement and metamorphosis in diverse animal phyla[1-10] and arginine is procured externally in most animals,[11] we propose that symbionts might play an equally critical regulatory role in this essential life cycle transition in other metazoans.}, }
@article {pmid33219271, year = {2020}, author = {Serra, V and Gammuto, L and Nitla, V and Castelli, M and Lanzoni, O and Sassera, D and Bandi, C and Sandeep, BV and Verni, F and Modeo, L and Petroni, G}, title = {Morphology, ultrastructure, genomics, and phylogeny of Euplotes vanleeuwenhoeki sp. nov. and its ultra-reduced endosymbiont "Candidatus Pinguicoccus supinus" sp. nov.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {20311}, pmid = {33219271}, issn = {2045-2322}, mesh = {Computational Biology ; DNA, Bacterial/isolation &amp; purification ; Euplotes/*classification/genetics/microbiology/ultrastructure ; Genome, Bacterial ; Genome, Mitochondrial ; Microscopy, Electron, Scanning ; Microscopy, Electron, Transmission ; Phylogeny ; Symbiosis/*genetics ; *Terminology as Topic ; Verrucomicrobia/*genetics/isolation &amp; purification ; }, abstract = {Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics and, more recently, on evolutionary relationships. With the birth of novel genomics/bioinformatics techniques and the increasing interest in microbiome studies, a further advance of taxonomic discipline appears not only possible but highly desirable. The present work proposes a new approach to modern taxonomy, consisting in the inclusion of novel descriptors in the organism characterization: (1) the presence of associated microorganisms (e.g.: symbionts, microbiome), (2) the mitochondrial genome of the host, (3) the symbiont genome. This approach aims to provide a deeper comprehension of the evolutionary/ecological dimensions of organisms since their very first description. Particularly interesting, are those complexes formed by the host plus associated microorganisms, that in the present study we refer to as "holobionts". We illustrate this approach through the description of the ciliate Euplotes vanleeuwenhoeki sp. nov. and its bacterial endosymbiont "Candidatus Pinguicoccus supinus" gen. nov., sp. nov. The endosymbiont possesses an extremely reduced genome (~ 163 kbp); intriguingly, this suggests a high integration between host and symbiont.}, }
@article {pmid33205966, year = {2020}, author = {Kelly, VW and Liang, BK and Sirk, SJ}, title = {Living Therapeutics: The Next Frontier of Precision Medicine.}, journal = {ACS synthetic biology}, volume = {9}, number = {12}, pages = {3184-3201}, doi = {10.1021/acssynbio.0c00444}, pmid = {33205966}, issn = {2161-5063}, mesh = {Antigens/genetics/metabolism ; Bacteria/genetics/metabolism ; Dysbiosis ; Gastrointestinal Microbiome ; Genetic Engineering ; Humans ; Metabolic Diseases/therapy ; Metabolic Engineering ; *Precision Medicine ; Probiotics/administration &amp; dosage ; }, abstract = {Modern medicine has long studied the mechanism and impact of pathogenic microbes on human hosts, but has only recently shifted attention toward the complex and vital roles that commensal and probiotic microbes play in both health and dysbiosis. Fueled by an enhanced appreciation of the human-microbe holobiont, the past decade has yielded countless insights and established many new avenues of investigation in this area. In this review, we discuss advances, limitations, and emerging frontiers for microbes as agents of health maintenance, disease prevention, and cure. We highlight the flexibility of microbial therapeutics across disease states, with special consideration for the rational engineering of microbes toward precision medicine outcomes. As the field advances, we anticipate that tools of synthetic biology will be increasingly employed to engineer functional living therapeutics with the potential to address longstanding limitations of traditional drugs.}, }
@article {pmid33193706, year = {2020}, author = {Djemiel, C and Goulas, E and Badalato, N and Chabbert, B and Hawkins, S and Grec, S}, title = {Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {581664}, pmid = {33193706}, issn = {1664-8021}, abstract = {The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.}, }
@article {pmid33175168, year = {2020}, author = {Whitelaw, BL and Cooke, IR and Finn, J and da Fonseca, RR and Ritschard, EA and Gilbert, MTP and Simakov, O and Strugnell, JM}, title = {Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss.}, journal = {GigaScience}, volume = {9}, number = {11}, pages = {}, pmid = {33175168}, issn = {2047-217X}, support = {P 30686/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Adaptation, Physiological ; Animals ; Genome ; Humans ; *Octopodiformes/genetics ; Tetrodotoxin/toxicity ; *Venoms ; }, abstract = {BACKGROUND: Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland.<br><br>FINDINGS: To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non-tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source.<br><br>CONCLUSIONS: We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.}, }
@article {pmid33141656, year = {2020}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {A comprehensive human minimal gut metagenome extends the host's metabolic potential.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33141656}, issn = {2057-5858}, mesh = {Bacteria/*genetics/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.}, }
@article {pmid33140282, year = {2021}, author = {Mote, S and Gupta, V and De, K and Nanajkar, M and Damare, SR and Ingole, B}, title = {Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India.}, journal = {Folia microbiologica}, volume = {66}, number = {2}, pages = {203-211}, pmid = {33140282}, issn = {1874-9356}, support = {GAP 2871//Rajiv Gandhi Science and Technology Commission, Government of Maharashtra/ ; }, mesh = {Animals ; Bacteria/genetics ; *Coral Reefs ; Ecosystem ; India ; *Porifera ; }, abstract = {The bacterial diversity associated with eroding sponges belonging to the Cliona viridis species complex is scarcely known. Cliona thomasi described from the West Coast of India is a new introduction to the viridis species complex. In this study, we determined the bacterial diversity associated with C. thomasi using next-generation sequencing. The results revealed the dominance of Proteobacteria followed by Cyanobacteria, Actinobacteria and Firmicutes. Among Proteobacteria, the Alphaproteobacteria were found to be the most dominant class. Furthermore, at the genus level, Rhodothalassium were highly abundant followed by Endozoicomonas in sponge samples. The beta-diversity and species richness measures showed remarkably lower diversity in Cliona thomasi than the ambient environment. The determined lower bacterial diversity in C. thomasi than the environmental samples, thus, categorized it as a low microbial abundance (LMA). Functional annotation of the C. thomasi-associated bacterial community indicates their possible role in photo-autotrophy, aerobic nitrification, coupling of sulphate reduction and sulphide oxidization. The present study unveils the bacterial diversity in bioeroding C. thomasi, which is a crucial step to determine the functions of the sponge holobiont in coral reef ecosystem.}, }
@article {pmid33138319, year = {2020}, author = {Boilard, A and Dubé, CE and Gruet, C and Mercière, A and Hernandez-Agreda, A and Derome, N}, title = {Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33138319}, issn = {2076-2607}, support = {6333//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Coral microbiomes are critical to holobiont health and functioning, but the stability of host-microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, "bleaching"), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont's diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.}, }
@article {pmid33135084, year = {2020}, author = {Panelli, S and Corbella, M and Gazzola, A and Piralla, A and Girello, A and Rampelli, S and Candela, M and Cambieri, P}, title = {Tracking over time the developing gut microbiota in newborns admitted to a neonatal intensive care unit during an outbreak caused by ESBL-producing Klebsiella pneumoniae.}, journal = {The new microbiologica}, volume = {43}, number = {4}, pages = {186-190}, pmid = {33135084}, issn = {1121-7138}, mesh = {*Cross Infection/epidemiology ; Disease Outbreaks ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Intensive Care Units, Neonatal ; *Klebsiella Infections/epidemiology ; Klebsiella pneumoniae/enzymology/genetics ; beta-Lactamases/genetics ; }, abstract = {The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and non-colonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual conditions, also in non-colonized patients.}, }
@article {pmid33127817, year = {2021}, author = {Goddard-Dwyer, M and López-Legentil, S and Erwin, PM}, title = {Microbiome Variability across the Native and Invasive Ranges of the Ascidian Clavelina oblonga.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {2}, pages = {}, pmid = {33127817}, issn = {1098-5336}, mesh = {Animals ; Bacteria/genetics ; Brazil ; DNA Barcoding, Taxonomic ; Florida ; *Introduced Species ; Italy ; *Microbiota ; North Carolina ; RNA, Ribosomal, 16S/genetics ; Seawater ; South Carolina ; Spain ; Symbiosis ; Urochordata/genetics/*microbiology ; }, abstract = {Ascidians are prolific colonizers of new environments and possess a range of well-studied features that contribute to their successful spread, but the role of their symbiotic microbial communities in their long-term establishment is mostly unknown. In this study, we utilized next-generation amplicon sequencing to provide a comprehensive description of the microbiome in the colonial ascidian Clavelina oblonga and examined differences in the composition, diversity, and structure of symbiont communities in the host's native and invasive ranges. To identify host haplotypes, we sequenced a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). C. oblonga harbored a diverse microbiome spanning 42 bacterial and three archaeal phyla. Colonies in the invasive range hosted significantly less diverse symbiont communities and exhibited lower COI haplotype diversity than colonies in the native range. Differences in microbiome structure were also detected across colonies in the native and invasive range, driven largely by novel bacteria representing symbiont lineages with putative roles in nitrogen cycling. Variability in symbiont composition was also observed among sites within each range. Together, these data suggest that C. oblonga hosts a dynamic microbiome resulting from (i) reductions in symbiont diversity due to founder effects in host populations and (ii) environmental selection of symbiont taxa in response to new habitats within a range. Further investigation is required to document the mechanisms behind these changes and to determine how changes in microbiome structure relate to holobiont function and the successful establishment of C. oblonga worldwide.IMPORTANCE Nonnative species destabilize coastal ecosystems and microbial symbionts may facilitate their spread by enhancing host survival and fitness. However, we know little of the microorganisms that live inside invasive species and whether they change as the host spreads to new areas. In this study, we investigated the microbial communities of an introduced ascidian (Clavelina oblonga) and tracked symbiont changes across locations within the host's native and invasive ranges. Ascidians in the invasive range had less-diverse microbiomes, as well as lower host haplotype diversity, suggesting that specific colonies reach new locations and carry select symbionts from native populations (i.e., founder effects). Further, ascidians in the invasive range hosted a different composition of symbionts, including microbes with the potential to aid in processes related to invasion success (e.g., nutrient cycling). We conclude that the putative functionality and observed flexibility of this introduced ascidian microbiome may represent an underappreciated factor in the successful establishment of nonnative species in new environments.}, }
@article {pmid33125870, year = {2021}, author = {Ramos-Madrigal, J and Sinding, MS and Carøe, C and Mak, SST and Niemann, J and Samaniego Castruita, JA and Fedorov, S and Kandyba, A and Germonpré, M and Bocherens, H and Feuerborn, TR and Pitulko, VV and Pavlova, EY and Nikolskiy, PA and Kasparov, AK and Ivanova, VV and Larson, G and Frantz, LAF and Willerslev, E and Meldgaard, M and Petersen, B and Sicheritz-Ponten, T and Bachmann, L and Wiig, &#xd8; and Hansen, AJ and Gilbert, MTP and Gopalakrishnan, S}, title = {Genomes of Pleistocene Siberian Wolves Uncover Multiple Extinct Wolf Lineages.}, journal = {Current biology : CB}, volume = {31}, number = {1}, pages = {198-206.e8}, pmid = {33125870}, issn = {1879-0445}, support = {/WT_/Wellcome Trust/United Kingdom ; UNS53502/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biodiversity ; *DNA, Ancient ; DNA, Mitochondrial/genetics ; Dogs/anatomy &amp; histology/*genetics ; Extinction, Biological ; Asia, Eastern ; Fossils ; *Genome ; Geography ; Phylogeny ; Siberia ; Skull/anatomy &amp; histology ; Wolves/anatomy &amp; histology/*genetics ; }, abstract = {Extant Canis lupus genetic diversity can be grouped into three phylogenetically distinct clades: Eurasian and American wolves and domestic dogs.[1] Genetic studies have suggested these groups trace their origins to a wolf population that expanded during the last glacial maximum (LGM)[1-3] and replaced local wolf populations.[4] Moreover, ancient genomes from the Yana basin and the Taimyr peninsula provided evidence of at least one extinct wolf lineage that dwelled in Siberia during the Pleistocene.[35] Previous studies have suggested that Pleistocene Siberian canids can be classified into two groups based on cranial morphology. Wolves in the first group are most similar to present-day populations, although those in the second group possess intermediate features between dogs and wolves.[67] However, whether this morphological classification represents distinct genetic groups remains unknown. To investigate this question and the relationships between Pleistocene canids, present-day wolves, and dogs, we resequenced the genomes of four Pleistocene canids from Northeast Siberia dated between >50 and 14 ka old, including samples from the two morphological categories. We found these specimens cluster with the two previously sequenced Pleistocene wolves, which are genetically more similar to Eurasian wolves. Our results show that, though the four specimens represent extinct wolf lineages, they do not form a monophyletic group. Instead, each Pleistocene Siberian canid branched off the lineage that gave rise to present-day wolves and dogs. Finally, our results suggest the two previously described morphological groups could represent independent lineages similarly related to present-day wolves and dogs.}, }
@article {pmid33123099, year = {2020}, author = {van de Water, JAJM and Coppari, M and Enrichetti, F and Ferrier-Pagès, C and Bo, M}, title = {Local Conditions Influence the Prokaryotic Communities Associated With the Mesophotic Black Coral Antipathella subpinnata.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {537813}, pmid = {33123099}, issn = {1664-302X}, abstract = {Black corals are important habitat-forming species in the mesophotic and deep-sea zones of the world's oceans because of their arborescent colony structure and tendency to form animal forests. Although we have started unraveling the ecology of mesophotic black corals, the importance of the associated microbes to their health has remained unexplored. Here, we provide in-depth assessments of black coral-microbe symbioses by investigating the spatial and temporal stability of these associations, and make comparisons with a sympatric octocoral with similar colony structure. To this end, we collected samples of Antipathella subpinnata colonies from three mesophotic shoals situated along the Ligurian Coast of the Mediterranean Sea (Bordighera, Portofino, Savona) in the spring of 2017. At the Portofino shoal, samples of A. subpinnata and the gorgonian Eunicella cavolini were collected in November 2016 and May 2017. Bacterial communities were profiled using 16S rRNA gene amplicon sequencing. The bacterial community of E. cavolini was consistently dominated by Endozoicomonas. Contrastingly, the black coral microbiome was more diverse, and was primarily composed of numerous Bacteroidetes, Alpha- and Gammaproteobacterial taxa, putatively involved in all steps of the nitrogen and sulfur cycles. Compositional differences in the A. subpinnata microbiome existed between all locations and both time points, and no phylotypes were consistently associated with A. subpinnata. This highlights that local conditions may influence the bacterial community structure and potentially nutrient cycling within the A. subpinnata holobiont. But it also suggests that this coral holobiont possesses a high degree of microbiome flexibility, which may be a mechanism to acclimate to environmental change.}, }
@article {pmid33122700, year = {2020}, author = {Chakraborty, A and Ashraf, MZ and Modlinger, R and Synek, J and Schlyter, F and Roy, A}, title = {Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18572}, pmid = {33122700}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/genetics/metabolism ; Coleoptera/metabolism/*microbiology ; Ecology ; Forests ; *Gastrointestinal Microbiome ; Nitrogen Fixation ; Phylogeny ; Trees/parasitology ; }, abstract = {Bark beetles often serve as forest damaging agents, causing landscape-level mortality. Understanding the biology and ecology of beetles are important for both, gathering knowledge about important forest insects and forest protection. Knowledge about the bark beetle gut-associated bacteria is one of the crucial yet surprisingly neglected areas of research with European tree-killing bark beetles. Hence, in this study, we survey the gut bacteriome from five Ips and one non-Ips bark beetles from Scolytinae. Results reveal 69 core bacterial genera among five Ips beetles that may perform conserved functions within the bark beetle holobiont. The most abundant bacterial genera from different bark beetle gut include Erwinia, Sodalis, Serratia, Tyzzerella, Raoultella, Rahnella, Wolbachia, Spiroplasma, Vibrio, and Pseudoxanthomonas. Notable differences in gut-associated bacterial community richness and diversity among the beetle species are observed. Furthermore, the impact of sampling location on the overall bark beetle gut bacterial community assemblage is also documented, which warrants further investigations. Nevertheless, our data expanded the current knowledge about core gut bacterial communities in Ips bark beetles and their putative function such as cellulose degradation, nitrogen fixation, detoxification of defensive plant compounds, and inhibition of pathogens, which could serve as a basis for further metatranscriptomics and metaproteomics investigations.}, }
@article {pmid33120157, year = {2021}, author = {da Silva Fonseca, J and Mies, M and Paranhos, A and Taniguchi, S and Güth, AZ and Bícego, MC and Marques, JA and Fernandes de Barros Marangoni, L and Bianchini, A}, title = {Isolated and combined effects of thermal stress and copper exposure on the trophic behavior and oxidative status of the reef-building coral Mussismilia harttii.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {268}, number = {Pt B}, pages = {115892}, doi = {10.1016/j.envpol.2020.115892}, pmid = {33120157}, issn = {1873-6424}, mesh = {Animals ; *Anthozoa ; Copper/toxicity ; Coral Reefs ; Oxidation-Reduction ; Oxidative Stress ; Symbiosis ; }, abstract = {Global warming and local disturbances such as pollution cause several impacts on coral reefs. Among them is the breakdown of the symbiosis between host corals and photosynthetic symbionts, which is often a consequence of oxidative stress. Therefore, we investigated if the combined effects of thermal stress and copper (Cu) exposure change the trophic behavior and oxidative status of the reef-building coral Mussismilia harttii. Coral fragments were exposed in a mesocosm system to three temperatures (25.0, 26.6 and 27.3 °C) and three Cu concentrations (2.9, 5.4 and 8.6 μg L[-1]). Samples were collected after 4 and 12 days of exposure. We then (i) performed fatty acid analysis by gas chromatography-mass spectrometry to quantify changes in stearidonic acid and docosapentaenoic acid (autotrophy markers) and cis-gondoic acid (heterotrophy marker), and (ii) assessed the oxidative status of both host and symbiont through analyses of lipid peroxidation (LPO) and total antioxidant capacity (TAC). Our findings show that trophic behavior was predominantly autotrophic and remained unchanged under individual and combined stressors for both 4- and 12-day experiments; for the latter, however, there was an increase in the heterotrophy marker. Results also show that 4 days was not enough to trigger changes in LPO or TAC for both coral and symbiont. However, the 12-day experiment showed a reduction in symbiont LPO associated with thermal stress alone, and the combination of stressors increased their TAC. For the coral, the isolated effects of increase in Cu and temperature led to an increase in LPO. The effects of combined stressors on trophic behavior and oxidative status were not much different than those from the isolated effects of each stressor. These findings highlight that host and symbionts respond differently to stress and are relevant as they show the physiological response of individual holobiont compartments to both global and local stressors.}, }
@article {pmid33117320, year = {2020}, author = {Cannicci, S and Fratini, S and Meriggi, N and Bacci, G and Iannucci, A and Mengoni, A and Cavalieri, D}, title = {To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {575372}, pmid = {33117320}, issn = {1664-302X}, abstract = {The transition to terrestrial environments by formerly aquatic species has occurred repeatedly in many animal phyla and lead to the vast diversity of extant terrestrial species. The differences between aquatic and terrestrial habitats are enormous and involved remarkable morphological and physiological changes. Convergent evolution of various traits is evident among phylogenetically distant taxa, but almost no information is available about the role of symbiotic microbiota in such transition. Here, we suggest that intertidal and terrestrial brachyuran crabs are a perfect model to study the evolutionary pathways and the ecological role of animal-microbiome symbioses, since their transition to land is happening right now, through a number of independent lineages. The microorganisms colonizing the gut of intertidal and terrestrial crabs are expected to play a major role to conquer the land, by reducing water losses and permitting the utilization of novel food sources. Indeed, it has been shown that the microbiomes hosted in the digestive system of terrestrial isopods has been critical to digest plant items, but nothing is known about the microbiomes present in the gut of truly terrestrial crabs. Other important physiological regulations that could be facilitated by microbiomes are nitrogen excretion and osmoregulation in the new environment. We also advocate for advances in comparative and functional genomics to uncover physiological aspects of these ongoing evolutionary processes. We think that the multidisciplinary study of microorganisms associated with terrestrial crabs will shed a completely new light on the biological and physiological processes involved in the sea-land transition.}, }
@article {pmid33117317, year = {2020}, author = {Cárdenas, A and Ye, J and Ziegler, M and Payet, JP and McMinds, R and Vega Thurber, R and Voolstra, CR}, title = {Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {572534}, pmid = {33117317}, issn = {1664-302X}, abstract = {Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatranscriptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, biological traits such as coral life history strategy correlated with patterns of viral diversity. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect protists and algal cells, respectively. Further, Myoviridae and Siphoviridae presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, whereas Hepadnaviridae and Retroviridae might infect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common among the viral sequences, corroborating a contribution of viruses to the holobiont's genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns.}, }
@article {pmid33087470, year = {2020}, author = {Mason, RAB and Wall, CB and Cunning, R and Dove, S and Gates, RD}, title = {High light alongside elevated PCO2 alleviates thermal depression of photosynthesis in a hard coral (Pocillopora acuta).}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 20}, pages = {}, doi = {10.1242/jeb.223198}, pmid = {33087470}, issn = {1477-9145}, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Chlorophyll A ; Coral Reefs ; Humans ; Hydrogen-Ion Concentration ; Oceans and Seas ; Photosynthesis ; Seawater ; Temperature ; }, abstract = {The absorbtion of human-emitted CO2 by the oceans (elevated PCO2) is projected to alter the physiological performance of coral reef organisms by perturbing seawater chemistry (i.e. ocean acidification). Simultaneously, greenhouse gas emissions are driving ocean warming and changes in irradiance (through turbidity and cloud cover), which have the potential to influence the effects of ocean acidification on coral reefs. Here, we explored whether physiological impacts of elevated PCO2 on a coral-algal symbiosis (Pocillopora acuta-Symbiodiniaceae) are mediated by light and/or temperature levels. In a 39 day experiment, elevated PCO2 (962 versus 431 µatm PCO2) had an interactive effect with midday light availability (400 versus 800 µmol photons m[-2] s[-1]) and temperature (25 versus 29°C) on areal gross and net photosynthesis, for which a decline at 29°C was ameliorated under simultaneous high-PCO2 and high-light conditions. Light-enhanced dark respiration increased under elevated PCO2 and/or elevated temperature. Symbiont to host cell ratio and chlorophyll a per symbiont increased at elevated temperature, whilst symbiont areal density decreased. The ability of moderately strong light in the presence of elevated PCO2 to alleviate the temperature-induced decrease in photosynthesis suggests that higher substrate availability facilitates a greater ability for photochemical quenching, partially offsetting the impacts of high temperature on the photosynthetic apparatus. Future environmental changes that result in moderate increases in light levels could therefore assist the P. acuta holobiont to cope with the 'one-two punch' of rising temperatures in the presence of an acidifying ocean.}, }
@article {pmid33086747, year = {2020}, author = {Wojciech, L and Tan, KSW and Gascoigne, NRJ}, title = {Taming the Sentinels: Microbiome-Derived Metabolites and Polarization of T Cells.}, journal = {International journal of molecular sciences}, volume = {21}, number = {20}, pages = {}, pmid = {33086747}, issn = {1422-0067}, support = {NUHSRO/2019/049/T1/SEED-MAR/02//NUS Seed Grant/ ; NUHSRO/2020/110/T1/SEED-MAR/06//NUS Seed Grant/ ; R-571-000-037-114//MOE Tier-1/ ; }, mesh = {Animals ; *Cell Polarity ; Fatty Acids/metabolism ; Homeostasis ; Humans ; *Metabolome ; *Microbiota ; T-Lymphocytes/*cytology ; }, abstract = {A global increase in the prevalence of metabolic syndromes and digestive tract disorders, like food allergy or inflammatory bowel disease (IBD), has become a severe problem in the modern world. Recent decades have brought a growing body of evidence that links the gut microbiome's complexity with host physiology. Hence, understanding the mechanistic aspects underlying the synergy between the host and its associated gut microbiome are among the most crucial questions. The functionally diversified adaptive immune system plays a central role in maintaining gut and systemic immune homeostasis. The character of the reciprocal interactions between immune components and host-dwelling microbes or microbial consortia determines the outcome of the organisms' coexistence within the holobiont structure. It has become apparent that metabolic by-products of the microbiome constitute crucial multimodal transmitters within the host-microbiome interactome and, as such, contribute to immune homeostasis by fine-tuning of the adaptive arm of immune system. In this review, we will present recent insights and discoveries regarding the broad landscape of microbiome-derived metabolites, highlighting the role of these small compounds in the context of the balance between pro- and anti-inflammatory mechanisms orchestrated by the host T cell compartment.}, }
@article {pmid33071821, year = {2020}, author = {Goulet, TL and Erill, I and Ascunce, MS and Finley, SJ and Javan, GT}, title = {Conceptualization of the Holobiont Paradigm as It Pertains to Corals.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {566968}, pmid = {33071821}, issn = {1664-042X}, abstract = {Corals' obligate association with unicellular dinoflagellates, family Symbiodiniaceae form the foundation of coral reefs. For nearly a century, researchers have delved into understanding the coral-algal mutualism from multiple levels of resolution and perspectives, and the questions and scope have evolved with each iteration of new techniques. Advances in genetic technologies not only aided in distinguishing between the multitude of Symbiodiniaceae but also illuminated the existence and diversity of other organisms constituting the coral microbiome. The coral therefore is a meta-organism, often referred to as the coral holobiont. In this review, we address the importance of including a holistic perspective to understanding the coral holobiont. We also discuss the ramifications of how different genotypic combinations of the coral consortium affect the holobiont entity. We highlight the paucity of data on most of the coral microbiome. Using Symbiodiniaceae data, we present evidence that the holobiont properties are not necessarily the sum of its parts. We then discuss the consequences of the holobiont attributes to the fitness of the holobiont and the myriad of organisms that contribute to it. Considering the complexity of host-symbiont genotypic combinations will aid in our understanding of coral resilience, robustness, acclimation, and/or adaptation in the face of environmental change and increasing perturbations.}, }
@article {pmid33071127, year = {2021}, author = {Chen, B and Yu, K and Liao, Z and Yu, X and Qin, Z and Liang, J and Wang, G and Wu, Q and Jiang, L}, title = {Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {142690}, doi = {10.1016/j.scitotenv.2020.142690}, pmid = {33071127}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; China ; Coral Reefs ; *Dinoflagellida ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Regional acclimatisation and microbial interactions significantly influence the resilience of reef-building corals facing anthropogenic climate change, allowing them to adapt to environmental stresses. However, the connections between community structure and microbial interactions of the endemic coral microbiome and holobiont acclimatisation remain unclear. Herein, we used generation sequencing of internal transcribed spacer (ITS2) and 16S rRNA genes to investigate the microbiome composition (Symbiodiniaceae and bacteria) and associated potential interactions of endemic dominant coral holobionts (Pocillopora verrucosa and Turbinaria peltata) in the South China Sea (SCS). We found that shifts in Symbiodiniaceae and bacterial communities of P. verrucosa were associated with latitudinal gradient and climate zone changes, respectively. The C1 sub-clade consistently dominated the Symbiodiniaceae community in T. peltata; yet, the bacterial community structure was spatially heterogeneous. The relative abundance of the core microbiome among P. verrucosa holobionts was reduced in the biogeographical transition zone, while bacterial taxa associated with anthropogenic activity (Escherichia coli and Sphingomonas) were identified in the core microbiomes. Symbiodiniaceae and bacteria potentially interact in microbial co-occurrence networks. Further, increased bacterial, and Symbiodiniaceae α-diversity was associated with increased and decreased network complexity, respectively. Hence, Symbiodiniaceae and bacteria demonstrated different flexibility in latitudinal or climatic environmental regimes, which correlated with holobiont acclimatisation. Core microbiome analysis has indicated that the function of core bacterial microbiota might have changed in distinct environmental regimes, implying potential human activity in the coral habitats. Increased bacterial α diversity may lead to a decline in the stability of coral-microorganism symbioses, whereas rare Symbiodiniaceae may help to retain symbioses. Cladocopium, γ-proteobacteria, while α-proteobacteria may have been the primary drivers in the Symbiodiniaceae-bacterial interactions (SBIs). Our study highlights the association between microbiome shift in distinct environmental regimes and holobiont acclimatisation, while providing insights into the impact of SBIs on holobiont health and acclimatisation during climate change.}, }
@article {pmid33065008, year = {2020}, author = {Barnett, R and Westbury, MV and Sandoval-Velasco, M and Vieira, FG and Jeon, S and Zazula, G and Martin, MD and Ho, SYW and Mather, N and Gopalakrishnan, S and Ramos-Madrigal, J and de Manuel, M and Zepeda-Mendoza, ML and Antunes, A and Baez, AC and De Cahsan, B and Larson, G and O'Brien, SJ and Eizirik, E and Johnson, WE and Koepfli, KP and Wilting, A and Fickel, J and Dalén, L and Lorenzen, ED and Marques-Bonet, T and Hansen, AJ and Zhang, G and Bhak, J and Yamaguchi, N and Gilbert, MTP}, title = {Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.}, journal = {Current biology : CB}, volume = {30}, number = {24}, pages = {5018-5025.e5}, pmid = {33065008}, issn = {1879-0445}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animal Distribution ; Animals ; Cuspid ; DNA, Ancient ; Extinction, Biological ; Felidae/anatomy &amp; histology/*genetics ; Fossils/anatomy &amp; histology ; *Genetic Drift ; *Genetic Speciation ; Genomics ; Hybridization, Genetic ; Phylogeny ; Recombination, Genetic ; }, abstract = {Homotherium was a genus of large-bodied scimitar-toothed cats, morphologically distinct from any extant felid species, that went extinct at the end of the Pleistocene [1-4]. They possessed large, saber-form serrated canine teeth, powerful forelimbs, a sloping back, and an enlarged optic bulb, all of which were key characteristics for predation on Pleistocene megafauna [5]. Previous mitochondrial DNA phylogenies suggested that it was a highly divergent sister lineage to all extant cat species [6-8]. However, mitochondrial phylogenies can be misled by hybridization [9], incomplete lineage sorting (ILS), or sex-biased dispersal patterns [10], which might be especially relevant for Homotherium since widespread mito-nuclear discrepancies have been uncovered in modern cats [10]. To examine the evolutionary history of Homotherium, we generated a ∼7x nuclear genome and a ∼38x exome from H. latidens using shotgun and target-capture sequencing approaches. Phylogenetic analyses reveal Homotherium as highly divergent (∼22.5 Ma) from living cat species, with no detectable signs of gene flow. Comparative genomic analyses found signatures of positive selection in several genes, including those involved in vision, cognitive function, and energy consumption, putatively consistent with diurnal activity, well-developed social behavior, and cursorial hunting [5]. Finally, we uncover relatively high levels of genetic diversity, suggesting that Homotherium may have been more abundant than the limited fossil record suggests [3, 4, 11-14]. Our findings complement and extend previous inferences from both the fossil record and initial molecular studies, enhancing our understanding of the evolution and ecology of this remarkable lineage.}, }
@article {pmid33060749, year = {2020}, author = {Vega de Luna, F and Córdoba-Granados, JJ and Dang, KV and Roberty, S and Cardol, P}, title = {In vivo assessment of mitochondrial respiratory alternative oxidase activity and cyclic electron flow around photosystem I on small coral fragments.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17514}, pmid = {33060749}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; Chlorophyll A/*chemistry ; Electron Transport ; Energy Metabolism ; Fluorescence ; Genotype ; Light ; Mitochondria/*enzymology ; Mitochondrial Proteins/*chemistry ; Oxidation-Reduction ; Oxidoreductases/*chemistry ; Oxygen/chemistry ; Oxygen Consumption ; Photosynthesis ; Photosystem I Protein Complex ; Photosystem II Protein Complex ; Plant Proteins/*chemistry ; Spectrophotometry ; *Symbiosis ; }, abstract = {The mutualistic relationship existing between scleractinian corals and their photosynthetic endosymbionts involves a complex integration of the metabolic pathways within the holobiont. Respiration and photosynthesis are the most important of these processes and although they have been extensively studied, our understanding of their interactions and regulatory mechanisms is still limited. In this work we performed chlorophyll-a fluorescence, oxygen exchange and time-resolved absorption spectroscopy measurements on small and thin fragments (0.3 cm[2]) of the coral Stylophora pistillata. We showed that the capacity of mitochondrial alternative oxidase accounted for ca. 25% of total coral respiration, and that the high-light dependent oxygen uptake, commonly present in isolated Symbiodiniaceae, was negligible. The ratio between photosystem I (PSI) and photosystem II (PSII) active centers as well as their respective electron transport rates, indicated that PSI cyclic electron flow occurred in high light in S. pistillata and in some branching and lamellar coral species freshly collected in the field. Altogether, these results show the potential of applying advanced biophysical and spectroscopic methods on small coral fragments to understand the complex mechanisms of coral photosynthesis and respiration and their responses to environmental changes.}, }
@article {pmid33057402, year = {2020}, author = {Eriksen, AMH and Nielsen, TK and Matthiesen, H and Carøe, C and Hansen, LH and Gregory, DJ and Turner-Walker, G and Collins, MJ and Gilbert, MTP}, title = {Bone biodeterioration-The effect of marine and terrestrial depositional environments on early diagenesis and bone bacterial community.}, journal = {PloS one}, volume = {15}, number = {10}, pages = {e0240512}, pmid = {33057402}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*growth &amp; development ; Bone and Bones/metabolism/*microbiology/*pathology ; Environmental Exposure/*analysis ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {Bacteria play an important role in the degradation of bone material. However, much remains to be learnt about the structure of their communities in degrading bone, and how the depositional environment influences their diversity throughout the exposure period. We genetically profiled the bacterial community in an experimental series of pig bone fragments (femur and humeri) deposited at different well-defined environments in Denmark. The bacterial community in the bone fragments and surrounding depositional environment were studied over one year, and correlated with the bioerosion damage patterns observed microscopically in the bones. We observed that the bacterial communities within the bones were heavily influenced by the local microbial community, and that the general bone microbial diversity increases with time after exposure. We found the presence of several known collagenase producing bacterial groups, and also observed increases in the relative abundance of several of these in bones with tunneling. We anticipate that future analyses using shotgun metagenomics on this and similar datasets will be able to provide insights into mechanisms of microbiome driven bone degradation.}, }
@article {pmid33053643, year = {2020}, author = {Baquiran, JIP and Nada, MAL and Campos, CLD and Sayco, SLG and Cabaitan, PC and Rosenberg, Y and Ayalon, I and Levy, O and Conaco, C}, title = {The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {33053643}, issn = {2076-2607}, support = {QMSR- MRRD-MEC-295-1449//Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development/ ; }, abstract = {Corals harbor a great diversity of symbiotic microorganisms that play pivotal roles in host nutrition, reproduction, and development. Changes in the ocean environment, such as increasing exposure to artificial light at night (ALAN), may alter these relationships and result in a decline in coral health. In this study, we examined the microbiome associated with gravid specimens of the reef-building coral Acropora digitifera. We also assessed the temporal effects of ALAN on the coral-associated microbial community using high-throughput sequencing of the 16S rRNA gene V4 hypervariable region. The A. digitifera microbial community was dominated by phyla Proteobacteria, Firmicutes, and Bacteroidetes. Exposure to ALAN had no large-scale effect on the coral microbiome, although taxa affiliated with Rhodobacteraceae, Caulobacteraceae, Burkholderiaceae, Lachnospiraceae, and Ruminococcaceae were significantly enriched in corals subjected to ALAN. We further noted an increase in the relative abundance of the family Endozoicomonadaceae (Endozoicomonas) as the spawning period approached, regardless of light treatment. These findings highlight the stability of the A. digitifera microbial community under short-term artificial light pollution and provide initial insights into the response of the collective holobiont to ALAN.}, }
@article {pmid33048474, year = {2020}, author = {de Oliveira, BFR and Freitas-Silva, J and Sánchez-Robinet, C and Laport, MS}, title = {Transmission of the sponge microbiome: moving towards a unified model.}, journal = {Environmental microbiology reports}, volume = {12}, number = {6}, pages = {619-638}, doi = {10.1111/1758-2229.12896}, pmid = {33048474}, issn = {1758-2229}, support = {140046/2020-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/International ; 140840/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/International ; Finance Code 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior - Brasil (CAPES)/International ; E-26/203.320/2017//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro (FAPERJ)/International ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Microbiota ; Models, Biological ; Phylogeny ; Porifera/growth &amp; development/*microbiology/physiology ; Symbiosis ; }, abstract = {Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.}, }
@article {pmid33041996, year = {2020}, author = {Martino, D and Johnson, I and Leckman, JF}, title = {What Does Immunology Have to Do With Normal Brain Development and the Pathophysiology Underlying Tourette Syndrome and Related Neuropsychiatric Disorders?.}, journal = {Frontiers in neurology}, volume = {11}, number = {}, pages = {567407}, pmid = {33041996}, issn = {1664-2295}, abstract = {Objective: The goal of this article is to review the past decade's literature and provide a critical commentary on the involvement of immunological mechanisms in normal brain development, as well as its role in the pathophysiology of Tourette syndrome, other Chronic tic disorders (CTD), and related neuropsychiatric disorders including Obsessive-compulsive disorder (OCD) and Attention deficit hyperactivity disorder (ADHD). Methods: We conducted a literature search using the Medline/PubMed and EMBASE electronic databases to locate relevant articles and abstracts published between 2009 and 2020, using a comprehensive list of search terms related to immune mechanisms and the diseases of interest, including both clinical and animal model studies. Results: The cellular and molecular processes that constitute our "immune system" are crucial to normal brain development and the formation and maintenance of neural circuits. It is also increasingly evident that innate and adaptive systemic immune pathways, as well as neuroinflammatory mechanisms, play an important role in the pathobiology of at least a subset of individuals with Tourette syndrome and related neuropsychiatric disorders In the conceptual framework of the holobiont theory, emerging evidence points also to the importance of the "microbiota-gut-brain axis" in the pathobiology of these neurodevelopmental disorders. Conclusions: Neural development is an enormously complex and dynamic process. Immunological pathways are implicated in several early neurodevelopmental processes including the formation and refinement of neural circuits. Hyper-reactivity of systemic immune pathways and neuroinflammation may contribute to the natural fluctuations of the core behavioral features of CTD, OCD, and ADHD. There is still limited knowledge of the efficacy of direct and indirect (i.e., through environmental modifications) immune-modulatory interventions in the treatment of these disorders. Future research also needs to focus on the key molecular pathways through which dysbiosis of different tissue microbiota influence neuroimmune interactions in these disorders, and how microbiota modification could modify their natural history. It is also possible that valid biomarkers will emerge that will guide a more personalized approach to the treatment of these disorders.}, }
@article {pmid33036916, year = {2021}, author = {Middleton, H and Yergeau, &#xc9; and Monard, C and Combier, JP and El Amrani, A}, title = {Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator.}, journal = {Trends in plant science}, volume = {26}, number = {2}, pages = {132-141}, doi = {10.1016/j.tplants.2020.09.005}, pmid = {33036916}, issn = {1878-4372}, mesh = {*MicroRNAs/genetics ; *Microbiota ; Plant Development ; Plants/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.}, }
@article {pmid33025575, year = {2021}, author = {Clowez, S and Renicke, C and Pringle, JR and Grossman, AR}, title = {Impact of Menthol on Growth and Photosynthetic Function of Breviolum Minutum (Dinoflagellata, Dinophyceae, Symbiodiniaceae) and Interactions with its Aiptasia Host.}, journal = {Journal of phycology}, volume = {57}, number = {1}, pages = {245-257}, doi = {10.1111/jpy.13081}, pmid = {33025575}, issn = {1529-8817}, mesh = {Animals ; *Dinoflagellida ; Menthol ; Photosynthesis ; *Sea Anemones ; Symbiosis ; }, abstract = {Environmental change, including global warming and chemical pollution, can compromise cnidarian-(e.g., coral-) dinoflagellate symbioses and cause coral bleaching. Understanding the mechanisms that regulate these symbioses will inform strategies for sustaining healthy coral-reef communities. A model system for corals is the symbiosis between the sea anemone Exaiptasia pallida (common name Aiptasia) and its dinoflagellate partners (family Symbiodiniaceae). To complement existing studies of the interactions between these organisms, we examined the impact of menthol, a reagent often used to render cnidarians aposymbiotic, on the dinoflagellate Breviolum minutum, both in culture and in hospite. In both environments, the growth and photosynthesis of this alga were compromised at either 100 or 300 µM menthol. We observed reduction in PSII and PSI functions, the abundances of reaction-center proteins, and, at 300 µM menthol, of total cellular proteins. Interestingly, for free-living algae exposed to 100 µM menthol, an initial decline in growth, photosynthetic activities, pigmentation, and protein abundances reversed after 5-15 d, eventually approaching control levels. This behavior was observed in cells maintained in continuous light, but not in cells experiencing a light-dark regimen, suggesting that B. minutum can detoxify menthol or acclimate and repair damaged photosynthetic complexes in a light- and/or energy-dependent manner. Extended exposures of cultured algae to 300 µM menthol ultimately resulted in algal death. Most symbiotic anemones were also unable to survive this menthol concentration for 30 d. Additionally, cells impaired for photosynthesis by pre-treatment with 300 µM menthol exhibited reduced efficiency in re-populating the anemone host.}, }
@article {pmid33011965, year = {2020}, author = {Riccio, P and Rossano, R}, title = {The human gut microbiota is neither an organ nor a commensal.}, journal = {FEBS letters}, volume = {594}, number = {20}, pages = {3262-3271}, doi = {10.1002/1873-3468.13946}, pmid = {33011965}, issn = {1873-3468}, mesh = {Biotransformation ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; *Symbiosis ; }, abstract = {The recent explosive increase in the number of works on gut microbiota has been accompanied by the spread of rather vague or improper definitions, chosen more for common use than for experimental evidence. Among them are those defining the human gut microbiota as an organ of our body or as a commensal. But, is the human gut microbiota an organ or a commensal? Here, we address this issue to spearhead a reflection on the real roles of the human gut microbiota in our life. Actually, the misuse of the vocabulary used to describe the properties and functions of the gut microbiota may generate confusion and cause misunderstandings both in the scientific community and among the general public.}, }
@article {pmid33008461, year = {2020}, author = {Pascelli, C and Laffy, PW and Botté, E and Kupresanin, M and Rattei, T and Lurgi, M and Ravasi, T and Webster, NS}, title = {Viral ecogenomics across the Porifera.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {144}, pmid = {33008461}, issn = {2049-2618}, mesh = {Animals ; Genome, Viral/*genetics ; Genomics ; *Microbiota ; Phylogeny ; Porifera/*virology ; *Symbiosis ; Viruses/*genetics/*isolation &amp; purification ; }, abstract = {BACKGROUND: Viruses directly affect the most important biological processes in the ocean via their regulation of prokaryotic and eukaryotic populations. Marine sponges form stable symbiotic partnerships with a wide diversity of microorganisms and this high symbiont complexity makes them an ideal model for studying viral ecology. Here, we used morphological and molecular approaches to illuminate the diversity and function of viruses inhabiting nine sponge species from the Great Barrier Reef and seven from the Red Sea.<br><br>RESULTS: Viromic sequencing revealed host-specific and site-specific patterns in the viral assemblages, with all sponge species dominated by the bacteriophage order Caudovirales but also containing variable representation from the nucleocytoplasmic large DNA virus families Mimiviridae, Marseilleviridae, Phycodnaviridae, Ascoviridae, Iridoviridae, Asfarviridae and Poxviridae. Whilst core viral functions related to replication, infection and structure were largely consistent across the sponge viromes, functional profiles varied significantly between species and sites largely due to differential representation of putative auxiliary metabolic genes (AMGs) and accessory genes, including those associated with herbicide resistance, heavy metal resistance and nylon degradation. Furthermore, putative AMGs varied with the composition and abundance of the sponge-associated microbiome. For instance, genes associated with antimicrobial activity were enriched in low microbial abundance sponges, genes associated with nitrogen metabolism were enriched in high microbial abundance sponges and genes related to cellulose biosynthesis were enriched in species that host photosynthetic symbionts.<br><br>CONCLUSIONS: Our results highlight the diverse functional roles that viruses can play in marine sponges and are consistent with our current understanding of sponge ecology. Differential representation of putative viral AMGs and accessory genes across sponge species illustrate the diverse suite of beneficial roles viruses can play in the functional ecology of these complex reef holobionts. Video Abstract.}, }
@article {pmid32990394, year = {2020}, author = {Massé, A and Tribollet, A and Meziane, T and Bourguet-Kondracki, ML and Yéprémian, C and Sève, C and Thiney, N and Longeon, A and Couté, A and Domart-Coulon, I}, title = {Functional diversity of microboring Ostreobium algae isolated from corals.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4825-4846}, doi = {10.1111/1462-2920.15256}, pmid = {32990394}, issn = {1462-2920}, support = {//Mus&#xe9;um national d'Histoire naturelle/ ; //Sorbonne-Universit&#xe9; (UPMC)/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Carbon/metabolism ; Chlorophyta/genetics/growth &amp; development/metabolism/*physiology ; Coral Reefs ; Fatty Acids/analysis/metabolism ; Nitrogen/metabolism ; Photosynthesis ; Pigments, Biological/analysis ; }, abstract = {The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated nine strains affiliated to two lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ[13] C and δ[15] N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8 h pulse-labeling with [13] C-bicarbonate and [15] N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.}, }
@article {pmid32985530, year = {2020}, author = {Carradec, Q and Poulain, J and Boissin, E and Hume, BCC and Voolstra, CR and Ziegler, M and Engelen, S and Cruaud, C and Planes, S and Wincker, P}, title = {A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15893}, pmid = {32985530}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*genetics ; *Coral Reefs ; Microbiota/*genetics ; Nanopore Sequencing ; Symbiosis ; }, abstract = {Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.}, }
@article {pmid32984975, year = {2021}, author = {Schmidt, R and Saha, M}, title = {Infochemicals in terrestrial plants and seaweed holobionts: current and future trends.}, journal = {The New phytologist}, volume = {229}, number = {4}, pages = {1852-1860}, doi = {10.1111/nph.16957}, pmid = {32984975}, issn = {1469-8137}, mesh = {Climate Change ; Droughts ; Ecology ; Ecosystem ; Rhizosphere ; *Seaweed ; }, abstract = {Since the holobiont concept came into the limelight ten years ago, we have become aware that responses of holobionts to climate change stressors may be driven by shifts in the microbiota. However, the complex interactions underlying holobiont responses across aquatic and terrestrial ecosystems remain largely unresolved. One of the key factors driving these responses is the infochemical-mediated communication in the holobiont. In order to come up with a holistic picture, in this Viewpoint we compare mechanisms and infochemicals in the rhizosphere of plants and the eco-chemosphere of seaweeds in response to climate change stressors and other environmental stressors, including drought, warming and nutrient stress. Furthermore, we discuss the inclusion of chemical ecology concepts that are of crucial importance in driving holobiont survival, adaptation and/or holobiont breakdown. Infochemicals can thus be regarded as a 'missing link' in our understanding of holobiont response to climate change and should be investigated while investigating the responses of plant and seaweed holobionts to climate change. This will set the basis for improving our understanding of holobiont responses to climate change stressors across terrestrial and aquatic ecosystems.}, }
@article {pmid32979529, year = {2020}, author = {Lee, JH and Lee, KA and Lee, WJ}, title = {Drosophila as a model system for deciphering the 'host physiology-nutrition-microbiome' axis.}, journal = {Current opinion in insect science}, volume = {41}, number = {}, pages = {112-119}, doi = {10.1016/j.cois.2020.09.005}, pmid = {32979529}, issn = {2214-5753}, mesh = {*Animal Nutritional Physiological Phenomena ; Animals ; Drosophila/*physiology ; *Gastrointestinal Microbiome ; Homeostasis ; Nutritional Status ; Signal Transduction ; }, abstract = {For metazoans, nutritional stressors, such as undernutrition during growth and development, results in serious outcomes, including growth impairments and organ wasting. When undernutrition is accompanied by other complications, including chronic inflammation, a more complex pathophysiology may emerge, such as environmental enteropathy. Although nutrition is one of the most important environmental factors that influences host physiology, the mechanism by which undernutrition induces host pathophysiology is not fully understood. Recently, gut microbiome was found to alleviate undernutrition-induced pathophysiology in an insect model, revealing the importance of nutrition-microbiome interactions. Here, we discussed how nutrition-microbiome interactions influence host physiology, including growth, tissue homeostasis, immunity, and behavior, by regulating the central metabolic signaling pathways with an emphasis on findings made through Drosophila, an insect model.}, }
@article {pmid32975356, year = {2020}, author = {Klinges, G and Maher, RL and Vega Thurber, RL and Muller, EM}, title = {Parasitic 'Candidatus Aquarickettsia rohweri' is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress.}, journal = {Environmental microbiology}, volume = {22}, number = {12}, pages = {5341-5355}, pmid = {32975356}, issn = {1462-2920}, support = {1314109//Division of Graduate Education/ ; 1840998//Division of Graduate Education/ ; 1452538//Division of Ocean Sciences/ ; 1923836//Division of Ocean Sciences/ ; }, mesh = {Alphaproteobacteria/*physiology ; Animals ; Anthozoa/*microbiology/physiology ; Disease Resistance ; Disease Susceptibility/*microbiology ; Genotype ; *Heat-Shock Response ; Host Microbial Interactions ; Hot Temperature ; Microbiota/*genetics ; }, abstract = {Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic bacteria in holobiont resistance and susceptibility to disease remains less well understood. This study thus characterizes the microbiome of disease-resistant and -susceptible Acropora cervicornis coral genotypes (hereafter referred to simply as 'genotypes') before and after high temperature-mediated bleaching. We found that the intracellular bacterial parasite 'Ca. Aquarickettsia rohweri' was strikingly abundant in disease-susceptible genotypes. Disease-resistant genotypes, however, had notably more diverse and even communities, with correspondingly low abundances of 'Ca. Aquarickettsia'. Bleaching caused a dramatic reduction of 'Ca. Aquarickettsia' within disease-susceptible corals and led to an increase in bacterial community dispersion, as well as the proliferation of opportunists. Our data support the hypothesis that 'Ca. Aquarickettsia' species increase coral disease risk through two mechanisms: (i) the creation of host nutritional deficiencies leading to a compromised host-symbiont state and (ii) the opening of niche space for potential pathogens during thermal stress.}, }
@article {pmid32950795, year = {2020}, author = {Letourneau, ML and Hopkinson, BM and Fitt, WK and Medeiros, PM}, title = {Molecular composition and biodegradation of loggerhead sponge Spheciospongia vesparium exhalent dissolved organic matter.}, journal = {Marine environmental research}, volume = {162}, number = {}, pages = {105130}, doi = {10.1016/j.marenvres.2020.105130}, pmid = {32950795}, issn = {1879-0291}, mesh = {Biodegradation, Environmental ; Carbon ; Florida ; *Microbiota ; *Seawater ; }, abstract = {Sponges are critical components of marine reefs due to their high filtering capacity, wide abundance, and alteration of biogeochemical cycling. Here, we characterized dissolved organic matter (DOM) composition in the sponge holobiont exhalent seawater of a loggerhead sponge (Spheciospongia vesparium) and in ambient seawater in Florida Bay (USA), as well as the microbial responses to each DOM pool through dark incubations. The sponge holobiont removed 6% of the seawater dissolved organic carbon (DOC), utilizing compounds that were low in carbon and oxygen, yet high in nitrogen content relative to the ambient seawater. The microbial community accessed 7% of DOC from the ambient seawater during a 5-day incubation but only 1% of DOC from the sponge exhalent seawater, suggesting a decrease in lability possibly due to holobiont removal of nitrogen-rich compounds. If this holds true for other sponges, it may have important implications for DOM lability and cycling in coastal environments.}, }
@article {pmid32947881, year = {2020}, author = {Cuffaro, B and Assohoun, ALW and Boutillier, D and Súkeníková, L and Desramaut, J and Boudebbouze, S and Salomé-Desnoulez, S and Hrdý, J and Waligora-Dupriet, AJ and Maguin, E and Grangette, C}, title = {In Vitro Characterization of Gut Microbiota-Derived Commensal Strains: Selection of Parabacteroides distasonis Strains Alleviating TNBS-Induced Colitis in Mice.}, journal = {Cells}, volume = {9}, number = {9}, pages = {}, pmid = {32947881}, issn = {2073-4409}, mesh = {Adult ; Animals ; Bacteroidetes/*genetics/*immunology/isolation &amp; purification ; Caco-2 Cells ; Colitis/*chemically induced/immunology/*microbiology ; DNA, Bacterial/genetics/metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Infant, Newborn ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestinal Mucosa/immunology ; Mice ; Mice, Inbred BALB C ; Real-Time Polymerase Chain Reaction ; T-Lymphocytes, Regulatory/immunology ; Trinitrobenzenesulfonic Acid/*adverse effects ; }, abstract = {Alterations in the gut microbiota composition and diversity seem to play a role in the development of chronic diseases, including inflammatory bowel disease (IBD), leading to gut barrier disruption and induction of proinflammatory immune responses. This opens the door for the use of novel health-promoting bacteria. We selected five Parabacteroides distasonis strains isolated from human adult and neonates gut microbiota. We evaluated in vitro their immunomodulation capacities and their ability to reinforce the gut barrier and characterized in vivo their protective effects in an acute murine model of colitis. The in vitro beneficial activities were highly strain dependent: two strains exhibited a potent anti-inflammatory potential and restored the gut barrier while a third strain reinstated the epithelial barrier. While their survival to in vitro gastric conditions was variable, the levels of P. distasonis DNA were higher in the stools of bacteria-treated animals. The strains that were positively scored in vitro displayed a strong ability to rescue mice from colitis. We further showed that two strains primed dendritic cells to induce regulatory T lymphocytes from naïve CD4[+] T cells. This study provides better insights on the functionality of commensal bacteria and crucial clues to design live biotherapeutics able to target inflammatory chronic diseases such as IBD.}, }
@article {pmid32943577, year = {2020}, author = {Becker, DM and Silbiger, NJ}, title = {Nutrient and sediment loading affect multiple facets of functionality in a tropical branching coral.}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 21}, pages = {}, doi = {10.1242/jeb.225045}, pmid = {32943577}, issn = {1477-9145}, mesh = {Animals ; *Anthozoa ; Chlorophyll A ; Coral Reefs ; Ecosystem ; Nutrients ; Polynesia ; }, abstract = {Coral reefs, one of the most diverse ecosystems in the world, face increasing pressures from global and local anthropogenic stressors. Therefore, a better understanding of the ecological ramifications of warming and land-based inputs (e.g. sedimentation and nutrient loading) on coral reef ecosystems is necessary. In this study, we measured how a natural nutrient and sedimentation gradient affected multiple facets of coral functionality, including endosymbiont and coral host response variables, holobiont metabolic responses and percent cover of Pocillopora acuta colonies in Mo'orea, French Polynesia. We used thermal performance curves to quantify the relationship between metabolic rates and temperature along the environmental gradient. We found that algal endosymbiont percent nitrogen content, endosymbiont densities and total chlorophyll a content increased with nutrient input, while endosymbiont nitrogen content per cell decreased, likely representing competition among the algal endosymbionts. Nutrient and sediment loading decreased coral metabolic responses to thermal stress in terms of their thermal performance and metabolic rate processes. The acute thermal optimum for dark respiration decreased, along with the maximal performance for gross photosynthetic and calcification rates. Gross photosynthetic and calcification rates normalized to a reference temperature (26.8°C) decreased along the gradient. Lastly, percent cover of P. acuta colonies decreased by nearly two orders of magnitude along the nutrient gradient. These findings illustrate that nutrient and sediment loading affect multiple levels of coral functionality. Understanding how local-scale anthropogenic stressors influence the responses of corals to temperature can inform coral reef management, particularly in relation to the mediation of land-based inputs into coastal coral reef ecosystems.}, }
@article {pmid32943559, year = {2020}, author = {Wicaksono, WA and Cernava, T and Grube, M and Berg, G}, title = {Assembly of Bacterial Genomes from the Metagenomes of Three Lichen Species.}, journal = {Microbiology resource announcements}, volume = {9}, number = {38}, pages = {}, pmid = {32943559}, issn = {2576-098X}, abstract = {Bacteria have recently emerged as important constituents of lichen holobionts. Here, 29 bacterial metagenome-assembled genome (MAG) sequences were reconstructed from lichen metagenomes and taxonomically classified in four phyla. These results provide a pivotal resource for further exploration of the ecological roles played by bacterial symbionts in lichen holobionts.}, }
@article {pmid32932829, year = {2020}, author = {Parisi, MG and Parrinello, D and Stabili, L and Cammarata, M}, title = {Cnidarian Immunity and the Repertoire of Defense Mechanisms in Anthozoans.}, journal = {Biology}, volume = {9}, number = {9}, pages = {}, pmid = {32932829}, issn = {2079-7737}, support = {PJ_RIC_FFABR_2017_161753 MGP//PJ_RIC_FFABR_2017_161753 MGP/ ; }, abstract = {Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes and gene families similar to those of the Bilateria. Evidence indicates that the Anthozoan innate immune system is not only involved in the disruption of harmful microorganisms, but is also crucial in structuring tissue-associated microbial communities that are essential components of the cnidarian holobiont and useful to the animal's health for several functions including metabolism, immune defense, development, and behavior. Here, we report on the current state of the art of Anthozoan immunity. Like other invertebrates, Anthozoans possess immune mechanisms based on self/non-self-recognition. Although lacking adaptive immunity, they use a diverse repertoire of immune receptor signaling pathways (PRRs) to recognize a broad array of conserved microorganism-associated molecular patterns (MAMP). The intracellular signaling cascades lead to gene transcription up to endpoints of release of molecules that kill the pathogens, defend the self by maintaining homeostasis, and modulate the wound repair process. The cells play a fundamental role in immunity, as they display phagocytic activities and secrete mucus, which acts as a physicochemical barrier preventing or slowing down the proliferation of potential invaders. Finally, we describe the current state of knowledge of some immune effectors in Anthozoan species, including the potential role of toxins and the inflammatory response in the Mediterranean Anthozoan Anemonia viridis following injection of various foreign particles differing in type and dimensions, including pathogenetic bacteria.}, }
@article {pmid32901388, year = {2021}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {471-482}, pmid = {32901388}, issn = {1432-184X}, support = {19-09072S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; CLU-2018-04//Junta de Castilla y Le&#xf3;n (ES)/ ; }, mesh = {Animals ; Antibiosis ; Arthrobacter/classification/genetics/*physiology ; Coleoptera/*microbiology ; DNA, Bacterial/genetics ; Fungi/growth &amp; development ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Host Microbial Interactions ; Phenotype ; Phylogeny ; Pinus/parasitology ; Plant Bark/*parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137[T] but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7[T] as the novel species Arthrobacter ipsi sp. nov. (type strain IA7[T] = CECT 30100[T] = LMG 31782[T]) and suggest its protective role for its host.}, }
@article {pmid32881650, year = {2020}, author = {Xie, H and Feng, X and Wang, M and Wang, Y and Kumar Awasthi, M and Xu, P}, title = {Implications of endophytic microbiota in Camellia sinensis: a review on current understanding and future insights.}, journal = {Bioengineered}, volume = {11}, number = {1}, pages = {1001-1015}, pmid = {32881650}, issn = {2165-5987}, mesh = {Camellia sinensis/genetics/*microbiology ; Gene Expression Regulation, Plant/genetics/physiology ; Microbiota ; }, abstract = {Endophytic fungi and bacteria are the most ubiquitous and representative commensal members that have been studied so far in various higher plants. Within colonization and interaction with their host plants, endophytic microbiota are reportedly to modulate not only the host's growth but also holobiont resilience to abiotic and biotic stresses, providing a natural reservoir and a promising solution for sustainable agricultural development challenged by global climate change. Moreover, possessing the talent to produce a wide array of high-value natural products, plant endophytic microbiota also serve as an alternative way for novel drug discovery. In this review, tea, one of the world's three largest nonalcoholic beverages and a worldwide economic woody crop, was highlighted in the context of endophytic microbiota. We explore the recent studies regarding isolation approaches, distribution characteristics and diversity, and also biological functions of endophytic microbiota in Camellia sinensis (L.) O. Kuntze. Profoundly, the future insight into interaction mechanism between endophytic microbiota and tea plants will shed light on in-depth exploration of tea microbial resources.}, }
@article {pmid32864518, year = {2020}, author = {Assefa, S and Köhler, G}, title = {Intestinal Microbiome and Metal Toxicity.}, journal = {Current opinion in toxicology}, volume = {19}, number = {}, pages = {21-27}, pmid = {32864518}, issn = {2468-2934}, support = {R15 GM110593/GM/NIGMS NIH HHS/United States ; }, abstract = {The human gut microbiome is considered critical for establishing and maintaining intestinal function and homeostasis throughout life. Evidence for bidirectional communication with the immune and nervous systems has spawned interest in the microbiome as a key factor for human and animal health. Consequently, appreciation of the microbiome as a target of xenobiotics, including environmental pollutants such as heavy metals, has risen steadily because disruption of a healthy microbiome (dysbiosis) has been linked to unfavorable health outcomes. Thus, toxicology must consider toxicant effects on the host's microbiome as an integral part of the holobiont. We discuss current findings on the impact of toxic metals on the composition, diversity, and function of the gut microbiome as well as the modulation of metal toxicity by the microbiome. Present limitations and future needs in elucidating microbiome-metal interactions and the potential of harnessing beneficial traits of the microbiota to counteract metal toxicity are also considered.}, }
@article {pmid32858775, year = {2020}, author = {Lindsay, EC and Metcalfe, NB and Llewellyn, MS}, title = {The potential role of the gut microbiota in shaping host energetics and metabolic rate.}, journal = {The Journal of animal ecology}, volume = {89}, number = {11}, pages = {2415-2426}, doi = {10.1111/1365-2656.13327}, pmid = {32858775}, issn = {1365-2656}, support = {BB/P001203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Diet ; Fishes ; *Gastrointestinal Microbiome ; Symbiosis ; }, abstract = {It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.}, }
@article {pmid32858771, year = {2020}, author = {Kenkel, CD and Mocellin, VJL and Bay, LK}, title = {Global gene expression patterns in Porites white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral.}, journal = {Molecular ecology}, volume = {29}, number = {20}, pages = {3907-3920}, doi = {10.1111/mec.15608}, pmid = {32858771}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Chlorophyll A ; Coral Reefs ; *Dinoflagellida/genetics ; Gene Expression ; Symbiosis/genetics ; }, abstract = {The mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing the process of symbiont loss from the thermal stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in Porites lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of disease and thermal stress from patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments combined with a lack of immune regulation suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. Expression in response to WPS also clustered independently of patterns in white syndrome impacted A. hyacinthus, further supporting a distinct aetiology of this syndrome. Expression patterns in WPS-affected tissues were significantly correlated with prior studies that examined short-term thermal stress responses independent of symbiotic state, suggesting that the majority of expression changes reflect a nonspecific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration and highlights distinct responses to bleaching in an anemone model.}, }
@article {pmid32855310, year = {2020}, author = {Fordham, DA and Jackson, ST and Brown, SC and Huntley, B and Brook, BW and Dahl-Jensen, D and Gilbert, MTP and Otto-Bliesner, BL and Svensson, A and Theodoridis, S and Wilmshurst, JM and Buettel, JC and Canteri, E and McDowell, M and Orlando, L and Pilowsky, JA and Rahbek, C and Nogues-Bravo, D}, title = {Using paleo-archives to safeguard biodiversity under climate change.}, journal = {Science (New York, N.Y.)}, volume = {369}, number = {6507}, pages = {}, doi = {10.1126/science.abc5654}, pmid = {32855310}, issn = {1095-9203}, support = {681605/ERC_/European Research Council/International ; }, mesh = {Animals ; Archives ; *Biodiversity ; Climate Change/*history ; *Conservation of Natural Resources ; *Extinction, Biological ; History, Ancient ; Paleontology ; }, abstract = {Strategies for 21st-century environmental management and conservation under global change require a strong understanding of the biological mechanisms that mediate responses to climate- and human-driven change to successfully mitigate range contractions, extinctions, and the degradation of ecosystem services. Biodiversity responses to past rapid warming events can be followed in situ and over extended periods, using cross-disciplinary approaches that provide cost-effective and scalable information for species' conservation and the maintenance of resilient ecosystems in many bioregions. Beyond the intrinsic knowledge gain such integrative research will increasingly provide the context, tools, and relevant case studies to assist in mitigating climate-driven biodiversity losses in the 21st century and beyond.}, }
@article {pmid32849407, year = {2020}, author = {Shiu, JH and Yu, SP and Fong, CL and Ding, JY and Tan, CJ and Fan, TY and Lu, CY and Tang, SL}, title = {Shifting in the Dominant Bacterial Group Endozoicomonas Is Independent of the Dissociation With Coral Symbiont Algae.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1791}, pmid = {32849407}, issn = {1664-302X}, abstract = {The coral-associated Endozoicomonas are dominant bacteria in the coral holobiont. Their relative abundance usually decreases with heat-induced coral bleaching and is proposed to be positively correlated with Symbiodiniaceae abundance. It remains unclear whether this phenomenon of decreased Endozoicomonas abundance is caused by temperature stress or a decreased abundance of Symbiodiniaceae. This study induced bleaching in the coral Euphyllia glabrescens using a dark treatment over 15 weeks. We examined shifts in Endozoicomonas abundance and experimentally reduced Symbiodiniaceae density. 16S rRNA gene amplicon sequencing was used to characterize the changes in bacterial community (incl. Endozoicomonas) over time, and the 16S rRNA gene copy number of Endozoicomonas was quantified by qPCR. We detected a high abundance of Endozoicomonas in E. glabrescens that underwent dark-induced bleaching. The results reveal that changes in the relative abundance of Endozoicomonas are unrelated to Symbiodiniaceae abundance, indicating that Endozoicomonas can be independent of Symbiodiniaceae in the coral holobiont.}, }
@article {pmid32831146, year = {2020}, author = {Wada, N and Yuasa, H and Kajitani, R and Gotoh, Y and Ogura, Y and Yoshimura, D and Toyoda, A and Tang, SL and Higashimura, Y and Sweatman, H and Forsman, Z and Bronstein, O and Eyal, G and Thongtham, N and Itoh, T and Hayashi, T and Yasuda, N}, title = {A ubiquitous subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {123}, pmid = {32831146}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics/*isolation &amp; purification ; Coral Reefs ; Indian Ocean ; Male ; Pacific Ocean ; Phylogeny ; *Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Starfish/genetics/*microbiology/*physiology ; *Symbiosis ; }, abstract = {BACKGROUND: Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on the dominant COTS-associated bacteria through a multifaceted molecular approach.<br><br>METHODS: A total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the bacterial genome from the hologenome sequence data.<br><br>RESULTS: We discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces.<br><br>CONCLUSIONS: COTS27 can be found in three allopatric COTS species, ranging from the northern Red Sea to the Pacific, implying that the symbiotic relationship arose before the speciation events (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS provides a useful model system for studying symbiont-host interactions in marine invertebrates and may have applications for coral reef conservation. Video Abstract.}, }
@article {pmid32827049, year = {2020}, author = {de Oliveira, BFR and Carr, CM and Dobson, ADW and Laport, MS}, title = {Harnessing the sponge microbiome for industrial biocatalysts.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {19}, pages = {8131-8154}, pmid = {32827049}, issn = {1432-0614}, support = {140840/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 304477/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 88887.341847/2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; E-26/203.320/2017//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; SSPC-3, 12/RC/2275_2/SFI_/Science Foundation Ireland/Ireland ; SSPC-2, 12/RC/2275/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bacteria/genetics ; Biotechnology ; Fungi ; *Microbiota ; Prospective Studies ; }, abstract = {Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.}, }
@article {pmid32811860, year = {2020}, author = {Zilius, M and Bonaglia, S and Broman, E and Chiozzini, VG and Samuiloviene, A and Nascimento, FJA and Cardini, U and Bartoli, M}, title = {N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13966}, pmid = {32811860}, issn = {2045-2322}, mesh = {Animals ; Biofilms/growth &amp; development ; Brachyura/*metabolism/*microbiology ; Decapoda/metabolism/microbiology ; Ecosystem ; Microbiota/genetics ; Nitrogen/metabolism ; Nitrogen Cycle/genetics/physiology ; Nitrogen Fixation/*physiology ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.}, }
@article {pmid32811423, year = {2020}, author = {Dunaj, SJ and Bettencourt, BR and Garb, JE and Brucker, RM}, title = {Spider phylosymbiosis: divergence of widow spider species and their tissues' microbiomes.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {104}, pmid = {32811423}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Female ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spiders/*classification/*microbiology ; *Symbiosis ; }, abstract = {BACKGROUND: Microbiomes can have profound impacts on host biology and evolution, but to date, remain vastly understudied in spiders despite their unique and diverse predatory adaptations. This study evaluates closely related species of spiders and their host-microbe relationships in the context of phylosymbiosis, an eco-evolutionary pattern where the microbial community profile parallels the phylogeny of closely related host species. Using 16S rRNA gene amplicon sequencing, we characterized the microbiomes of five species with known phylogenetic relationships from the family Theridiidae, including multiple closely related widow spiders (L. hesperus, L. mactans, L. geometricus, S. grossa, and P. tepidariorum).<br><br>RESULTS: We compared whole animal and tissue-specific microbiomes (cephalothorax, fat bodies, venom glands, silk glands, and ovary) in the five species to better understand the relationship between spiders and their microbial symbionts. This showed a strong congruence of the microbiome beta-diversity of the whole spiders, cephalothorax, venom glands, and silk glands when compared to their host phylogeny. Our results support phylosymbiosis in these species and across their specialized tissues. The ovary tissue microbial dendrograms also parallel the widow phylogeny, suggesting vertical transfer of species-specific bacterial symbionts. By cross-validating with RNA sequencing data obtained from the venom glands, silk glands and ovaries of L. hesperus, L. geometricus, S. grossa, and P. tepidariorum we confirmed that several microbial symbionts of interest are viably active in the host.<br><br>CONCLUSION: Together these results provide evidence that supports the importance of host-microbe interactions and the significant role microbial communities may play in the evolution and adaptation of their hosts.}, }
@article {pmid32806647, year = {2020}, author = {Poquita-Du, RC and Goh, YL and Huang, D and Chou, LM and Todd, PA}, title = {Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32806647}, issn = {2076-2607}, support = {MSRDP-P03//National Research Foundation Singapore/ ; MSRDP-P05//National Research Foundation Singapore/ ; }, abstract = {The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts' Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.}, }
@article {pmid32796689, year = {2020}, author = {Fujii, T and Tanaka, Y and Maki, K and Saotome, N and Morimoto, N and Watanabe, A and Miyajima, T}, title = {Organic Carbon and Nitrogen Isoscapes of Reef Corals and Algal Symbionts: Relative Influences of Environmental Gradients and Heterotrophy.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32796689}, issn = {2076-2607}, support = {21370008//Japan Society for the Promotion of Science/ ; 20121007//Japan Society for the Promotion of Science/ ; 4-1806//Environmental Restoration and Conservation Agency/ ; }, abstract = {The elemental (C/N) and stable isotopic (δ[13]C, δ[15]N) compositions and compound-specific δ[15]N values of amino acids (δ[15]NAA) were evaluated for coral holobionts as diagnostic tools to detect spatiotemporal environmental heterogeneity and its effects on coral health. Hermatypic coral samples of eight species were collected at 12 reef sites with differing levels of pollution stress. The C/N ratios, δ[13]C values, and δ[15]N values of coral tissues and endosymbiotic algae were determined for 193 coral holobionts, and the amino acid composition and δ[15]NAA values of selected samples were analyzed. δ[15]N values were influenced most by pollution stress, while C/N ratios and δ[13]C values depended most strongly on species. The results imply that δ[13]C and δ[15]N values are useful indicators for distinguishing the ecological niches of sympatric coral species based on microhabitat preference and resource selectivity. Using δ[15]NAA values, the trophic level (TL) of the examined coral samples was estimated to be 0.71 to 1.53, i.e., purely autotrophic to partially heterotrophic. Significant portions of the variation in bulk δ[15]N and δ[13]C values could be explained by the influence of heterotrophy. The TL of symbionts covaried with that of their hosts, implying that amino acids acquired through host heterotrophy are translocated to symbionts. Dependence on heterotrophy was stronger at polluted sites, indicating that the ecological role of corals changes in response to eutrophication.}, }
@article {pmid32795355, year = {2020}, author = {Ronai, I and Greslehner, GP and Boem, F and Carlisle, J and Stencel, A and Suárez, J and Bayir, S and Bretting, W and Formosinho, J and Guerrero, AC and Morgan, WH and Prigot-Maurice, C and Rodeck, S and Vasse, M and Wallis, JM and Zacks, O}, title = {"Microbiota, symbiosis and individuality summer school" meeting report.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {117}, pmid = {32795355}, issn = {2049-2618}, mesh = {*Biomedical Research ; Europe ; Health ; Humans ; *Individuality ; *Interdisciplinary Studies ; *Microbiota ; *Schools ; Seasons ; *Symbiosis ; }, abstract = {How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.}, }
@article {pmid32794337, year = {2020}, author = {Berlanga-Clavero, MV and Molina-Santiago, C and de Vicente, A and Romero, D}, title = {More than words: the chemistry behind the interactions in the plant holobiont.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4532-4544}, doi = {10.1111/1462-2920.15197}, pmid = {32794337}, issn = {1462-2920}, support = {BacBio 637971//H2020 European Research Council/ ; PID2019-107724GB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; AGL2016-78662R//Secretar&#xed;a de Estado de Investigaci&#xf3;n, Desarrollo e Innovaci&#xf3;n/ ; }, mesh = {Bacteria/*metabolism ; Germination/physiology ; Microbial Interactions/physiology ; Microbiota/physiology ; Plant Development/*physiology ; Plant Roots/microbiology ; Plants/metabolism/*microbiology ; Rhizosphere ; Seeds/growth &amp; development/microbiology ; Signal Transduction/physiology ; Symbiosis/*physiology ; Virulence Factors/metabolism ; }, abstract = {Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.}, }
@article {pmid32788054, year = {2020}, author = {Triviño, V and Suárez, J}, title = {Holobionts: Ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systems.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {84}, number = {}, pages = {101323}, doi = {10.1016/j.shpsc.2020.101323}, pmid = {32788054}, issn = {1879-2499}, mesh = {Animals ; Biological Evolution ; *Biota ; Invertebrates/*microbiology ; Metaphysics ; *Microbiota ; Plants/*microbiology ; *Symbiosis ; Vertebrates/*microbiology ; }, abstract = {Holobionts are symbiotic assemblages composed by a macrobe host (animal or plant) plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl's account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host's microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective.}, }
@article {pmid32777774, year = {2020}, author = {Nyholm, L and Koziol, A and Marcos, S and Botnen, AB and Aizpurua, O and Gopalakrishnan, S and Limborg, MT and Gilbert, MTP and Alberdi, A}, title = {Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research.}, journal = {iScience}, volume = {23}, number = {8}, pages = {101414}, pmid = {32777774}, issn = {2589-0042}, abstract = {From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions by combining multi-omic data from both hosts and microbes. However, exploring the full extent of these interactions requires careful consideration of study design for the efficient generation and optimal integration of data derived from (meta)genomics, (meta)transcriptomics, (meta)proteomics, and (meta)metabolomics. In this perspective, we introduce the holo-omic approach that incorporates multi-omic data from both host and microbiota domains to untangle the interplay between the two. We revisit the recent literature on biomolecular host-microbe interactions and discuss the implementation and current limitations of the holo-omic approach. We anticipate that the application of this approach can contribute to opening new research avenues and discoveries in biomedicine, biotechnology, agricultural and aquacultural sciences, nature conservation, as well as basic ecological and evolutionary research.}, }
@article {pmid32772673, year = {2020}, author = {Fontaine, SS and Kohl, KD}, title = {Optimal integration between host physiology and functions of the gut microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190594}, pmid = {32772673}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Host Microbial Interactions/*physiology ; Invertebrates/microbiology/*physiology ; *Symbiosis ; Vertebrates/microbiology/*physiology ; }, abstract = {Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772672, year = {2020}, author = {van Oppen, MJH and Medina, M}, title = {Coral evolutionary responses to microbial symbioses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190591}, pmid = {32772672}, issn = {1471-2970}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; *Biological Evolution ; Dinoflagellida/*physiology ; Global Warming ; *Microbiota ; *Symbiosis ; }, abstract = {This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772670, year = {2020}, author = {Moeller, AH and Sanders, JG}, title = {Roles of the gut microbiota in the adaptive evolution of mammalian species.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190597}, pmid = {32772670}, issn = {1471-2970}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mammals/*microbiology ; }, abstract = {Every mammalian species harbours a gut microbiota, and variation in the gut microbiota within mammalian species can have profound effects on host phenotypes. In this review, we summarize recent evidence that gut microbiotas have influenced the course of mammalian adaptation and diversification. Associations with gut microbiotas have: (i) promoted the diversification of mammalian species by enabling dietary transitions onto difficult-to-digest carbon sources and toxic food items; (ii) shaped the evolution of adaptive phenotypic plasticity in mammalian species through the amplification of signals from the external environment and from postnatal developmental processes; and (iii) generated selection for host mechanisms, including innate and adaptive immune mechanisms, to control the gut microbiota for the benefit of host fitness. The stability of specific gut microbiotas within host species lineages varies substantially across the mammalian phylogeny, and this variation may alter the ultimate evolutionary outcomes of relationships with gut microbiotas in different mammalian clades. In some mammalian species, including humans, relationships with host species-specific gut microbiotas appear to have led to the evolution of host dependence on the gut microbiota for certain functions. These studies implicate the gut microbiota as a significant environmental factor and selective agent shaping the adaptive evolution of mammalian diet, phenotypic plasticity, gastrointestinal morphology and immunity. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772660, year = {2020}, author = {Koskella, B and Bergelson, J}, title = {The study of host-microbiome (co)evolution across levels of selection.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190604}, pmid = {32772660}, issn = {1471-2970}, mesh = {*Biological Coevolution ; *Host Microbial Interactions ; *Microbiota ; *Selection, Genetic ; }, abstract = {Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772380, year = {2021}, author = {Ravanbakhsh, M and Kowalchuk, GA and Jousset, A}, title = {Targeted plant hologenome editing for plant trait enhancement.}, journal = {The New phytologist}, volume = {229}, number = {2}, pages = {1067-1077}, pmid = {32772380}, issn = {1469-8137}, mesh = {*Arabidopsis/genetics ; Ethylenes ; Genes, Plant ; Phenotype ; Plant Breeding ; }, abstract = {Breeding better crops is a cornerstone of global food security. While efforts in plant genetic improvement show promise, it is increasingly becoming apparent that the plant phenotype should be treated as a function of the holobiont, in which plant and microbial traits are deeply intertwined. Using a minimal holobiont model, we track ethylene production and plant nutritional value in response to alterations in plant ethylene synthesis (KO mutation in ETO1), which induces 1-aminocyclopropane-1-carboxylic acid (ACC) synthase 5 (ACS5), or microbial degradation of ACC (KO mutation in microbial acdS), preventing the breakdown of the plant ACC pool, the product of ACS5. We demonstrate that similar plant phenotypes can be generated by either specific mutations of plant-associated microbes or alterations in the plant genome. Specifically, we could equally increase plant nutritional value by either altering the plant ethylene synthesis gene ETO1, or the microbial gene acdS. Both mutations yielded a similar plant phenotype with increased ethylene production and higher shoot micronutrient concentrations. Restoring bacterial AcdS enzyme activity also rescued the plant wild-t8yp phenotype in an eto1 background. Plant and bacterial genes build an integrated plant-microbe regulatory network amenable to genetic improvement from both the plant and microbial sides.}, }
@article {pmid32767091, year = {2021}, author = {Vargas, S and Leiva, L and Wörheide, G}, title = {Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {213-222}, pmid = {32767091}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; Climate Change ; Cyanobacteria/*classification/genetics/isolation &amp; purification ; Hot Temperature ; Microbiota/*genetics ; Planctomycetales/*classification/genetics/isolation &amp; purification ; Porifera/*microbiology ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Thermotolerance/genetics ; }, abstract = {Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.}, }
@article {pmid32765431, year = {2020}, author = {Friel, AD and Neiswenter, SA and Seymour, CO and Bali, LR and McNamara, G and Leija, F and Jewell, J and Hedlund, BP}, title = {Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs (Limulus polyphemus) Into a Touch-Tank Exhibit.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1398}, pmid = {32765431}, issn = {1664-302X}, abstract = {The Atlantic horseshoe crab (Limulus polyphemus) is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adult L. polyphemus in a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. The wild population hosted diverse and distinct microbiomes on the carapace (260 ± 96 amplicon sequence variants or ASVs), cloaca (345 ± 77 ASVs), gills (309 ± 36 ASVs), and oral cavity (359 ± 37 ASVs), which were dominated by classes Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria. A rapid decline in richness across all body locations was observed within 1 month of captivity, with tank-acclimated (>2 years) animals having <5% of the initial microbiome richness and a nearly completely restructured microbial community. Tank-acclimated horseshoe crabs possessed distinct microbiomes that were highly uneven and low in species richness on the carapace (31 ± 7 ASVs), cloaca (53 ± 19 ASVs), gills (17 ± 2 ASVs), and oral cavity (31 ± 13 ASVs). The carapace, oral cavity, and gills of the tank-acclimated animals hosted abundant populations of Aeromonas (>60%) and Pseudomonas (>20%), both of which are known opportunistic pathogens of aquatic animals and can express chitinases, providing a plausible mechanism for the development of the carapace lesion pathology observed in this and other studies. The cloaca of the tank-acclimated animals was slightly more diverse than the other body locations with Aeromonas, Enterococcus, Shewanella, and Vagococcus dominating the community. These results provide an important baseline on the microbiomes of both wild and tank-acclimated horseshoe crabs and underscore the need to continue to investigate how native microbial populations may protect animals from pathogens.}, }
@article {pmid32762039, year = {2021}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Rouillé, T and Ajdic, D and Uchida, Y and Di Nardo, A and Bosch, TCG and Paus, R}, title = {Exploring the human hair follicle microbiome.}, journal = {The British journal of dermatology}, volume = {184}, number = {5}, pages = {802-815}, doi = {10.1111/bjd.19461}, pmid = {32762039}, issn = {1365-2133}, support = {//University of Miami/ ; //DFG CRC 1182/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; //DFG CRC 1182 (TPC4.2)/ ; }, mesh = {*Alopecia Areata ; *Folliculitis ; Hair Follicle ; *Hidradenitis Suppurativa ; Humans ; *Microbiota ; }, abstract = {Human hair follicles (HFs) carry complex microbial communities that differ from the skin surface microbiota. This likely reflects that the HF epithelium differs from the epidermal barrier in that it provides a moist, less acidic, and relatively ultraviolet light-protected environment, part of which is immune-privileged, thus facilitating microbial survival. Here we review the current understanding of the human HF microbiome and its potential physiological and pathological functions, including in folliculitis, acne vulgaris, hidradenitis suppurativa, alopecia areata and cicatricial alopecias. While reviewing the main human HF bacteria (such as Propionibacteria, Corynebacteria, Staphylococci and Streptococci), viruses, fungi and parasites as human HF microbiome constituents, we advocate a broad view of the HF as an integral part of the human holobiont. Specifically, we explore how the human HF may manage its microbiome via the regulated production of antimicrobial peptides (such as cathelicidin, psoriasin, RNAse7 and dermcidin) by HF keratinocytes, how the microbiome may impact on cytokine and chemokine release from the HF, and examine hair growth-modulatory effects of antibiotics, and ask whether the microbiome affects hair growth in turn. We highlight major open questions and potential novel approaches to the management of hair diseases by targeting the HF microbiome.}, }
@article {pmid32743860, year = {2020}, author = {Duarte, CM and Ngugi, DK and Alam, I and Pearman, J and Kamau, A and Eguiluz, VM and Gojobori, T and Acinas, SG and Gasol, JM and Bajic, V and Irigoien, X}, title = {Sequencing effort dictates gene discovery in marine microbial metagenomes.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4589-4603}, pmid = {32743860}, issn = {1462-2920}, support = {//King Abdullah University of Science and Technology/ ; BB123456/NH/NIH HHS/United States ; AA123456/NH/NIH HHS/United States ; CSD2008-00077//Spanish Ministry of Science and Innovation/ ; }, mesh = {Alphaproteobacteria/genetics ; Aquatic Organisms/*genetics/microbiology ; Diatoms/genetics ; Flavobacteriaceae/genetics ; Gammaproteobacteria/genetics ; Genetic Association Studies ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Metagenome/*genetics ; Metagenomics/methods ; Plankton/*genetics/microbiology ; Water Microbiology ; }, abstract = {Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red Sea plankton community to uncover that the rate of gene discovery increases continuously with sequencing effort, with no indication that the retrieved 2.83 million non-redundant (complete) genes predicted from the experiment represented a nearly complete inventory of the genes present in the sampled community (i.e., no evidence of saturation). The underlying reason is the Pareto-like distribution of the abundance of genes in the plankton community, resulting in a very long tail of millions of genes present at remarkably low abundances, which can only be retrieved through massive sequencing. Microbial metagenomic projects retrieve a variable number of unique genes per Tera base-pair (Tbp), with a median value of 14.7 million unique genes per Tbp sequenced across projects. The increase in the rate of gene discovery in microbial metagenomes with sequencing effort implies that there is ample room for new gene discovery in further ocean and holobiont sequencing studies.}, }
@article {pmid32738355, year = {2020}, author = {Miller, WB and Baluška, F and Torday, JS}, title = {Cellular senomic measurements in Cognition-Based Evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {156}, number = {}, pages = {20-33}, doi = {10.1016/j.pbiomolbio.2020.07.002}, pmid = {32738355}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Biology/trends ; Cell Communication ; *Cognition ; Homeostasis ; Humans ; Models, Biological ; Thermodynamics ; }, abstract = {All living entities are cognitive and dependent on ambiguous information. Any assessment of that imprecision is necessarily a measuring function. Individual cells measure information to sustain self-referential homeostatic equipoise (self-identity) in juxtaposition to the external environment. The validity of that information is improved by its collective assessment. The reception of cellular information obliges thermodynamic reactions that initiate a self-reinforcing work channel. This expresses as natural cellular engineering and niche constructions which become the complex interrelated tissue ecologies of holobionts. Multicellularity is collaborative cellular information management directed towards the optimization of information quality through its collective measured assessment. Biology and its evolution can now be re-framed as the continuous process of self-referential cellular measurement in the perpetual defense of individual cellular self-identities through the collective form.}, }
@article {pmid32731457, year = {2020}, author = {Lifshitz, N and Hazanov, L and Fine, M and Yarden, O}, title = {Seasonal Variations in the Culturable Mycobiome of Acropora loripes along a Depth Gradient.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32731457}, issn = {2076-2607}, support = {888/19//Israel Science Foundation/ ; }, abstract = {Coral associated fungi are widespread, highly diverse and are part and parcel of the coral holobiont. To study how environmental conditions prevailing near the coral-host may affect fungal diversity, the culturable (isolated on potato dextrose agar) mycobiome associated with Acropora loripes colonies was seasonally sampled along a depth gradient in the Gulf of Aqaba. Fragments were sampled from both apparently healthy coral colonies as well as those exhibiting observable lesions. Based on phylogenetic analysis of 197 fungal sequences, Ascomycota were the most prevalent (91.9%). The abundance of fungi increased with increasing water depth, where corals sampled at 25 m yielded up to 70% more fungal colony forming units (CFUs) than those isolated at 6 m. Fungal diversity at 25 m was also markedly higher, with over 2-fold more fungal families represented. Diversity was also higher in lesioned coral samples, when compared to apparently healthy colonies. In winter, concurrent with water column mixing and increased levels of available nutrients, at the shallow depths, Saccharomytacea and Sporidiobolacea were more prevalent, while in spring and fall Trichocomacea (overall, the most prevalent family isolated throughout this study) were the most abundant taxa isolated at these depths as well as at deeper sampling sites. Our results highlight the dynamic nature of the culturable coral mycobiome and its sensitivity to environmental conditions and coral health.}, }
@article {pmid32727134, year = {2020}, author = {Biagi, E and Mengucci, C and Barone, M and Picone, G and Lucchi, A and Celi, P and Litta, G and Candela, M and Manfreda, G and Brigidi, P and Capozzi, F and De Cesare, A}, title = {Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32727134}, issn = {2076-2607}, support = {77/2018//Universit&#xe0; di Bologna/ ; }, abstract = {The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota-host relationship can improve chickens' immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3-V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.}, }
@article {pmid32714292, year = {2020}, author = {Li, Z and Wang, X and Alberdi, A and Deng, J and Zhong, Z and Si, H and Zheng, C and Zhou, H and Wang, J and Yang, Y and Wright, AG and Mao, S and Zhang, Z and Guan, L and Li, G}, title = {Comparative Microbiome Analysis Reveals the Ecological Relationships Between Rumen Methanogens, Acetogens, and Their Hosts.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1311}, pmid = {32714292}, issn = {1664-302X}, abstract = {Ruminant methane, which is generated by methanogens through the consumption of hydrogen and supports the normal function of the rumen ecosystem, is a major source of greenhouse gases. Reductive acetogenesis by acetogens is a possible alternative sink that can dispose of hydrogen for acetate production. However, the distribution of rumen methanogens and acetogens along with the relationships among methanogens, acetogens, and their host are poorly understood. Therefore, we investigated the rumen methanogen and acetogen communities of 97 individual animals representing 14 ruminant species within three ruminant families Cervidae (deer), Bovidae (bovid), and Moschidae (musk deer). The results showed that the Methanobrevibacter spp. and acetogens associated with Eubacteriaceae were the most widespread methanogens and acetogens, respectively. However, other methanogens and acetogens exhibited host specificity in the rumen of reindeer and Chinese muntjac deer. Acetogen and methanogen communities were not correlated in these species, and the phylosymbiosis signature between host phylogeny and the composition of both communities was lacking. The abundance of Methanobrevibacter gottschalkii was negatively correlated with the degree of papillation of the rumen wall. Finally, co-occurrence analysis showed that the variation of the predicted methane yields was characterized by the interactive patterns between methanogens, acetogens, and concentrations of rumen metabolites. Our results show that rumen methanogen and acetogen communities have low compositional interdependence and do not exhibit parallel host evolution, which suggests that the strategies for mitigating methane production should be based on a species-specific rumen microbiota analysis.}, }
@article {pmid32710518, year = {2020}, author = {Allgeier, JE and Andskog, MA and Hensel, E and Appaldo, R and Layman, C and Kemp, DW}, title = {Rewiring coral: Anthropogenic nutrients shift diverse coral-symbiont nutrient and carbon interactions toward symbiotic algal dominance.}, journal = {Global change biology}, volume = {26}, number = {10}, pages = {5588-5601}, doi = {10.1111/gcb.15230}, pmid = {32710518}, issn = {1365-2486}, support = {OCE #0746164//National Science Foundation/ ; OCE #2023507//National Science Foundation/ ; OCE #1948622//National Science Foundation/ ; //University of Alabama at Birmingham/ ; }, mesh = {Animals ; *Anthozoa ; Carbon ; Coral Reefs ; Nutrients ; Symbiosis ; }, abstract = {Improving coral reef conservation requires heightened understanding of the mechanisms by which coral cope with changing environmental conditions to maintain optimal health. We used a long-term (10 month) in situ experiment with two phylogenetically diverse scleractinians (Acropora palmata and Porites porites) to test how coral-symbiotic algal interactions changed under real-world conditions that were a priori expected to be beneficial (fish-mediated nutrients) and to be harmful, but non-lethal, for coral (fish + anthropogenic nutrients). Analyzing nine response variables of nutrient stoichiometry and stable isotopes per coral fragment, we found that nutrients from fish positively affected coral growth, and moderate doses of anthropogenic nutrients had no additional effects. While growing, coral maintained homeostasis in their nutrient pools, showing tolerance to the different nutrient regimes. Nonetheless, structural equation models revealed more nuanced relationships, showing that anthropogenic nutrients reduced the diversity of coral-symbiotic algal interactions and caused nutrient and carbon flow to be dominated by the symbiont. Our findings show that nutrient and carbon pathways are fundamentally "rewired" under anthropogenic nutrient regimes in ways that could increase corals' susceptibility to further stressors. We hypothesize that our experiment captured coral in a previously unrecognized transition state between mutualism and antagonism. These findings highlight a notable parallel between how anthropogenic nutrients promote symbiont dominance with the holobiont, and how they promote macroalgal dominance at the coral reef scale. Our findings suggest more realistic experimental conditions, including studies across gradients of anthropogenic nutrient enrichment as well as the incorporation of varied nutrient and energy pathways, may facilitate conservation efforts to mitigate coral loss.}, }
@article {pmid32686736, year = {2020}, author = {Fernandes de Barros Marangoni, L and Ferrier-Pagès, C and Rottier, C and Bianchini, A and Grover, R}, title = {Unravelling the different causes of nitrate and ammonium effects on coral bleaching.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11975}, pmid = {32686736}, issn = {2045-2322}, mesh = {Ammonium Compounds/*pharmacology ; Analysis of Variance ; Animals ; Anthozoa/drug effects/*physiology ; Antioxidants/metabolism ; Calcification, Physiologic/drug effects ; Chlorophyll/metabolism ; Energy Metabolism/drug effects ; Lactic Acid/metabolism ; Lipid Peroxidation/drug effects ; Models, Biological ; Nitrates/*pharmacology ; Nitric Oxide/biosynthesis ; Nitrosation ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Reactive Oxygen Species/metabolism ; Symbiosis/drug effects ; Tyrosine/metabolism ; }, abstract = {Mass coral bleaching represents one of the greatest threats to coral reefs and has mainly been attributed to seawater warming. However, reduced water quality can also interact with warming to increase coral bleaching, but this interaction depends on nutrient ratios and forms. In particular, nitrate (NO3[-]) enrichment reduces thermal tolerance while ammonium (NH4[+]) enrichment tends to benefit coral health. The biochemical mechanisms underpinning the different bleaching responses of corals exposed to DIN enrichment still need to be investigated. Here, we demonstrated that the coral Stylophora pistillata underwent a severe oxidative stress condition and reduced aerobic scope when exposed to NO3[-] enrichment combined with thermal stress. Such condition resulted in increased bleaching intensity compared to a low-nitrogen condition. On the contrary, NH4[+] enrichment was able to amend the deleterious effects of thermal stress by favoring the oxidative status and energy metabolism of the coral holobiont. Overall, our results demonstrate that the opposite effects of nitrate and ammonium enrichment on coral bleaching are related to the effects on corals' energy/redox status. As nitrate loading in coastal waters is predicted to significantly increase in the future due to agriculture and land-based pollution, there is the need for urgent management actions to prevent increases in nitrate levels in seawater. In addition, the maintenance of important fish stocks, which provide corals with recycled nitrogen such as ammonium, should be favoured.}, }
@article {pmid32686311, year = {2021}, author = {Li, J and Long, L and Zou, Y and Zhang, S}, title = {Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {826-843}, pmid = {32686311}, issn = {1462-2920}, support = {2017A030306025//Guangdong Natural Science Funds for Distinguished Young Scholars/ ; 2017YFC0506303//National Key R&amp;D Program of China/ ; 41676155//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; 2017396//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; Anthozoa/*genetics/growth &amp; development/*microbiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Coral Reefs ; Dinoflagellida/genetics/physiology ; Hot Temperature ; *Microbiota ; Seawater/*chemistry/microbiology/parasitology ; Symbiosis ; Temperature ; Transcription, Genetic ; }, abstract = {A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease-associated bacteria increased at 32°C, which may affect immune responses in heat-stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non-selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.}, }
@article {pmid32684958, year = {2020}, author = {Angers, B and Perez, M and Menicucci, T and Leung, C}, title = {Sources of epigenetic variation and their applications in natural populations.}, journal = {Evolutionary applications}, volume = {13}, number = {6}, pages = {1262-1278}, pmid = {32684958}, issn = {1752-4571}, abstract = {Epigenetic processes manage gene expression and products in a real-time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet-hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.}, }
@article {pmid32681284, year = {2021}, author = {Varasteh, T and Hamerski, L and Tschoeke, D and Lima, AS and Garcia, G and Cosenza, CAN and Thompson, C and Thompson, F}, title = {Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {267-277}, pmid = {32681284}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Antioxidants/*metabolism ; Bacteroidetes/genetics/isolation &amp; purification/*metabolism ; Brazil ; Carotenoids/metabolism ; Catalase/biosynthesis ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Oxidoreductases/biosynthesis ; Paracoccus/genetics/isolation &amp; purification/*metabolism ; Peroxidase/biosynthesis ; Pigments, Biological/genetics/*metabolism ; Pseudoalteromonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.}, }
@article {pmid32676070, year = {2020}, author = {Mensch, B and Neulinger, SC and Künzel, S and Wahl, M and Schmitz, RA}, title = {Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1471}, pmid = {32676070}, issn = {1664-302X}, abstract = {Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10-11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and-particularly during spring and summer-an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem.}, }
@article {pmid32669465, year = {2020}, author = {Yergaliyev, TM and Alexander-Shani, R and Dimerets, H and Pivonia, S and Bird, DM and Rachmilevitch, S and Szitenberg, A}, title = {Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32669465}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/metabolism ; DNA Barcoding, Taxonomic ; Genetic Variation ; *Host Microbial Interactions ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology/*parasitology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; Tylenchoidea/*microbiology/physiology ; }, abstract = {Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.}, }
@article {pmid32664706, year = {2020}, author = {Malassigné, S and Valiente Moro, C and Luis, P}, title = {Mosquito Mycobiota: An Overview of Non-Entomopathogenic Fungal Interactions.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {7}, pages = {}, pmid = {32664706}, issn = {2076-0817}, support = {(IDEX Lyon - Universit&#xe9; de Lyon)//Scientific Breakthrough Program Micro-be-have/ ; }, abstract = {The growing expansion of mosquito vectors leads to the emergence of vector-borne diseases in new geographic areas and causes major public health concerns. In the absence of effective preventive treatments against most pathogens transmitted, vector control remains one of the most suitable strategies to prevent mosquito-borne diseases. Insecticide overuse raises mosquito resistance and deleterious impacts on the environment and non-target species. Growing knowledge of mosquito biology has allowed the development of alternative control methods. Following the concept of holobiont, mosquito-microbiota interactions play an important role in mosquito biology. Associated microbiota is known to influence many aspects of mosquito biology such as development, survival, immunity or even vector competence. Mosquito-associated microbiota is composed of bacteria, fungi, protists, viruses and nematodes. While an increasing number of studies have focused on bacteria, other microbial partners like fungi have been largely neglected despite their huge diversity. A better knowledge of mosquito-mycobiota interactions offers new opportunities to develop innovative mosquito control strategies. Here, we review the recent advances concerning the impact of mosquito-associated fungi, and particularly nonpathogenic fungi, on life-history traits (development, survival, reproduction), vector competence and behavior of mosquitoes by focusing on Culex, Aedes and Anopheles species.}, }
@article {pmid32662980, year = {2020}, author = {Mohanty, I and Moore, SG and Yi, D and Biggs, JS and Gaul, DA and Garg, N and Agarwal, V}, title = {Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids.}, journal = {ACS chemical biology}, volume = {15}, number = {8}, pages = {2185-2194}, pmid = {32662980}, issn = {1554-8937}, support = {K99 ES026620/ES/NIEHS NIH HHS/United States ; R00 ES026620/ES/NIEHS NIH HHS/United States ; }, mesh = {Alkaloids/*biosynthesis/*chemistry ; Animals ; Imidazoles/*chemistry ; *Metabolome ; Microbiota ; Phylogeny ; Porifera/*metabolism ; Pyrroles/*chemistry ; }, abstract = {Pyrrole-imidazole alkaloids are natural products isolated from marine sponges, holobiont metazoans that are associated with symbiotic microbiomes. Pyrrole-imidazole alkaloids have attracted attention due to their chemical complexity and their favorable pharmacological properties. However, insights into how these molecules are biosynthesized within the sponge holobionts are scarce. Here, we provide a multiomic profiling of the microbiome and metabolomic architectures of three sponge genera that are prolific producers of pyrrole-imidazole alkaloids. Using a retrobiosynthetic scheme as a guide, we mine the metabolomes of these sponges to detect intermediates in pyrrole-imidazole alkaloid biosynthesis. Our findings reveal that the nonproteinogenic amino acid homoarginine is a critical branch point that connects primary metabolite lysine to the production of pyrrole-imidazole alkaloids. These insights are derived from the polar metabolomes of these sponges which additionally reveal the presence of zwitterionic betaines that may serve important ecological roles in marine habitats. We also establish that metabolomic richness does not correlate with microbial diversity of the sponge holobiont for neither the polar nor the nonpolar metabolomes. Our findings now provide the biochemical foundation for genomic interrogation of the sponge holobiont to establish biogenetic routes for pyrrole-imidazole alkaloid production.}, }
@article {pmid32645351, year = {2020}, author = {Groussin, M and Mazel, F and Alm, EJ}, title = {Co-evolution and Co-speciation of Host-Gut Bacteria Systems.}, journal = {Cell host &amp; microbe}, volume = {28}, number = {1}, pages = {12-22}, doi = {10.1016/j.chom.2020.06.013}, pmid = {32645351}, issn = {1934-6069}, mesh = {Animals ; Bacteria/genetics/immunology ; *Biological Coevolution ; *Gastrointestinal Microbiome ; *Genetic Speciation ; Host Microbial Interactions ; Humans ; Mammals/genetics/immunology/microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Mammalian gut microbiomes profoundly influence host fitness, but the processes that drive the evolution of host-microbiome systems are poorly understood. Recent studies suggest that mammals and their individual gut symbionts can have parallel evolutionary histories, as represented by their congruent phylogenies. These "co-phylogenetic" patterns are signatures of ancient co-speciation events and illustrate the cohesiveness of the mammalian host-gut microbiome entity over evolutionary times. Theory predicts that co-speciation between mammals and their gut symbionts could result from their co-evolution. However, there is only limited evidence of such co-evolution. Here, we propose a model that explains cophylogenetic patterns without relying on co-evolution. Specifically, we suggest that individual gut bacteria are likely to diverge in patterns recapitulating host phylogeny when hosts undergo allopatric speciation, limiting inter-host bacterial dispersal and genomic recombination. We provide evidence that the model is empirically grounded and propose a series of observational and experimental approaches to test its validity.}, }
@article {pmid32635154, year = {2020}, author = {Bertazzon, N and Chitarra, W and Angelini, E and Nerva, L}, title = {Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {7}, pages = {}, pmid = {32635154}, issn = {2223-7747}, support = {VITE 4.0//Cassa di Risparmio di Cuneo/ ; DiBIO - Subproject BIOPRIME//Ministero delle Politiche Agricole Alimentari e Forestali/ ; }, abstract = {The concept of plant as a holobiont is now spreading among the scientific community and the importance to study plant-associated microorganisms is becoming more and more necessary. Along with bacteria and fungi, also viruses can play important roles during the holobiont-environment interactions. In grapevine, viruses are studied mainly as pathological agents, and many species (more than 80) are known to be able to replicate inside its tissues. In this study two new viral species associated with grape wood tissues are presented, one belongs to the Potyviridae family and one to the Bunyavirales order. Due to the ability of potyviruses to enhance heterologous virus replication, it will be important to assess the presence of such a virus in the grapevine population to understand its ecological role. Furthermore, the association of the cogu-like virus with esca symptomatic samples opens new questions and the necessity of a more detailed characterization of this virus.}, }
@article {pmid32627905, year = {2020}, author = {Herrera, M and Klein, SG and Schmidt-Roach, S and Campana, S and Cziesielski, MJ and Chen, JE and Duarte, CM and Aranda, M}, title = {Unfamiliar partnerships limit cnidarian holobiont acclimation to warming.}, journal = {Global change biology}, volume = {26}, number = {10}, pages = {5539-5553}, pmid = {32627905}, issn = {1365-2486}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Heat-Shock Response ; Symbiosis ; }, abstract = {Enhancing the resilience of corals to rising temperatures is now a matter of urgency, leading to growing efforts to explore the use of heat tolerant symbiont species to improve their thermal resilience. The notion that adaptive traits can be retained by transferring the symbionts alone, however, challenges the holobiont concept, a fundamental paradigm in coral research. Holobiont traits are products of a specific community (holobiont) and all its co-evolutionary and local adaptations, which might limit the retention or transference of holobiont traits by exchanging only one partner. Here we evaluate how interchanging partners affect the short- and long-term performance of holobionts under heat stress using clonal lineages of the cnidarian model system Aiptasia (host and Symbiodiniaceae strains) originating from distinct thermal environments. Our results show that holobionts from more thermally variable environments have higher plasticity to heat stress, but this resilience could not be transferred to other host genotypes through the exchange of symbionts. Importantly, our findings highlight the role of the host in determining holobiont productivity in response to thermal stress and indicate that local adaptations of holobionts will likely limit the efficacy of interchanging unfamiliar compartments to enhance thermal tolerance.}, }
@article {pmid32620152, year = {2020}, author = {Clerissi, C and Guillou, L and Escoubas, JM and Toulza, E}, title = {Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {193}, pmid = {32620152}, issn = {1471-2180}, mesh = {Alveolata/*classification/genetics/isolation &amp; purification ; Animals ; Crassostrea/*parasitology ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA/methods ; Stramenopiles/*classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far.<br><br>RESULTS: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples.<br><br>CONCLUSIONS: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.}, }
@article {pmid32616905, year = {2020}, author = {Breusing, C and Mitchell, J and Delaney, J and Sylva, SP and Seewald, JS and Girguis, PR and Beinart, RA}, title = {Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2568-2579}, pmid = {32616905}, issn = {1751-7370}, mesh = {Animals ; Ecosystem ; *Gammaproteobacteria/genetics ; *Hydrothermal Vents ; Phylogeny ; Symbiosis ; }, abstract = {Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host-symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.}, }
@article {pmid32614866, year = {2020}, author = {Vogel, MA and Mason, OU and Miller, TE}, title = {Host and environmental determinants of microbial community structure in the marine phyllosphere.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235441}, pmid = {32614866}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Fresh Water/*microbiology ; Gulf of Mexico ; Host Microbial Interactions ; Hydrocharitaceae/*microbiology/physiology ; *Microbiota ; Phylogeny ; Plant Leaves/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Wetlands ; }, abstract = {Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.}, }
@article {pmid32612612, year = {2020}, author = {Dierking, K and Pita, L}, title = {Receptors Mediating Host-Microbiota Communication in the Metaorganism: The Invertebrate Perspective.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1251}, pmid = {32612612}, issn = {1664-3224}, mesh = {Animals ; Biodiversity ; Homeostasis ; *Host Microbial Interactions/immunology ; Humans ; Invertebrates ; *Microbiota/immunology ; Protein Binding ; Receptors, Pattern Recognition/*metabolism ; *Signal Transduction ; Species Specificity ; }, abstract = {Multicellular organisms live in close association with a plethora of microorganism, which have a profound effect on multiple host functions. As such, the microbiota and its host form an intimate functional entity, termed the metaorganism or holobiont. But how does the metaorganism communicate? Which receptors recognize microbial signals, mediate the effect of the microbiota on host physiology or regulate microbiota composition and homeostasis? In this review we provide an overview on the function of different receptor classes in animal host-microbiota communication. We put a special focus on invertebrate hosts, including both traditional invertebrate models such as Drosophila melanogaster and Caenorhabditis elegans and "non-model" invertebrates in microbiota research. Finally, we highlight the potential of invertebrate systems in studying mechanism of host-microbiota interactions.}, }
@article {pmid32587579, year = {2020}, author = {Bourgin, M and Labarthe, S and Kriaa, A and Lhomme, M and Gérard, P and Lesnik, P and Laroche, B and Maguin, E and Rhimi, M}, title = {Exploring the Bacterial Impact on Cholesterol Cycle: A Numerical Study.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1121}, pmid = {32587579}, issn = {1664-302X}, abstract = {High blood cholesterol levels are often associated with cardiovascular diseases. Therapeutic strategies, targeting different functions involved in cholesterol transport or synthesis, were developed to control cholesterolemia in human. However, the gut microbiota is also involved in cholesterol regulation by direct biotransformation of luminal cholesterol or conversion of bile salts, opening the way to the design of new strategies to manage cholesterol level. In this report, we developed for the first time a whole-body human model of cholesterol metabolism including the gut microbiota in order to investigate the relative impact of host and microbial pathways. We first used an animal model to investigate the ingested cholesterol distribution in vivo. Then, using in vitro bacterial growth experiments and metabolite measurements, we modeled the population dynamics of bacterial strains in the presence of cholesterol or bile salts, together with their bioconversion function. Next, after correct rescaling to mimic the activity of a complex microbiota, we developed a whole body model of cholesterol metabolism integrating host and microbiota mechanisms. This global model was validated with the animal experiments. Finally, the model was numerically explored to give a further insight into the different flux involved in cholesterol turn-over. According to this model, bacterial pathways appear as an important driver of cholesterol regulation, reinforcing the need for development of novel "bacteria-based" strategies for cholesterol management.}, }
@article {pmid32566125, year = {2020}, author = {Gacesa, R and Hung, JY and Bourne, DG and Long, PF}, title = {Horizontal transfer of a natterin-like toxin encoding gene within the holobiont of the reef building coral Acropora digitifera (Cnidaria: Anthozoa: Scleractinia) and across multiple animal linages.}, journal = {Journal of venom research}, volume = {10}, number = {}, pages = {7-12}, pmid = {32566125}, issn = {2044-0324}, abstract = {Phylogenetic evidence is provided for horizontal transfer of a natterin-like toxin encoding gene from fungi into the genome of the coral Acropora digitifera. Sequencing analysis of the coral tissues supported that a fungal taxon predicted to be the most likely gene donor was represented in the coral microbiome. Further bioinformatics data suggested widespread recruitment of the natterin-like gene into venomous terrestrial invertebrates, and repositioning of this gene to non-toxic functions in non-venomous teleost fish.}, }
@article {pmid32555283, year = {2020}, author = {Guibert, I and Bourdreux, F and Bonnard, I and Pochon, X and Dubousquet, V and Raharivelomanana, P and Berteaux-Lecellier, V and Lecellier, G}, title = {Dimethylsulfoniopropionate concentration in coral reef invertebrates varies according to species assemblages.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9922}, pmid = {32555283}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*metabolism ; Bivalvia/*metabolism ; *Coral Reefs ; Sulfonium Compounds/*metabolism ; Sulfur/*metabolism ; *Symbiosis ; }, abstract = {Dimethylsulfoniopropionate (DMSP) is a key compound in the marine sulfur cycle, and is produced in large quantities in coral reefs. In addition to Symbiodiniaceae, corals and associated bacteria have recently been shown to play a role in DMSP metabolism. Numerous ecological studies have focused on DMSP concentrations in corals, which led to the hypothesis that increases in DMSP levels might be a general response to stress. Here we used multiple species assemblages of three common Indo-Pacific holobionts, the scleractinian corals Pocillopora damicornis and Acropora cytherea, and the giant clam Tridacna maxima and examined the DMSP concentrations associated with each species within different assemblages and thermal conditions. Results showed that the concentration of DMSP in A. cytherea and T. maxima is modulated according to the complexity of species assemblages. To determine the potential importance of symbiotic dinoflagellates in DMSP production, we then explored the relative abundance of Symbiodiniaceae clades in relation to DMSP levels using metabarcoding, and found no significant correlation between these factors. Finally, this study also revealed the existence of homologs involved in DMSP production in giant clams, suggesting for the first time that, like corals, they may also contribute to DMSP production. Taken together, our results demonstrated that corals and giant clams play important roles in the sulfur cycle. Because DMSP production varies in response to specific species-environment interactions, this study offers new perspectives for future global sulfur cycling research.}, }
@article {pmid32554943, year = {2020}, author = {Chiba, Y and Tomaru, Y and Shimabukuro, H and Kimura, K and Hirai, M and Takaki, Y and Hagiwara, D and Nunoura, T and Urayama, SI}, title = {Viral RNA Genomes Identified from Marine Macroalgae and a Diatom.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, pmid = {32554943}, issn = {1347-4405}, mesh = {Biodiversity ; Diatoms/*virology ; Double Stranded RNA Viruses/classification/*genetics/isolation &amp; purification ; Genome, Viral/*genetics ; Phylogeny ; Seawater/*virology ; Seaweed/*virology ; Viral Proteins/genetics ; Virome ; }, abstract = {Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.}, }
@article {pmid32550573, year = {2019}, author = {Ul-Hasan, S and Rodríguez-Román, E and Reitzel, AM and Adams, RMM and Herzig, V and Nobile, CJ and Saviola, AJ and Trim, SA and Stiers, EE and Moschos, SA and Keiser, CN and Petras, D and Moran, Y and Colston, TJ}, title = {The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP).}, journal = {Toxicon: X}, volume = {4}, number = {}, pages = {100016}, pmid = {32550573}, issn = {2590-1710}, abstract = {Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium.}, }
@article {pmid32548850, year = {2020}, author = {Voolstra, CR and Ziegler, M}, title = {Adapting with Microbial Help: Microbiome Flexibility Facilitates Rapid Responses to Environmental Change.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {7}, pages = {e2000004}, doi = {10.1002/bies.202000004}, pmid = {32548850}, issn = {1521-1878}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota ; Symbiosis ; }, abstract = {Animals and plants are metaorganisms and associate with microbes that affect their physiology, stress tolerance, and fitness. Here the hypothesis that alteration of the microbiome may constitute a fast-response mechanism to environmental change is examined. This is supported by recent reciprocal transplant experiments with reef corals, which have shown that their microbiome adapts to thermally variable habitats and changes over time when transplanted into different environments. Further, inoculation of corals with beneficial bacteria increases their stress tolerance. But corals differ in their ability to flexibly associate with different bacteria. How scales of microbiome flexibility may reflect different metaorganism adaptation mechanisms is discussed and future directions for research are pinpointed. It is posited that microbiome flexibility is a broad phenomenon that contributes to the ability of organisms to respond to environmental change. Importantly, adapting with microbial help may provide an alternate route to organismal adaptation that facilitates rapid responses.}, }
@article {pmid32544798, year = {2020}, author = {Zelante, T and Costantini, C and Romani, L}, title = {Microbiome-mediated regulation of anti-fungal immunity.}, journal = {Current opinion in microbiology}, volume = {58}, number = {}, pages = {8-14}, doi = {10.1016/j.mib.2020.05.002}, pmid = {32544798}, issn = {1879-0364}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Fungi/genetics/immunology/*physiology ; Humans ; Immunity ; *Microbiota ; Mycoses/*immunology/microbiology ; }, abstract = {Anti-fungal immunity is characterized by the continuous interplay between immune activation and immune regulation processes. These processes have now been clearly shown not only in animal pre-clinical models but also in humans. To create and maintain this immune homeostasis, reciprocal interactions among the host immune system, fungal pathogens, and the microbiome are crucial. Notably, the microbiome exerts multiple direct and indirect antifungal effects that are particularly aimed at minimizing host tissue damage. Thus, in this microbiome era, the architecture of 3D culture system or 'tissue organoids' might finally represent a simple but effective in vitro 'holobiont' to unravel the diverse interactions and adaptations that evolve to overcome fungal infections.}, }
@article {pmid32542933, year = {2020}, author = {Bohmann, K and Mirarab, S and Bafna, V and Gilbert, MTP}, title = {Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification.}, journal = {Molecular ecology}, volume = {29}, number = {14}, pages = {2521-2534}, pmid = {32542933}, issn = {1365-294X}, support = {R01 GM114362/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *DNA ; *DNA Barcoding, Taxonomic ; DNA Primers ; Databases, Genetic ; Genomics/*methods ; Polymerase Chain Reaction ; }, abstract = {Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based "genome skimming" alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its "DNA-mark") for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such "DNA-marks," it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.}, }
@article {pmid32542314, year = {2020}, author = {Kusstatscher, P and Cernava, T and Abdelfattah, A and Gokul, J and Korsten, L and Berg, G}, title = {Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {7}, pages = {}, doi = {10.1093/femsec/fiaa119}, pmid = {32542314}, issn = {1574-6941}, mesh = {Bacteria/genetics ; Fruit ; Fungi ; *Microbiota ; *Vegetables ; }, abstract = {Microbes play an important role in plants and interact closely with their host starting from sprouting seeds, continuing during growth and after harvest. The discovery of their importance for plant and postharvest health initiated a biotechnological development of various antagonistic bacteria and fungi for disease control. Nevertheless, their application often showed inconsistent effects. Recently, high-throughput sequencing-based techniques including advanced microscopy reveal fruits and vegetables as holobionts. At harvest, all fruits and vegetables harbor a highly abundant and specific microbiota including beneficial, pathogenic and spoilage microorganisms. Especially, a high microbial diversity and resilient microbial networks were shown to be linked to fruit and vegetable health, while diseased products showed severe dysbiosis. Field and postharvest handling of fruits and vegetables was shown to affect the indigenous microbiome and therefore has a substantial impact on the storability of fruits and vegetables. Microbiome tracking can be implemented as a new tool to evaluate and assess all postharvest processes and contribute to fruit and vegetable health. Here, we summarize current research advancements in the emerging field of postharvest microbiomes and elaborate its importance. The generated knowledge provides profound insights into postharvest microbiome dynamics and sets a new basis for targeted, microbiome-driven and sustainable control strategies.}, }
@article {pmid32537770, year = {2020}, author = {Fields, C and Levin, M}, title = {Scale-Free Biology: Integrating Evolutionary and Developmental Thinking.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {8}, pages = {e1900228}, doi = {10.1002/bies.201900228}, pmid = {32537770}, issn = {1521-1878}, support = {12171//Paul G. Allen Frontiers Group/International ; TWCF0089/AB55//Templeton World Charity Foundation/International ; //Paul G. Allen Frontiers Group/International ; }, mesh = {*Biological Evolution ; *Developmental Biology ; Humans ; }, abstract = {When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and selection become, for example, bidirectional information flows between scales, while the notions of "cooperation" and "competition" become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale-free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system.}, }
@article {pmid32528423, year = {2020}, author = {Saad, OS and Lin, X and Ng, TY and Li, L and Ang, P and Lin, S}, title = {Genome Size, rDNA Copy, and qPCR Assays for Symbiodiniaceae.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {847}, pmid = {32528423}, issn = {1664-302X}, abstract = {Symbiodiniaceae community structure in corals is crucial for understanding the plasticity of different holobionts under environmental stress. While this relies on molecular analyses, accuracy of molecular quantification, as influenced by DNA extraction efficiency and rDNA copy number variations in particular, has rarely been systematically investigated. Here, we report the development of a set of genus-specific qPCR assays. First, a protocol for efficient DNA isolation and accurate measurements of genome size and rDNA copy number was established. Second, seven newly designed genus-specific ITS2 primer sets were validated using computational and empirical analyses and qPCR assays were developed. We find that while the genome size ranges between 1.75 ± 0.21 and 4.5 ± 0.96 Gbp, rDNA copy number shows over 10-fold variation among Symbiodiniaceae species. Our protocol produced standard curves with high efficiencies (89.8-99.3%; R [2] ≥ 0.999) and tight Cq values over different PCR conditions, illustrating high specificity and sensitivity of the qPCR assays. Tested on mock communities of mixed culture species, our qPCR results agreed well with microscopic counts and facilitated calibration of metabarcoding data. To test the applicability of our protocol for field samples, we analyzed three different Hong Kong coral samples. Six Symbiodiniaceae genera were detected in Acropora valida, Oulastrea crispata, and Platygyra acuta, with Breviolum, Effrenium, Fugacium, and Gerakladium sp. being reported for the first time. Our results suggest that aggressively disrupting cells to ensure thorough cell lysis, estimating cell loss and DNA loss, and validating qPCR assays are critical for success. The number of species examined here is limited, but the primers are potentially applicable to most species in respective genera, and the protocol and the approach to develop it provide a base and template toward a standardized procedure for quantitatively characterizing Symbiodiniaceae communities in corals.}, }
@article {pmid32521261, year = {2020}, author = {Vandehoef, C and Molaei, M and Karpac, J}, title = {Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP.}, journal = {Cell reports}, volume = {31}, number = {10}, pages = {107736}, pmid = {32521261}, issn = {2211-1247}, support = {F30 DK117538/DK/NIDDK NIH HHS/United States ; P40 OD010949/OD/NIH HHS/United States ; R01 DK108930/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Diet ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/metabolism/*microbiology ; Female ; Intracellular Signaling Peptides and Proteins/*metabolism ; Male ; *Microbiota ; NF-kappa B/*metabolism ; Peptide Initiation Factors/*metabolism ; Signal Transduction ; }, abstract = {Dietary nutrients shape complex interactions between hosts and their commensal gut bacteria, further promoting flexibility in host-microbiota associations that can drive nutritional symbiosis. However, it remains less clear if diet-dependent host signaling mechanisms also influence these associations. Using Drosophila, we show here that nuclear factor κB (NF-κB)/Relish, an innate immune transcription factor emerging as a signaling node linking nutrient-immune-metabolic interactions, is vital to adapt gut microbiota species composition to host diet macronutrient composition. We find that Relish is required within midgut enterocytes to amplify host-Lactobacillus associations, an important bacterial mediator of nutritional symbiosis, and thus modulate microbiota composition in response to dietary adaptation. Relish limits diet-dependent transcriptional inducibility of the cap-dependent translation inhibitor 4E-BP/Thor to control microbiota composition. Furthermore, maintaining cap-dependent translation in response to dietary adaptation is critical to amplify host-Lactobacillus associations. These results highlight that NF-κB-dependent host signaling mechanisms, in coordination with host translation control, shape diet-microbiota interactions.}, }
@article {pmid32518251, year = {2020}, author = {Bovo, S and Utzeri, VJ and Ribani, A and Cabbri, R and Fontanesi, L}, title = {Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9279}, pmid = {32518251}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Bees ; DNA, Environmental/*analysis/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Plant/genetics ; Genome, Protozoan/genetics ; Genome, Viral/genetics ; Honey/*analysis ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.}, }
@article {pmid32517729, year = {2020}, author = {Pagliai, G and Dinu, M and Fiorillo, C and Becatti, M and Turroni, S and Emmi, G and Sofi, F}, title = {Modulation of gut microbiota through nutritional interventions in Behçet's syndrome patients (the MAMBA study): study protocol for a randomized controlled trial.}, journal = {Trials}, volume = {21}, number = {1}, pages = {511}, pmid = {32517729}, issn = {1745-6215}, support = {GR-2016-02361162//Italian Ministry of Health/ ; }, mesh = {Behcet Syndrome/*etiology/microbiology ; Body Composition ; Butyrates/*administration &amp; dosage ; Cross-Over Studies ; *Diet, Mediterranean ; *Diet, Vegetarian ; Dietary Supplements ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Randomized Controlled Trials as Topic ; Risk ; }, abstract = {BACKGROUND: Behçet's syndrome (BS) is a systemic inflammatory disorder of unknown etiology, and it is characterized by a wide range of potential clinical manifestations. Recent evidence suggests that the gut microbiota (GM) in BS has low biodiversity with a significant depletion in butyrate producers. The aim of the present project is to investigate whether a dietary intervention could ameliorate the clinical manifestations and modulate the GM of individuals with BS.<br><br>METHODS: This is a randomized, open, cross-over study that involves 90 individuals with BS, who will be randomly assigned to one of three different diets for 3&#x2009;months: a lacto-ovo-vegetarian diet (VD), a Mediterranean diet (MD), or a Mediterranean diet supplemented with butyrate (MD-Bt). The VD will contain inulin-resistant and resistant-starch-rich foods, eggs, and dairy in addition to plant-based food, but it will not contain meat, poultry, or fish. The MD will contain all food categories and will provide two portions per week of fish and three portions per week of fresh and processed meat. The MD-Bt will be similar to the MD but supplemented with 1.8&#x2009;g/day of oral butyrate. The three different diets will be isocaloric and related to the participants' nutritional requirements. Anthropometric measurements, body composition, blood, and fecal samples will be obtained from each participant at the beginning and the end of each intervention phase. The primary outcomes will be represented by the change from baseline of the BS gastrointestinal and systemic symptoms. Changes from baseline in GM composition, short-chain fatty acid (SCFA) production, and the inflammatory and antioxidant profile will be considered as secondary outcomes.<br><br>DISCUSSION: BS is a rare disease, and, actually, not all the available treatments are target therapies. A supportive treatment based on dietary and lifestyle issues, able to restore immune system homeostasis, could have a high impact on cost sustainability for the treatment of such a chronic and disabling inflammatory condition.<br><br>TRIAL REGISTRATION: clinicaltrials.gov: NCT03962335. Registered on 21 May 2019.}, }
@article {pmid32513310, year = {2020}, author = {Douglas, GM and Bielawski, JP and Langille, MGI}, title = {Re-evaluating the relationship between missing heritability and the microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {87}, pmid = {32513310}, issn = {2049-2618}, support = {CMF-108026//CIHR/Canada ; }, mesh = {Genetic Variation ; Genome, Human ; *Genome-Wide Association Study ; Humans ; *Microbiota/genetics ; Phenotype ; }, abstract = {Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typical GWASs. The human microbiome is potentially related to both of these explanations, but it has been more commonly considered as a source of unmeasured genetic variation. In particular, it has recently been argued that the genetic variation within the human microbiome should be included when estimating trait heritability. We outline issues with this argument, which in its strictest form depends on the holobiont model of human-microbiome interactions. Instead, we argue that the microbiome could be leveraged to help control for environmental variation across a population, although that remains to be determined. We discuss potential approaches that could be explored to determine whether integrating microbiome sequencing data into GWASs is useful. Video abstract.}, }
@article {pmid32510843, year = {2020}, author = {Alonso, P and Blondin, L and Gladieux, P and Mahé, F and Sanguin, H and Ferdinand, R and Filloux, D and Desmarais, E and Cerqueira, F and Jin, B and Huang, H and He, X and Morel, JB and Martin, DP and Roumagnac, P and Vernière, C}, title = {Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3429-3445}, pmid = {32510843}, issn = {1462-2920}, support = {//National Research Foundation of South Africa/International ; //INRAE/Yunnan Agricultural University/International ; //International Associated Laboratory Plantomix/International ; //Yunnan Agricultural University/International ; ANR-17-CE32-0011//French National Research Agency/International ; //E-Space Flagship Program/International ; 1504-004//Agropolis Fondation/International ; //French International and Agricultural Research Agency (CIRAD)/International ; }, mesh = {Agriculture/methods ; *Biodiversity ; China ; Humans ; Microbiota/*genetics ; Oryza/*microbiology ; Plant Diseases/microbiology ; }, abstract = {The Honghe Hani rice terraces system (HHRTS) is a traditional rice cultivation system where Hani people cultivate remarkably diverse rice varieties. Recent introductions of modern rice varieties to the HHRTS have significantly increased the severity of rice diseases within the terraces. Here, we determine the impacts of these recent introductions on the composition of the rice-associated microbial communities. We confirm that the HHRTS contains a range of both traditional HHRTS landraces and introduced modern rice varieties and find differences between the microbial communities of these two groups. However, this introduction of modern rice varieties has not strongly impacted the overall diversity of the HHRTS rice microbial community. Furthermore, we find that the rice varieties (i.e. groups of closely related genotypes) have significantly structured the rice microbial community composition (accounting for 15%-22% of the variance) and that the core microbial community of HHRTS rice plants represents less than 3.3% of all the microbial taxa identified. Collectively, our study suggests a highly diverse HHRTS rice holobiont (host with its associated microbes) where the diversity of rice hosts mirrors the diversity of their microbial communities. Further studies will be needed to better determine how such changes might impact the sustainability of the HHRTS.}, }
@article {pmid32510361, year = {2020}, author = {Yu, X and Yu, K and Liao, Z and Liang, J and Deng, C and Huang, W and Huang, Y}, title = {Potential molecular traits underlying environmental tolerance of Pavona decussata and Acropora pruinosa in Weizhou Island, northern South China Sea.}, journal = {Marine pollution bulletin}, volume = {156}, number = {}, pages = {111199}, doi = {10.1016/j.marpolbul.2020.111199}, pmid = {32510361}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa ; Bacteria ; China ; *Dinoflagellida ; Islands ; }, abstract = {Coral species display varying susceptibilities to biotic or abiotic stress. To address the causes underlying this phenomenon, we profiled the Symbiodiniaceae clade type, bacterial communities and coral transcriptome responses in Pavona decussata and Acropora pruinosa, two species displaying different environmental tolerances in the Weizhou Island. We found that C1 was the most dominant Symbiodiniaceae subclade, with no difference detected between A. pruinosa and P. decussata. Nevertheless, P. decussata exhibited higher microbial diversity and significantly different community structure compared with that of A. pruinosa. Transcriptome analysis revealed that coral genes with significantly high expression in P. decussata were mostly related to immune and stress-resistance responses, whereas, those with significantly low expression were metabolism-related. We postulate that the higher tolerance of P. decussata as compared with that of A. pruinosa is the result of several traits, such as higher microbial diversity, different dominant bacteria, higher immune and stress-resistant response, and lower metabolic rate.}, }
@article {pmid32508779, year = {2020}, author = {Jorge, F and Dheilly, NM and Poulin, R}, title = {Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {954}, pmid = {32508779}, issn = {1664-302X}, abstract = {Animal microbiomes influence their development, behavior and interactions with other organisms. Parasitic metazoans also harbor microbial communities; although they are likely to modulate host-parasite interactions, little is known about parasite microbiomes. The persistence of microbial communities throughout the life of a parasite is particularly challenging for helminths with complex life cycles. These parasites undergo major morphological changes during their life, and parasitize host species that are immunologically, physiologically, and phylogenetically very different. Here, using 16S amplicon sequencing, we characterize the microbiome of the trematode Coitocaecum parvum across four of its life stages: sporocysts, metacercariae and adults inhabiting (respectively) snails, crustaceans and fish, as well as free-living cercariae. Our results demonstrate that, at each life stage, the parasite possesses a phylogenetically diverse microbiome, distinct from that of its hosts or the external environment. The parasite's microbiome comprises bacterial taxa specific to each life stage in different hosts, as well as a small core set of taxa that persists across the parasite's whole life. The apparent existence of an ontogenetically and vertically transmitted core microbiome is supported by the findings that the diversity and taxonomic composition of the microbiome does not vary significantly among life stages, and that the main source of microbial taxa at any life stage is the previous life stage. Our results suggest that microbes are an integrated component of the trematode, possibly shaping its phenotype and host-parasite interactions.}, }
@article {pmid32507851, year = {2020}, author = {McCauley, EP and Piña, IC and Thompson, AD and Bashir, K and Weinberg, M and Kurz, SL and Crews, P}, title = {Highlights of marine natural products having parallel scaffolds found from marine-derived bacteria, sponges, and tunicates.}, journal = {The Journal of antibiotics}, volume = {73}, number = {8}, pages = {504-525}, pmid = {32507851}, issn = {1881-1469}, support = {R01 AI141511/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Aquatic Organisms/*chemistry ; Bacteria/*chemistry ; Biological Products/*chemistry ; Metagenomics/methods ; Porifera/*chemistry ; Urochordata/*chemistry ; }, abstract = {Marine-derived bacteria are a prolific source of a wide range of structurally diverse natural products. This review, dedicated to Professor William Fenical, begins by showcasing many seminal discoveries made at the University of California San Diego from marine-derived actinomycetes. Discussed early on is the 20-year journey of discovery and advancement of the seminal actinomycetes natural product salinosporamide A into Phase III anticancer clinical trials. There are many fascinating parallels discussed that were gleaned from the comparative literature of marine sponge, tunicate, and bacteria-derived natural products. Identifying bacterial biosynthetic machinery housed in sponge and tunicate holobionts through both culture-independent and culture-dependent approaches is another important and expanding subject that is analyzed. Work reviewed herein also evaluates the hypotheses that many marine invertebrate-derived natural products are biosynthesised by associated or symbiotic bacteria. The insights and outcomes from metagenomic sequencing and synthetic biology to expand molecule discovery continue to provide exciting outcomes and they are predicted to be the source of the next generation of novel marine natural product chemical scaffolds.}, }
@article {pmid32504001, year = {2020}, author = {Gouveia, D and Pible, O and Culotta, K and Jouffret, V and Geffard, O and Chaumot, A and Degli-Esposti, D and Armengaud, J}, title = {Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {23}, pmid = {32504001}, issn = {2055-5008}, mesh = {Amphipoda/*microbiology ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Gastrointestinal Microbiome ; Phylogeny ; Proteogenomics/*methods ; Proteomics/*methods ; Sequence Analysis, RNA ; Tandem Mass Spectrometry ; }, abstract = {Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.}, }
@article {pmid32498449, year = {2020}, author = {Murray, AE and Avalon, NE and Bishop, L and Davenport, KW and Delage, E and Dichosa, AEK and Eveillard, D and Higham, ML and Kokkaliari, S and Lo, CC and Riesenfeld, CS and Young, RM and Chain, PSG and Baker, BJ}, title = {Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica.}, journal = {Marine drugs}, volume = {18}, number = {6}, pages = {}, pmid = {32498449}, issn = {1660-3397}, support = {R21 CA205932/CA/NCI NIH HHS/United States ; OPP-0442857, ANT-0838776, PLR-1341339, ANT-0632389, DBI-0532893//National Science Foundation/ ; CA205932/NH/NIH HHS/United States ; }, mesh = {Animals ; Antarctic Regions ; Islands ; Macrolides/*analysis ; *Microbiota ; RNA, Ribosomal, 16S ; Urochordata/*microbiology ; }, abstract = {Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3-V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)-20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.}, }
@article {pmid32498442, year = {2020}, author = {Gamalero, E and Bona, E and Todeschini, V and Lingua, G}, title = {Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction.}, journal = {Biology}, volume = {9}, number = {6}, pages = {}, pmid = {32498442}, issn = {2079-7737}, abstract = {Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world's population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.}, }
@article {pmid32497352, year = {2020}, author = {Speare, L and Davies, SW and Balmonte, JP and Baumann, J and Castillo, KD}, title = {Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef.}, journal = {Molecular ecology}, volume = {29}, number = {13}, pages = {2334-2348}, doi = {10.1111/mec.15497}, pmid = {32497352}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; *Bacteria/classification ; Belize ; Coral Reefs ; *Dinoflagellida/classification ; *Microbiota ; }, abstract = {A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.}, }
@article {pmid32484275, year = {2020}, author = {Hawksworth, DL and Grube, M}, title = {Lichens redefined as complex ecosystems.}, journal = {The New phytologist}, volume = {227}, number = {5}, pages = {1281-1283}, pmid = {32484275}, issn = {1469-8137}, mesh = {Biodiversity ; Ecosystem ; *Lichens ; Saccharomyces cerevisiae ; Symbiosis ; }, abstract = {This article is a Commentary on Mark et al. (2020), 227: 1362–1375.}, }
@article {pmid32483294, year = {2020}, author = {Calusinska, M and Marynowska, M and Bertucci, M and Untereiner, B and Klimek, D and Goux, X and Sillam-Dussès, D and Gawron, P and Halder, R and Wilmes, P and Ferrer, P and Gerin, P and Roisin, Y and Delfosse, P}, title = {Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {275}, pmid = {32483294}, issn = {2399-3642}, mesh = {Adaptation, Biological ; Animals ; Bacteria/*enzymology ; Diet ; Digestion ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/physiology ; *Gene Expression ; Isoptera/*physiology ; Poaceae/*chemistry ; }, abstract = {Miscanthus sp. biomass could satisfy future biorefinery value chains. However, its use is largely untapped due to high recalcitrance. The termite and its gut microbiome are considered the most efficient lignocellulose degrading system in nature. Here, we investigate at holobiont level the dynamic adaptation of Cortaritermes sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose recalcitrance. We use an integrative omics approach combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Modified gene expression profiles of gut bacteria suggest a shift towards utilisation of cellulose and arabinoxylan, two main components of Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to closely related species supports the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.}, }
@article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, }
@article {pmid32477316, year = {2020}, author = {Corbin, KR and Bolt, B and Rodríguez López, CM}, title = {Breeding for Beneficial Microbial Communities Using Epigenomics.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {937}, pmid = {32477316}, issn = {1664-302X}, }
@article {pmid32471941, year = {2020}, author = {Vollmar, S and Wellmann, R and Borda-Molina, D and Rodehutscord, M and Camarinha-Silva, A and Bennewitz, J}, title = {The Gut Microbial Architecture of Efficiency Traits in the Domestic Poultry Model Species Japanese Quail (Coturnix japonica) Assessed by Mixed Linear Models.}, journal = {G3 (Bethesda, Md.)}, volume = {10}, number = {7}, pages = {2553-2562}, pmid = {32471941}, issn = {2160-1836}, mesh = {Animals ; *Coturnix/genetics ; *Gastrointestinal Microbiome/genetics ; Linear Models ; Poultry ; RNA, Ribosomal, 16S/genetics ; }, abstract = {It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.}, }
@article {pmid32467266, year = {2020}, author = {Zhang, XL and Yang, X and Wang, SJ and Jiang, ZW and Xie, ZX and Zhang, L and Dai, J and Fan, CQ and Tian, XQ and Yang, Q}, title = {Draft Genome Sequences of Nine Cultivable Heterotrophic Proteobacteria Isolated from Phycosphere Microbiota of Toxic Alexandrium catenella LZT09.}, journal = {Microbiology resource announcements}, volume = {9}, number = {22}, pages = {}, pmid = {32467266}, issn = {2576-098X}, abstract = {Microscopic interactions between phycosphere microbiota and host algae play crucial roles in aquatic ecosystems. Despite their significance, there is a scarcity of available genome sequences derived from the phycosphere microbiome. Here, we report the draft genome sequences of nine heterotrophic proteobacterial strains isolated from the toxic dinoflagellate Alexandrium catenella LZT09 during execution of our Phycosphere Microbiome Project. Further exploration of the genomic features of the alga-associated bacterial community will profoundly help in deeply deciphering the processes and mechanisms governing the host-microbe interactome within algal holobionts in the ocean.}, }
@article {pmid32467160, year = {2020}, author = {Daybog, I and Kolodny, O}, title = {Simplified model assumptions artificially constrain the parameter range in which selection at the holobiont level can occur.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {11862-11863}, pmid = {32467160}, issn = {1091-6490}, mesh = {*Microbiota ; Symbiosis ; }, }
@article {pmid32467159, year = {2020}, author = {van Vliet, S and Doebeli, M}, title = {Reply to Daybog and Kolodny: Necessary requirements for holobiont-level selection are robust to model assumptions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {11864}, pmid = {32467159}, issn = {1091-6490}, mesh = {*Microbiota ; Symbiosis ; }, }
@article {pmid32466246, year = {2020}, author = {Ben-Eliahu, N and Herut, B and Rahav, E and Abramovich, S}, title = {Shell Growth of Large Benthic Foraminifera under Heavy Metals Pollution: Implications for Geochemical Monitoring of Coastal Environments.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {10}, pages = {}, pmid = {32466246}, issn = {1660-4601}, mesh = {Chlorophyll A ; Environmental Monitoring ; *Foraminifera ; Geologic Sediments ; Metals, Heavy/*analysis/toxicity ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {This study was promoted by the recent efforts using larger benthic foraminiferal (LBF) shells geochemistry for the monitoring of heavy metals (HMs) pollution in the marine environment. The shell itself acts as a recorder of the ambient water chemistry in low to extreme HMs-polluted environments, allowing the monitoring of recent-past pollution events. This concept, known as sclerochronology, requires the addition of new parts (i.e., new shell) even in extreme pollution events. We evaluated the physiological resilience of three LBF species with different shell types and symbionts to enriched concentrations of Cd, Cu, and Pb at levels several folds higher than the ecological criteria maximum concentration (CMC) (165-166, 33-43, 1001-1206 µg L[-1], respectively), which is derived from aquatic organisms' toxicity tests. The physiological response of the holobiont was expressed by growth rates quantified by the addition of new chambers (new shell parts), and by the chlorophyll a of the algal symbionts. The growth rate decrease varied between 0% and 30% compared to the unamended control for all HMs tested, whereas the algal symbionts exhibited a general non-fatal but significant response to Pb and Cu. Our results highlight that shell growth inhibition of LBF is predicted in extreme concentrations of 57 × CMC of Cu and 523 × CMC of Cd, providing a proof of concept for shell geochemistry monitoring, which is currently not used in the regulatory sectors.}, }
@article {pmid32461810, year = {2020}, author = {Kumar, A and Dubey, A}, title = {Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production.}, journal = {Journal of advanced research}, volume = {24}, number = {}, pages = {337-352}, pmid = {32461810}, issn = {2090-1232}, abstract = {Plants in nature are constantly exposed to a variety of abiotic and biotic stresses which limits their growth and production. Enhancing crop yield and production to feed exponentially growing global population in a sustainable manner by reduced chemical fertilization and agrochemicals will be a big challenge. Recently, the targeted application of beneficial plant microbiome and their cocktails to counteract abiotic and biotic stress is gaining momentum and becomes an exciting frontier of research. Advances in next generation sequencing (NGS) platform, gene editing technologies, metagenomics and bioinformatics approaches allows us to unravel the entangled webs of interactions of holobionts and core microbiomes for efficiently deploying the microbiome to increase crops nutrient acquisition and resistance to abiotic and biotic stress. In this review, we focused on shaping rhizosphere microbiome of susceptible host plant from resistant plant which comprises of specific type of microbial community with multiple potential benefits and targeted CRISPR/Cas9 based strategies for the manipulation of susceptibility genes in crop plants for improving plant health. This review is significant in providing first-hand information to improve fundamental understanding of the process which helps in shaping rhizosphere microbiome.}, }
@article {pmid32451122, year = {2020}, author = {Arif, I and Batool, M and Schenk, PM}, title = {Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience.}, journal = {Trends in biotechnology}, volume = {38}, number = {12}, pages = {1385-1396}, doi = {10.1016/j.tibtech.2020.04.015}, pmid = {32451122}, issn = {1879-3096}, mesh = {*Crops, Agricultural/microbiology ; *Microbiota ; Plant Roots/microbiology ; *Soil Microbiology ; }, abstract = {Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.}, }
@article {pmid32446076, year = {2020}, author = {Yu, X and Yu, K and Huang, W and Liang, J and Qin, Z and Chen, B and Yao, Q and Liao, Z}, title = {Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139319}, doi = {10.1016/j.scitotenv.2020.139319}, pmid = {32446076}, issn = {1879-1026}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Symbiosis ; *Thermotolerance ; }, abstract = {Field ecological observations indicate that scleractinian coral exposed to early thermal stress are likely to develop higher tolerance to subsequent heat stress. The causes of this phenomenon, however, remain enigmatic. To unravel the mechanisms underlying the increased heat tolerance, we applied different thermal treatments to the scleractinian coral Acropora pruinosa and studied the resulting differences in appearance, physiological index, Symbiodiniaceae and bacterial communities, and transcriptome response. We found that early heat stress improved the thermal tolerance of the coral holobiont. After thermal acclimation, the community structure and symbiotic bacterial diversity in the microbiota were reorganized, whereas those of Symbiodiniaceae remained stable. RNA-seq analysis revealed that the downregulated coral host genes were mainly involved in pathways relating to metabolism, particularly the nitrogen metabolism pathway. This indicates that thermal acclimation led to decrease in the metabolism level in the coral host, which might be a self-protection mechanism. We suggest that thermal acclimation may increase scleractinian coral thermal tolerance by slowing host metabolism, altering the dominant bacterial population, and increasing bacterial diversity. This study offers new insights into the adaptive potential of scleractinian coral to heat stress from global warming.}, }
@article {pmid32431680, year = {2020}, author = {Newkirk, CR and Frazer, TK and Martindale, MQ and Schnitzler, CE}, title = {Adaptation to Bleaching: Are Thermotolerant Symbiodiniaceae Strains More Successful Than Other Strains Under Elevated Temperatures in a Model Symbiotic Cnidarian?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {822}, pmid = {32431680}, issn = {1664-302X}, abstract = {The ability of some symbiotic cnidarians to resist and better withstand stress factors that cause bleaching is a trait that is receiving increased attention. The adaptive bleaching hypothesis postulates that cnidarians that can form a stable symbiosis with thermotolerant Symbiodiniaceae strains may cope better with increasing seawater temperatures. We used polyps of the scyphozoan, Cassiopea xamachana, as a model system to test symbiosis success under heat stress. We sought to determine: (1) if aposymbiotic C. xamachana polyps could establish and maintain a symbiosis with both native and non-native strains of Symbiodiniaceae that all exhibit different tolerances to heat, (2) whether polyps with these newly acquired Symbiodiniaceae strains would strobilate (produce ephyra), and (3) if thermally tolerant Symbiodiniaceae strains that established and maintained a symbiosis exhibited greater success in response to heat stress (even if they are not naturally occurring in Cassiopea). Following recolonization of aposymbiotic C. xamachana polyps with different strains, we found that: (1) strains Smic, Stri, Slin, and Spil all established a stable symbiosis that promoted strobilation and (2) strains Bmin1 and Bmin2 did not establish a stable symbiosis and strobilation did not occur. Strains Smic, Stri, Slin, and Spil were used in a subsequent bleaching experiment; each of the strains was introduced to a subset of aposymbiotic polyps and once polyp tissues were saturated with symbionts they were subjected to elevated temperatures - 32°C and 34°C - for 2 weeks. Our findings indicate that, in general, pairings of polyps with Symbiodiniaceae strains that are native to Cassiopea (Stri and Smic) performed better than a non-native strain (Slin) even though this strain has a high thermotolerance. This suggests a degree of partner specificity that may limit the adaptive potential of certain cnidarians to increased ocean warming. We also observed that the free-living, non-native thermotolerant strain Spil was relatively successful in resisting bleaching during experimental trials. This suggests that free-living Symbiodiniaceae may provide a supply of potentially "new" thermotolerant strains to cnidarians following a bleaching event.}, }
@article {pmid32429344, year = {2020}, author = {Sariola, S and Gilbert, SF}, title = {Toward a Symbiotic Perspective on Public Health: Recognizing the Ambivalence of Microbes in the Anthropocene.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32429344}, issn = {2076-2607}, support = {316941//Academy of Finland/ ; SFG//Swarthmore College Faculty Research/ ; }, abstract = {Microbes evolve in complex environments that are often fashioned, in part, by human desires. In a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. The germ theory of disease cast microbes as enemies of the body and the body politic. Antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. Public health perspectives such as "Precision Public Health" and "One Health" have recently been proposed to further manage microbial populations. However, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. We propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. This perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the "One Health" model with the genomic methodologies utilized in the "Precision Public Health" model. In the Anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions.}, }
@article {pmid32429044, year = {2020}, author = {Pavagadhi, S and Swarup, S}, title = {Metabolomics for Evaluating Flavor-Associated Metabolites in Plant-Based Products.}, journal = {Metabolites}, volume = {10}, number = {5}, pages = {}, pmid = {32429044}, issn = {2218-1989}, support = {NRF-CRP 16-2015-04//National Research Foundation Singapore/ ; Holobiont Cluster (core funding)//Singapore Centre for Environmental Life Sciences Engineering/ ; }, abstract = {Plant-based diets (PBDs) are associated with environmental benefits, human health promotion and animal welfare. There is a worldwide shift towards PBDs, evident from the increased global demand for fresh plant-based products (PBPs). Such shifts in dietary preferences accompanied by evolving food palates, create opportunities to leverage technological advancements and strict quality controls in developing PBPs that can drive consumer acceptance. Flavor, color and texture are important sensory attributes of a food product and, have the largest influence on consumer appeal and acceptance. Among these, flavor is considered the most dominating quality attribute that significantly affects overall eating experience. Current state-of-art technologies rely on physicochemical estimations and sensory-based tests to assess flavor-related attributes in fresh PBPs. However, these methodologies often do not provide any indication about the metabolic features associated with unique flavor profiles and, consequently, can be used in a limited way to define the quality attributes of PBPs. To this end, a systematic understanding of metabolites that contribute to the flavor profiles of PBPs is warranted to complement the existing methodologies. This review will discuss the use of metabolomics for evaluating flavor-associated metabolites in fresh PBPs at post-harvest stage, alongside its applications for quality assessment and grading. We will summarize the current research in this area, discuss technical challenges and considerations pertaining to sampling and analytical techniques, as well as s provide future perspectives and directions for government organizations, industries and other stakeholders associated with the quality assessment of fresh PBPs.}, }
@article {pmid32426508, year = {2020}, author = {Buerger, P and Alvarez-Roa, C and Coppin, CW and Pearce, SL and Chakravarti, LJ and Oakeshott, JG and Edwards, OR and van Oppen, MJH}, title = {Heat-evolved microalgal symbionts increase coral bleaching tolerance.}, journal = {Science advances}, volume = {6}, number = {20}, pages = {eaba2498}, pmid = {32426508}, issn = {2375-2548}, mesh = {Animals ; *Anthozoa/genetics/metabolism ; Coral Bleaching ; Coral Reefs ; *Dinoflagellida/genetics ; Hot Temperature ; *Microalgae ; Reactive Oxygen Species/metabolism ; Symbiosis/genetics ; }, abstract = {Coral reefs worldwide are suffering mass mortalities from marine heat waves. With the aim of enhancing coral bleaching tolerance, we evolved 10 clonal strains of a common coral microalgal endosymbiont at elevated temperatures (31°C) for 4 years in the laboratory. All 10 heat-evolved strains had expanded their thermal tolerance in vitro following laboratory evolution. After reintroduction into coral host larvae, 3 of the 10 heat-evolved endosymbionts also increased the holobionts' bleaching tolerance. Although lower levels of secreted reactive oxygen species (ROS) accompanied thermal tolerance of the heat-evolved algae, reduced ROS secretion alone did not predict thermal tolerance in symbiosis. The more tolerant symbiosis exhibited additional higher constitutive expression of algal carbon fixation genes and coral heat tolerance genes. These findings demonstrate that coral stock with enhanced climate resilience can be developed through ex hospite laboratory evolution of their microalgal endosymbionts.}, }
@article {pmid32408381, year = {2020}, author = {Bonthond, G and Bayer, T and Krueger-Hadfield, SA and Barboza, FR and Nakaoka, M and Valero, M and Wang, G and Künzel, S and Weinberger, F}, title = {How do microbiota associated with an invasive seaweed vary across scales?.}, journal = {Molecular ecology}, volume = {29}, number = {11}, pages = {2094-2108}, doi = {10.1111/mec.15470}, pmid = {32408381}, issn = {1365-294X}, mesh = {Introduced Species ; *Microbiota/genetics ; Rhodophyta/*microbiology ; Seaweed/*microbiology ; }, abstract = {Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro- and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non-native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.}, }
@article {pmid32406121, year = {2020}, author = {Suárez, J and Stencel, A}, title = {A part-dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {5}, pages = {1308-1324}, doi = {10.1111/brv.12610}, pmid = {32406121}, issn = {1469-185X}, support = {FFI2016-76799-P//Ministerio de Econom&#xed;a y Competitividad/International ; FFU16/02570//Ministerio de Educaci&#xf3;n, Cultura y Deporte/International ; 2018/28/T/HS1/00201//Narodowe Centrum Nauki/International ; //University of Sydney/International ; //University of Bordeaux/International ; //University of Barcelona/International ; //University of Exeter/International ; }, mesh = {Biological Evolution ; Humans ; *Microbiota ; Symbiosis ; }, abstract = {Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont - that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome - be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part-dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of the part of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host-relative or microbe-relative. We support the claim that biological individuality is part-dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the 'demibiont'. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates.}, }
@article {pmid32390975, year = {2020}, author = {Tong, H and Cai, L and Zhou, G and Zhang, W and Huang, H and Qian, PY}, title = {Correlations Between Prokaryotic Microbes and Stress-Resistant Algae in Different Corals Subjected to Environmental Stress in Hong Kong.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {686}, pmid = {32390975}, issn = {1664-302X}, abstract = {Coral reefs are extremely vulnerable to global climate change, as evidenced by increasing bleaching events. Previous studies suggest that both algal and microbial partners benefit coral hosts, but the nature of interactions between Symbiodiniaceae and prokaryotic microbes and their effects on coral hosts remains unclear. In the present study, we examined correlations between Symbiodiniaceae and prokaryotic microbes in Montipora spp. and Porites lutea sampled from two sites in Hong Kong with contrasting environmental conditions in March and October 2014. The results showed that the prokaryotic microbial communities had adaptable structures in both Montipora spp. and P. lutea, and environmental conditions had greater effects on the algal/microbial communities in Montipora spp. than in P. lutea. Further network analysis revealed a greater number of prokaryotic microbes were significantly correlated with potentially stress-resistant Symbiodiniaceae in P. lutea than in Montipora spp. Stress-resistant Symbiodiniaceae played more important roles in the community and in the algal-microbial correlations in P. lutea than in Montipora spp. Since P. lutea is faring better in Hong Kong as the seawater temperature gradually increases, the results suggest that the correlations between stress-resistant algae and prokaryotic microbes could provide a compensation mechanism allowing coral hosts to adapt to higher temperatures, particularly as the prokaryotic microbes correlated with Symbiodiniaceae provide the ecological functions of photosynthesis and nitrogen fixation.}, }
@article {pmid32390855, year = {2020}, author = {Zhang, R and Gao, X and Bai, H and Ning, K}, title = {Traditional Chinese Medicine and Gut Microbiome: Their Respective and Concert Effects on Healthcare.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {538}, pmid = {32390855}, issn = {1663-9812}, abstract = {Advances in systems biology, particularly based on the omics approaches, have resulted in a paradigm shift in both traditional Chinese medicine (TCM) and the gut microbiome research. In line with this paradigm shift, the importance of TCM and gut microbiome in healthcare, as well as their interplay, has become clearer. Firstly, we briefly summarize the current status of three topics in this review: microbiome, TCM, and relationship of TCM and microbiome. Second, we focused on TCM's therapeutic effects and gut microbiome's mediation roles, including the relationships among diet, gut microbiome, and health care. Third, we have summarized some databases and tools to help understand the impact of TCM and gut microbiome on diagnosis and treatment at the molecular level. Finally, we introduce the effects of gut microbiome on TCM and host health, with two case studies, one on the metabolic effect of gut microbiome on TCM, and another on cancer treatment. In summary, we have reviewed the current status of the two components of healthcare: TCM and gut microbiome, as well as their concert effects. It is quite clear that as the holobiont, the maintenance of the health status of human would depend heavily on TCM, gut microbiome, and their combined effects.}, }
@article {pmid32372688, year = {2020}, author = {Perry, WB and Lindsay, E and Payne, CJ and Brodie, C and Kazlauskaite, R}, title = {The role of the gut microbiome in sustainable teleost aquaculture.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1926}, pages = {20200184}, pmid = {32372688}, issn = {1471-2954}, mesh = {Animal Feed ; Animals ; *Aquaculture ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Sustainable Development ; }, abstract = {As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.}, }
@article {pmid32354088, year = {2020}, author = {Roberty, S and Béraud, E and Grover, R and Ferrier-Pagès, C}, title = {Coral Productivity Is Co-Limited by Bicarbonate and Ammonium Availability.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32354088}, issn = {2076-2607}, abstract = {The nitrogen environment and nitrogen status of reef-building coral endosymbionts is one of the important factors determining the optimal assimilation of phototrophic carbon and hence the growth of the holobiont. However, the impact of inorganic nutrient availability on the photosynthesis and physiological state of the coral holobiont is partly understood. This study aimed to determine if photosynthesis of the endosymbionts associated with the coral Stylophora pistillata and the overall growth of the holobiont were limited by the availability of dissolved inorganic carbon and nitrogen in seawater. For this purpose, colonies were incubated in absence or presence of 4 µM ammonium and/or 6 mM bicarbonate. Photosynthetic performances, pigments content, endosymbionts density and growth rate of the coral colonies were monitored for 3 weeks. Positive effects were observed on coral physiology with the supplementation of one or the other nutrient, but the most important changes were observed when both nutrients were provided. The increased availability of DIC and NH4[+] significantly improved the photosynthetic efficiency and capacity of endosymbionts, in turn enhancing the host calcification rate. Overall, these results suggest that in hospite symbionts are co-limited by nitrogen and carbon availability for an optimal photosynthesis.}, }
@article {pmid32326359, year = {2020}, author = {Gong, S and Jin, X and Ren, L and Tan, Y and Xia, X}, title = {Unraveling Heterogeneity of Coral Microbiome Assemblages in Tropical and Subtropical Corals in the South China Sea.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32326359}, issn = {2076-2607}, support = {GML2019ZD0405//Key Ecological Processes and Health Regulation Principles of Marine Ecosystem in Guangdong-Hong Kong-Macao Greater Bay Area/ ; Y8SL031001, Y9YB021001//the CAS Pioneer Hundred Talents Program and the South China Sea Institute of Oceanography/ ; 31971501//National Natural Science Foundation of China/ ; }, abstract = {Understanding the coral microbiome is critical for predicting the fidelity of coral symbiosis with growing surface seawater temperature (SST). However, how the coral microbiome will respond to increasing SST is still understudied. Here, we compared the coral microbiome assemblages among 73 samples across six typical South China Sea coral species in two thermal regimes. The results revealed that the composition of microbiome varied across both coral species and thermal regimes, except for Porites lutea. The tropical coral microbiome displayed stronger heterogeneity and had a more un-compacted ecological network than subtropical coral microbiome. The coral microbiome was more strongly determined by environmental factors than host specificity. γ- (32%) and α-proteobacteria (19%), Bacteroidetes (14%), Firmicutes (14%), Actinobacteria (6%) and Cyanobacteria (2%) dominated the coral microbiome. Additionally, bacteria inferred to play potential roles in host nutrients metabolism, several keystone bacteria detected in human and plant rhizospheric microbiome were retrieved in explored corals. This study not only disentangles how different host taxa and microbiome interact and how such an interaction is affected by thermal regimes, but also identifies previously unrecognized keystone bacteria in corals, and also infers the community structure of coral microbiome will be changed from a compacted to an un-compacted network under elevated SST.}, }
@article {pmid32314003, year = {2020}, author = {Parker, ES and Newton, ILG and Moczek, AP}, title = {(My Microbiome) Would Walk 10,000 miles: Maintenance and Turnover of Microbial Communities in Introduced Dung Beetles.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {435-446}, doi = {10.1007/s00248-020-01514-9}, pmid = {32314003}, issn = {1432-184X}, support = {1901680//Division of Integrative Organismal Systems/ ; 1256689//Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; }, mesh = {Animals ; Australian Capital Territory ; Bacteria/*isolation &amp; purification ; Coleoptera/*microbiology ; Introduced Species ; Italy ; *Microbiota ; *Symbiosis ; West Virginia ; }, abstract = {Host-associated microbes facilitate diverse biotic and abiotic interactions between hosts and their environments. Experimental alterations of host-associated microbial communities frequently decrease host fitness, yet much less is known about if and how host-microbiome interactions are altered by natural perturbations, such as introduction events. Here, we begin to assess this question in Onthophagus dung beetles, a species-rich and geographically widely distributed genus whose members rely on vertically transmitted microbiota to support normal development. Specifically, we investigated to what extent microbiome community membership shifts during host introduction events and the relative significance of ancestral associations and novel environmental conditions in the structuring of microbial communities of introduced host species. Our results demonstrate that both evolutionary history and local environmental forces structure the microbial communities of these animals, but that their relative importance is shaped by the specific circumstances that characterize individual introduction events. Furthermore, we identify microbial taxa such as Dysgonomonas that may constitute members of the core Onthophagus microbiome regardless of host population or species, but also Wolbachia which associates with Onthophagus beetles in a species or even population-specific manner. We discuss the implications of our results for our understanding of the evolutionary ecology of symbiosis in dung beetles and beyond.}, }
@article {pmid32307770, year = {2020}, author = {Kriaa, A and Jablaoui, A and Mkaouar, H and Akermi, N and Maguin, E and Rhimi, M}, title = {Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {6}, pages = {7270-7282}, doi = {10.1096/fj.202000031RR}, pmid = {32307770}, issn = {1530-6860}, mesh = {Animals ; Bacteria/metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; Inflammation/*metabolism ; Inflammatory Bowel Diseases/*metabolism ; Serine Proteases/*metabolism ; }, abstract = {Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.}, }
@article {pmid32294545, year = {2020}, author = {Muggia, L and Nelsen, MP and Kirika, PM and Barreno, E and Beck, A and Lindgren, H and Lumbsch, HT and Leavitt, SD and , }, title = {Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy.}, journal = {Molecular phylogenetics and evolution}, volume = {149}, number = {}, pages = {106821}, doi = {10.1016/j.ympev.2020.106821}, pmid = {32294545}, issn = {1095-9513}, mesh = {*Biodiversity ; Chlorophyta/anatomy &amp; histology/*classification/genetics/ultrastructure ; Genetic Loci ; Lichens/*classification/genetics/ultrastructure ; *Phylogeny ; Species Specificity ; }, abstract = {Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.}, }
@article {pmid32282951, year = {2020}, author = {Lin, D and Lacey, EA and Bach, BH and Bi, K and Conroy, CJ and Suvorov, A and Bowie, RCK}, title = {Gut microbial diversity across a contact zone for California voles: Implications for lineage divergence of hosts and mitonuclear mismatch in the assembly of the mammalian gut microbiome.}, journal = {Molecular ecology}, volume = {29}, number = {10}, pages = {1873-1889}, doi = {10.1111/mec.15443}, pmid = {32282951}, issn = {1365-294X}, mesh = {Animals ; Arvicolinae/*microbiology ; California ; *Gastrointestinal Microbiome/genetics ; Mammals ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbial diversity is thought to reflect the co-evolution of microbes and their hosts as well as current host-specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition of California voles (Microtus californicus) across a contact zone between two recently diverged lineages of this species. Because this contact zone contains individuals with mismatched mitochondrial-nuclear genomes (cybrids), it provides an important opportunity to explore how different components of the genotype contribute to gut microbial diversity. Analyses of bacterial 16S rRNA sequences and joint species distribution modelling revealed that host genotypes and genetic differentiation among host populations together explained more than 50% of microbial community variation across our sampling transect. The ranked importance (most to least) of factors contributing to gut microbial diversity in our study populations were: genome-wide population differentiation, local environmental conditions, and host genotypes. However, differences in microbial communities among vole populations (β-diversity) did not follow patterns of lineage divergence (i.e., phylosymbiosis). Instead, among-population variation was best explained by the spatial distribution of hosts, as expected if the environment is a primary source of gut microbial diversity (i.e., dispersal limitation hypothesis). Across the contact zone, several bacterial taxa differed in relative abundance between the two parental lineages as well as among individuals with mismatched mitochondrial and nuclear genomes. Thus, genetic divergence among host lineages and mitonuclear genomic mismatches may also contribute to microbial diversity by altering interactions between host genomes and gut microbiota (i.e., hologenome speciation hypothesis).}, }
@article {pmid32275303, year = {2020}, author = {Renoud, S and Bouffaud, ML and Dubost, A and Prigent-Combaret, C and Legendre, L and Moënne-Loccoz, Y and Muller, D}, title = {Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, doi = {10.1093/femsec/fiaa062}, pmid = {32275303}, issn = {1574-6941}, mesh = {Deamination ; Nitrogen Fixation ; *Rhizosphere ; Soil Microbiology ; *Zea mays ; }, abstract = {The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.}, }
@article {pmid32275297, year = {2020}, author = {Simonin, M and Dasilva, C and Terzi, V and Ngonkeu, ELM and Diouf, D and Kane, A and Béna, G and Moulin, L}, title = {Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa067}, pmid = {32275297}, issn = {1574-6941}, mesh = {France ; Fungi ; Genotype ; Italy ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.}, }
@article {pmid32269559, year = {2020}, author = {Paix, B and Carriot, N and Barry-Martinet, R and Greff, S and Misson, B and Briand, JF and Culioli, G}, title = {A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {494}, pmid = {32269559}, issn = {1664-302X}, abstract = {Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.}, }
@article {pmid32269511, year = {2020}, author = {Elmassry, MM and Piechulla, B}, title = {Volatilomes of Bacterial Infections in Humans.}, journal = {Frontiers in neuroscience}, volume = {14}, number = {}, pages = {257}, pmid = {32269511}, issn = {1662-4548}, abstract = {Sense of smell in humans has the capacity to detect certain volatiles from bacterial infections. Our olfactory senses were used in ancient medicine to diagnose diseases in patients. As humans are considered holobionts, each person's unique odor consists of volatile organic compounds (VOCs, volatilome) produced not only by the humans themselves but also by their beneficial and pathogenic micro-habitants. In the past decade it has been well documented that microorganisms (fungi and bacteria) are able to emit a broad range of olfactory active VOCs [summarized in the mVOC database (http://bioinformatics.charite.de/mvoc/)]. During microbial infection, the equilibrium between the human and its microbiome is altered, followed by a change in the volatilome. For several decades, physicians have been trying to utilize these changes in smell composition to develop fast and efficient diagnostic tools, particularly because volatiles detection is non-invasive and non-destructive, which would be a breakthrough in many therapies. Within this review, we discuss bacterial infections including gastrointestinal, respiratory or lung, and blood infections, focusing on the pathogens and their known corresponding volatile biomarkers. Furthermore, we cover the potential role of the human microbiota and their volatilome in certain diseases such as neurodegenerative diseases. We also report on discrete mVOCs that affect humans.}, }
@article {pmid32266849, year = {2020}, author = {Boem, F and Nannini, G and Amedei, A}, title = {Not just 'immunity': how the microbiota can reshape our approach to cancer immunotherapy.}, journal = {Immunotherapy}, volume = {12}, number = {6}, pages = {407-416}, doi = {10.2217/imt-2019-0192}, pmid = {32266849}, issn = {1750-7448}, mesh = {*Gastrointestinal Microbiome ; Humans ; Immune System ; Immunologic Factors ; Immunotherapy/methods ; *Microbiota ; *Neoplasms/therapy ; }, abstract = {Cancer immunotherapy refers to a set of approaches aiming at enhancing the immune system to fight cancer growth and spread. This variety of therapeutic approaches, especially those inhibiting immune checkpoints, have shown very promising results. Nevertheless, patients may respond differently to treatments and the efficacy of immunotherapy seems to be dependent on several factors that go beyond the molecular targeting of immune cells modulation. Here, we review how the activity of gut microbiota appears to be crucial in determining the effectiveness of some immunotherapeutic treatments, fostering or impeding the conditions under which treatments can work or not. Moreover, we discuss how these findings suggest not only extending the range of immunotherapeutic approaches but also reshaping our understanding of immunotherapy itself.}, }
@article {pmid32253628, year = {2020}, author = {Nisenbaum, M and Corti-Monzón, G and Villegas-Plazas, M and Junca, H and Mangani, A and Patat, ML and González, JF and Murialdo, SE}, title = {Enrichment and key features of a robust and consistent indigenous marine-cognate microbial consortium growing on oily bilge wastewaters.}, journal = {Biodegradation}, volume = {31}, number = {1-2}, pages = {91-108}, doi = {10.1007/s10532-020-09896-w}, pmid = {32253628}, issn = {1572-9729}, support = {VT38-UNMdP10982//Universidad Nacional de Mar del Plata/International ; PIT-AP-BA-2016//Consejo de Investigaciones Cient&#xed;ficas y T&#xe9;cnicas de la Provincia de Buenos Aires/International ; PICT 2014-1567//Fondo para la Investigaci&#xf3;n Cient&#xed;fica y Tecnol&#xf3;gica/International ; }, mesh = {Biodegradation, Environmental ; Hydrocarbons ; Microbial Consortia ; *Petroleum ; *Wastewater ; }, abstract = {Oily bilge wastewater (OBW) is a hazardous hydrocarbon-waste generated by ships worldwide. In this research, we enriched, characterized and study the hydrocarbon biodegradation potential of a microbial consortium from the bilges of maritime ships. The consortium cZ presented a biodegradation efficiency of 66.65% for total petroleum hydrocarbons, 72.33% for aromatics and 97.76% removal of n-alkanes. This consortium showed the ability to grow in OBWs of diverse origin and concentration. A 67-fold increase in biomass was achieved using a Sequential Batch Reactor with OBW as the only carbon and energy source. The bacterial community composition of the enriched OBW bacterial consortium at the final stable stage was characterized by 16S amplicon Illumina sequencing showing that 25 out of 915 of the emerged predominant bacterial types detected summed up for 84% of total composition. Out of the 140 taxa detected, 13 alone accumulated 94.9% of the reads and were classified as Marinobacter, Alcanivorax, Parvibaculum, Flavobacteriaceae, Gammaproteobacteria PYR10d3, Novispirillum and Xanthomonadaceae among the most predominant, followed by Thalassospira, Shewanella, Rhodospirillaceae, Gammaprotobacteria, Rhodobacteriaceae and Achromobacter. The microbial community from OBW bioreactor enrichments is intrinsically diverse with clear selection of predominant types and remarkably exhibiting consistent and efficient biodegradation achieved without any nutrient or surfactant addition. Due to there is very little information available in the OBW biodegradation field, this work contributes to the body of knowledge surrounding the treatment improvement of this toxic waste and its potential application in wastewater management.}, }
@article {pmid32251879, year = {2020}, author = {Biagi, E and Caroselli, E and Barone, M and Pezzimenti, M and Teixido, N and Soverini, M and Rampelli, S and Turroni, S and Gambi, MC and Brigidi, P and Goffredo, S and Candela, M}, title = {Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents.}, journal = {The Science of the total environment}, volume = {724}, number = {}, pages = {138048}, doi = {10.1016/j.scitotenv.2020.138048}, pmid = {32251879}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Coral Reefs ; Hydrogen-Ion Concentration ; Italy ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Seawater ; }, abstract = {Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO2 provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO2 vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO2 vent system.}, }
@article {pmid32245478, year = {2020}, author = {Corona, G and Kreimes, A and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Costabile, A}, title = {Impact of lignans in oilseed mix on gut microbiome composition and enterolignan production in younger healthy and premenopausal women: an in vitro pilot study.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {82}, pmid = {32245478}, issn = {1475-2859}, mesh = {Case-Control Studies ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lignans/*chemistry ; Pilot Projects ; Plant Oils/*chemistry ; Premenopause ; }, abstract = {BACKGROUND: Dietary lignans belong to the group of phytoestrogens together with coumestans, stilbenes and isoflavones, and themselves do not exhibit oestrogen-like properties. Nonetheless, the gut microbiota converts them into enterolignans, which show chemical similarity to the human oestrogen molecule. One of the richest dietary sources of lignans are oilseeds, including flaxseed. The aim of this pilot study was to determine the concentration of the main dietary lignans in an oilseed mix, and explore the gut microbiota-dependent production of enterolignans for oestrogen substitution in young and premenopausal women. The oilseed mix was fermented in a pH-controlled batch culture system inoculated with women's faecal samples. The lignan content and enterolignan production were measured by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and the faecal-derived microbial communities were profiled by 16S rRNA gene-based next-generation sequencing.<br><br>RESULTS: In vitro batch culture fermentation of faecal samples inoculated with oilseed mix for 24&#xa0;h resulted in a substantial increase in enterolactone production in younger women and an increase in enterodiol in the premenopausal group. As for the gut microbiota, different baseline profiles were observed as well as different temporal dynamics, mainly related to Clostridiaceae, and Klebsiella and Collinsella spp.<br><br>CONCLUSIONS: Despite the small sample size, our pilot study revealed that lignan-rich oilseeds could strongly influence the faecal microbiota of both younger and premenopausal females, leading to a different enterolignan profile being produced. Further studies in larger cohorts are needed to evaluate the long-term effects of lignan-rich diets on the gut microbiota and find out how enterolactone-producing bacterial species could be increased. Diets rich in lignans could potentially serve as a safe supplement of oestrogen analogues to meet the cellular needs of endogenous oestrogen and deliver numerous health benefits, provided that the premenopausal woman microbiota is capable of converting dietary precursors into enterolignans.}, }
@article {pmid32230931, year = {2020}, author = {Leitão, AL and Costa, MC and Gabriel, AF and Enguita, FJ}, title = {Interspecies Communication in Holobionts by Non-Coding RNA Exchange.}, journal = {International journal of molecular sciences}, volume = {21}, number = {7}, pages = {}, pmid = {32230931}, issn = {1422-0067}, mesh = {Animals ; Anthozoa/physiology ; Bacteria ; Bacterial Physiological Phenomena ; Cell Communication/*genetics/*physiology ; Dysbiosis ; Mammals ; Metagenome ; MicroRNAs ; Microbiota/physiology ; Plant Physiological Phenomena ; Plants ; RNA, Untranslated/*genetics/*metabolism ; *Signal Transduction ; Symbiosis/genetics/physiology ; Transcriptome ; }, abstract = {Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.}, }
@article {pmid32209692, year = {2020}, author = {Storey, MA and Andreassend, SK and Bracegirdle, J and Brown, A and Keyzers, RA and Ackerley, DF and Northcote, PT and Owen, JG}, title = {Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32209692}, issn = {2150-7511}, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*classification/isolation &amp; purification ; Biosynthetic Pathways ; Metabolome ; *Metagenomics ; Microbiota ; Multigene Family ; Phylogeny ; Polyketides/*metabolism ; Porifera/*microbiology ; Secondary Metabolism ; *Symbiosis ; }, abstract = {Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCEMycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.}, }
@article {pmid32208346, year = {2020}, author = {Vanwonterghem, I and Webster, NS}, title = {Coral Reef Microorganisms in a Changing Climate.}, journal = {iScience}, volume = {23}, number = {4}, pages = {100972}, pmid = {32208346}, issn = {2589-0042}, abstract = {Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.}, }
@article {pmid32194470, year = {2020}, author = {Suárez, J and Triviño, V}, title = {What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems.}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {187}, pmid = {32194470}, issn = {1664-1078}, abstract = {Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.}, }
@article {pmid32193752, year = {2020}, author = {Corti-Monzón, G and Nisenbaum, M and Villegas-Plazas, M and Junca, H and Murialdo, S}, title = {Enrichment and characterization of a bilge microbial consortium with oil in water-emulsions breaking ability for oily wastewater treatment.}, journal = {Biodegradation}, volume = {31}, number = {1-2}, pages = {57-72}, doi = {10.1007/s10532-020-09894-y}, pmid = {32193752}, issn = {1572-9729}, support = {Resoluci&#xf3;n N&#xba; 428/16 y 429/16//Comisi&#xf3;n de Investigaciones Cient&#xed;ficas/International ; VT38-UNMdP10982//Ministerio de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Productiva/International ; }, mesh = {Biodegradation, Environmental ; Emulsions ; *Microbial Consortia ; RNA, Ribosomal, 16S ; Shewanella ; *Wastewater ; }, abstract = {Oily bilge wastewater is one of the main sources of hydrocarbons pollution in marine environments due to accidental or clandestine discharges. The main technical challenge for its effective treatment is the presence of stable oil-in-water (O/W) emulsions. In this work we are reporting an enriched microbial consortium from bilge wastewater with remarkable ability to demulsify oil in water emulsions. The consortium showed emulsion-breaking ratios up to 72.6% in the exponential growth phase, while the values range from 11.9 to 8.5% in stationary phase. A positive association was observed between demulsifying ability and microbial adhesion to hydrocarbons, as well as between cell concentration and demulsifying ability. Also, an interesting ability to demulsify under different temperatures, conditions of agitation, and bilge emulsions from different vessels was observed. The Bacterial and Archaeal composition was analyzed by 16S rRNA gene amplicon lllumina sequencing analyses, revealing an assemblage composed of bacterial types highly related to well characterized bacterial isolates and also to non-yet cultured bacterial types previously detected in marine and sediment samples. Hydrocarbonoclastic microbial types such as Marinobacter, Flavobacteriaceae, Alcanivorax and Gammaproteobacteria PYR10d3 were found in high relative abundance (27.0%-11.1%) and types of marine oligotrophs and surfactant degraders such as Thallasospira, Parvibaculum, Novospirillum, Shewanella algae, and Opitutae were in a group of middle predominance (1.7-3.5%). The microbial consortium reported has promising potential for the biological demulsification of bilge wastewater and other oily wastewaters.}, }
@article {pmid32190114, year = {2020}, author = {Bredon, M and Herran, B and Bertaux, J and Grève, P and Moumen, B and Bouchon, D}, title = {Isopod holobionts as promising models for lignocellulose degradation.}, journal = {Biotechnology for biofuels}, volume = {13}, number = {}, pages = {49}, pmid = {32190114}, issn = {1754-6834}, abstract = {BACKGROUND: Isopods have colonized all environments, partly thanks to their ability to decompose the organic matter. Their enzymatic repertoire, as well as the one of their associated microbiota, has contributed to their colonization success. Together, these holobionts have evolved several interesting life history traits to degrade the plant cell walls, mainly composed of lignocellulose. It has been shown that terrestrial isopods achieve lignocellulose degradation thanks to numerous and diverse CAZymes provided by both the host and its microbiota. Nevertheless, the strategies for lignocellulose degradation seem more diversified in isopods, in particular in aquatic species which are the least studied. Isopods could be an interesting source of valuable enzymes for biotechnological industries of biomass conversion.<br><br>RESULTS: To provide new features on the lignocellulose degradation in isopod holobionts, shotgun sequencing of 36 metagenomes of digestive and non-digestive tissues was performed from several populations of four aquatic and terrestrial isopod species. Combined to the 15 metagenomes of an additional species from our previous study, as well as the host transcriptomes, this large dataset allowed us to identify the CAZymes in both the host and the associated microbial communities. Analyses revealed the dominance of Bacteroidetes and Proteobacteria in the five species, covering 36% and 56% of the total bacterial community, respectively. The identification of CAZymes and new enzymatic systems for lignocellulose degradation, such as PULs, cellulosomes and LPMOs, highlights the richness of the strategies used by the isopods and their associated microbiota.<br><br>CONCLUSIONS: Altogether, our results show that the isopod holobionts are promising models to study lignocellulose degradation. These models can provide new enzymes and relevant lignocellulose-degrading bacteria strains for the biotechnological industries of biomass conversion.}, }
@article {pmid32181589, year = {2020}, author = {Gaona, O and Cerqueda-García, D and Moya, A and Neri-Barrios, X and Falcón, LI}, title = {Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae.}, journal = {MicrobiologyOpen}, volume = {9}, number = {6}, pages = {1113-1127}, pmid = {32181589}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; Chiroptera/*microbiology ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Lactation ; Mexico ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Social Isolation ; }, abstract = {In this paper, we explore how two discrete and geographically separated populations of the lesser long-nosed bat (Leptonycteris yerbabuenae)-one in central and the other in the Pacific region of Mexico-differ in their fecal microbiota composition. Considering the microbiota-host as a unity, in which extrinsic (as food availability and geography) or intrinsic factors (as physiology) play an important role in the microbiota composition, we would expect differentiation in the microbiota of two geographically separated populations. The Amplicon Sequences Variants (ASVs) of the V4 region of the 16s rRNA gene from 68 individuals were analyzed using alpha and beta diversity metrics. We obtained a total of 11 566 (ASVs). The bacterial communities in the Central and Pacific populations had a diversity of 6,939 and 4,088 ASVs, respectively, sharing a core microbiota of 539 ASVs accounting for 75% of the relative abundance, suggesting stability over evolutionary time. The Weighted UniFrac metrics tested by a PERMANOVA showed that lactating and pregnant females had significant beta diversity differences in the two populations compared with other reproductive stages. This could be a consequence of the increased energy requirements of these physiological stages, more than the variation due to geographical separation. In contrast, a positive correlation of the observed ASVs of fecal microbiota with the observed ASVs of plastids related to the diet was observed in the juveniles and adults, suggesting that in these physiological stages an extrinsic factor as the diet shapes the microbiota composition. The results provide a baseline for future studies of the microbiome in these two wild populations of the lesser long-nosed bat, the main pollinator of the Agaves from which the beverages tequila and mezcal are made.}, }
@article {pmid32175570, year = {2020}, author = {Ruiz, C and Villegas-Plazas, M and Thomas, OP and Junca, H and Pérez, T}, title = {Specialized microbiome of the cave-dwelling sponge Plakina kanaky (Porifera, Homoscleromorpha).}, journal = {FEMS microbiology ecology}, volume = {96}, number = {4}, pages = {}, doi = {10.1093/femsec/fiaa043}, pmid = {32175570}, issn = {1574-6941}, mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The recent description of the polychromatic sponge Plakina kanaky revealed original microsymbionts, with some morphotypes recorded for the first time in Homoscleromorpha and others never before observed in other sponge groups. Illumina 16S amplicon sequencing was used to characterize this microbial community by comparing contents of seven specimens of this Plakinidae with five other sponge species: one Homoscleromopha of the Oscarellidae family and four Demospongiae. A total of 256 458 sequences of the hypervariable V5-V6 region of the 16S rRNA gene were clustered into 2,829 OTUs at 97% similarity, with Proteobacteria, Poribacteria and Chloroflexi being the most abundant phyla. The Plakina kanaky specific community appeared to be mainly composed by five OTUs representing about 10% of the total microbiome. Among these, the filamentous bacterium Candidatus Entotheonella, which was among the dominant morphotypes previously observed in the mesohyl and the larvae of P. kanaky, was detected in all studied specimens. However, other original and dominant morphotypes could not be assigned to a known prokaryotic taxon. This cave dwelling sponge species harbors a distinctive microbiome composition of potential taxonomic and metabolic novelties that may be linked to its ecological success in such extreme environments.}, }
@article {pmid32174904, year = {2020}, author = {Clerissi, C and de Lorgeril, J and Petton, B and Lucasson, A and Escoubas, JM and Gueguen, Y and Dégremont, L and Mitta, G and Toulza, E}, title = {Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {311}, pmid = {32174904}, issn = {1664-302X}, abstract = {Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from each family were either sampled for individual microbiota analyses using 16S rRNA gene-metabarcoding or transferred into facilities to record their survival using controlled condition. As expected, all oysters from susceptible families died, and all oysters from the resistant family survived. Quantification of OsHV-1 and bacteria showed that 5 days of transplantation were long enough to contaminate oysters by POMS, but not for entering the pathogenesis process. Thus, it was possible to compare microbiota characteristics between resistant and susceptible oysters families at the early steps of infection. Strikingly, we found that microbiota evenness and abundances of Cyanobacteria (Subsection III, family I), Mycoplasmataceae, Rhodobacteraceae, and Rhodospirillaceae were significantly different between resistant and susceptible oyster families. We concluded that these microbiota characteristics might predict oyster mortalities.}, }
@article {pmid32167987, year = {2020}, author = {Donovan, SM}, title = {Evolution of the gut microbiome in infancy within an ecological context.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {23}, number = {3}, pages = {223-227}, pmid = {32167987}, issn = {1473-6519}, support = {R01 DK107561/DK/NIDDK NIH HHS/United States ; }, mesh = {Ecological and Environmental Phenomena/*physiology ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Pregnancy ; *Prenatal Nutritional Physiological Phenomena ; }, abstract = {PURPOSE OF REVIEW: Humans and their commensal microbiota coexist in a complex ecosystem molded by evolutionary and ecological factors. Ecological opportunity is the prospective, lineage-specific characteristic of an environment that contains both niche availability leading to persistence coupled with niche discordance that drives selection within that lineage. The newborn gut ecosystem presents vast ecological opportunity. Herein, factors affecting perinatal infant microbiome composition are discussed.<br><br>RECENT FINDINGS: Establishing a healthy microbiota in early life is required for immunological programming and prevention of both short-term and long-term health outcomes. The holobiont theory infers that host genetics contributes to microbiome composition. However, in most human studies, environmental factors are predominantly responsible for microbiome composition and function. Key perinatal elements are route of delivery, diet and the environment in which that infant resides. Vaginal delivery seeds an initial microbiome, and breastfeeding refines the community by providing additional microbes, human milk oligosaccharides and immunological proteins.<br><br>SUMMARY: Early life represents an opportunity to implement clinical practices that promote the optimal seeding and feeding of the gut microbial ecosystem. These include reducing nonemergent cesarean deliveries, avoiding the use of antibiotics, and promoting exclusive breastfeeding.}, }
@article {pmid32163141, year = {2020}, author = {Greshake Tzovaras, B and Segers, FHID and Bicker, A and Dal Grande, F and Otte, J and Anvar, SY and Hankeln, T and Schmitt, I and Ebersberger, I}, title = {What Is in Umbilicaria pustulata? A Metagenomic Approach to Reconstruct the Holo-Genome of a Lichen.}, journal = {Genome biology and evolution}, volume = {12}, number = {4}, pages = {309-324}, pmid = {32163141}, issn = {1759-6653}, mesh = {Ascomycota/*genetics/growth &amp; development ; *Genome, Fungal ; Lichens/*genetics/growth &amp; development ; *Metagenome ; Phylogeny ; *Symbiosis ; }, abstract = {Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis-the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)-were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.}, }
@article {pmid32157287, year = {2020}, author = {Saad, MM and Eida, AA and Hirt, H}, title = {Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application.}, journal = {Journal of experimental botany}, volume = {71}, number = {13}, pages = {3878-3901}, pmid = {32157287}, issn = {1460-2431}, mesh = {*Agricultural Inoculants ; Agriculture ; Fertilizers ; Plant Development ; Plants ; Soil Microbiology ; }, abstract = {Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.}, }
@article {pmid32155796, year = {2020}, author = {Meron, D and Maor-Landaw, K and Eyal, G and Elifantz, H and Banin, E and Loya, Y and Levy, O}, title = {The Complexity of the Holobiont in the Red Sea Coral Euphyllia paradivisa under Heat Stress.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32155796}, issn = {2076-2607}, abstract = {The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral-with photosymbionts, and without photosymbionts (apo-symbiotic)-to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community's composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host's differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.}, }
@article {pmid32146404, year = {2020}, author = {Robinson, JM and Breed, MF}, title = {The Lovebug Effect: Is the human biophilic drive influenced by interactions between the host, the environment, and the microbiome?.}, journal = {The Science of the total environment}, volume = {720}, number = {}, pages = {137626}, doi = {10.1016/j.scitotenv.2020.137626}, pmid = {32146404}, issn = {1879-1026}, mesh = {Brain ; Humans ; *Microbiota ; }, abstract = {Psychological frameworks are often used to investigate the mechanisms involved with our affinity towards, and connection with nature--such as the Biophilia Hypothesis and Nature Connectedness. Recent revelations from microbiome science suggest that animal behaviour can be strongly influenced by the host's microbiome--for example, via the bidirectional communication properties of the gut-brain axis. Here, we build on this theory to hypothesise that a microbially-influenced mechanism could also contribute to the human biophilic drive - the tendency for humans to affiliate and connect with nature. Humans may be at an evolutionary advantage through health-regulating exchange of environmental microbiota, which in turn could influence our nature affinity. We present a conceptual model for microbially-influenced nature affinity, calling it the Lovebug Effect. We present an overview of the potential mechanistic pathways involved in the Lovebug Effect, and consider its dependence on the hologenome concept of evolution, direct behavioural manipulation, and host-microbiota associated phenotypes independent of these concepts. We also discuss its implications for human health and ecological resilience. Finally, we highlight several possible approaches to scrutinise the hypothesis. The Lovebug Effect could have important implications for our understanding of exposure to natural environments for health and wellbeing, and could contribute to an ecologically resilient future.}, }
@article {pmid32132275, year = {2020}, author = {Gignoux-Wolfsohn, SA and Precht, WF and Peters, EC and Gintert, BE and Kaufman, LS}, title = {Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {3}, pages = {217-237}, doi = {10.3354/dao03441}, pmid = {32132275}, issn = {0177-5103}, mesh = {Animals ; *Anthozoa ; Bacteria ; Coral Reefs ; Disease Outbreaks ; Ecosystem ; Florida ; }, abstract = {This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.}, }
@article {pmid32130695, year = {2020}, author = {Baffy, G}, title = {Gut Microbiota and Cancer of the Host: Colliding Interests.}, journal = {Advances in experimental medicine and biology}, volume = {1219}, number = {}, pages = {93-107}, pmid = {32130695}, issn = {0065-2598}, mesh = {Dysbiosis ; Gastrointestinal Microbiome/immunology/*physiology ; Humans ; Intestines/immunology/microbiology ; Neoplasms/immunology/*metabolism/therapy ; Tumor Microenvironment ; }, abstract = {Cancer develops in multicellular organisms from cells that ignore the rules of cooperation and escape the mechanisms of anti-cancer surveillance. Tumorigenesis is jointly encountered by the host and microbiota, a vast collection of microorganisms that live on the external and internal epithelial surfaces of the body. The largest community of human microbiota resides in the gastrointestinal tract where commensal, symbiotic and pathogenic microorganisms interact with the intestinal barrier and gut mucosal lymphoid tissue, creating a tumor microenvironment in which cancer cells thrive or perish. Aberrant composition and function of the gut microbiota (dysbiosis) has been associated with tumorigenesis by inducing inflammation, promoting cell growth and proliferation, weakening immunosurveillance, and altering food and drug metabolism or other biochemical functions of the host. However, recent research has also identified several mechanisms through which gut microbiota support the host in the fight against cancer. These mechanisms include the use of antigenic mimicry, biotransformation of chemotherapeutic agents, and other mechanisms to boost anti-cancer immune responses and improve the efficacy of cancer immunotherapy. Further research in this rapidly advancing field is expected to identify additional microbial metabolites with tumor suppressing properties, map the complex interactions of host-microbe 'transkingdom network' with cancer cells, and elucidate cellular and molecular pathways underlying the impact of specific intestinal microbial configurations on immune checkpoint inhibitor therapy.}, }
@article {pmid32127450, year = {2020}, author = {Lima, LFO and Weissman, M and Reed, M and Papudeshi, B and Alker, AT and Morris, MM and Edwards, RA and de Putron, SJ and Vaidya, NK and Dinsdale, EA}, title = {Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32127450}, issn = {2150-7511}, support = {T32 GM128596/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Bermuda ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Models, Theoretical ; Mucus/microbiology ; *Temperature ; }, abstract = {Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.}, }
@article {pmid32126507, year = {2020}, author = {Yin, J and Yu, Y and Zhang, Z and Chen, L and Ruan, L}, title = {Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato.}, journal = {Microbiological research}, volume = {234}, number = {}, pages = {126446}, doi = {10.1016/j.micres.2020.126446}, pmid = {32126507}, issn = {1618-0623}, abstract = {The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.}, }
@article {pmid32123705, year = {2020}, author = {Butina, TV and Khanaev, IV and Kravtsova, LS and Maikova, OO and Bukin, YS}, title = {Metavirome datasets from two endemic Baikal sponges Baikalospongia bacillifera.}, journal = {Data in brief}, volume = {29}, number = {}, pages = {105260}, pmid = {32123705}, issn = {2352-3409}, abstract = {Sponges are ecologically important components of marine and freshwater benthic environments; these holobionts contain a variety of microorganisms and viruses. For the metagenomic characterization of potential taxonomic and functional diversity of sponge-associated dsDNA viruses, we surveyed two samples of Baikal endemic sponge Baikalospongia bacillifera (diseased and visually healthy). In total, after quality processing, we have obtained 3 375 063 and 4 063 311 reads; of these 97 557 and 88 517 sequences, accounting for ca. 2.9 and 2.2% of datasets, have been identified as viral. We have revealed approximately 28 viral families, among which the bacteriophages of the Myoviridae, Siphoviridae and Podoviridae families, as well as the viruses of the Phycodnaviridae and Poxviridae families, dominated in the samples. Analysis of viral sequences using the COG database has indicated 22 functional categories of proteins. Viral communities of visually healthy and diseased Baikal sponges were significantly different. The metagenome sequence data were deposited to NCBI SRA as BioProject PRJNA577390.}, }
@article {pmid32123297, year = {2020}, author = {Glasl, B and Robbins, S and Frade, PR and Marangon, E and Laffy, PW and Bourne, DG and Webster, NS}, title = {Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1435-1450}, pmid = {32123297}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomass ; Coral Reefs ; Metagenome ; *Microbiota ; Porifera/*microbiology ; Seasons ; Seawater/microbiology ; Seaweed/classification/*genetics ; }, abstract = {Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.}, }
@article {pmid32123172, year = {2020}, author = {Alberdi, A and Razgour, O and Aizpurua, O and Novella-Fernandez, R and Aihartza, J and Budinski, I and Garin, I and Ibáñez, C and Izagirre, E and Rebelo, H and Russo, D and Vlaschenko, A and Zhelyazkova, V and Zrnčić, V and Gilbert, MTP}, title = {DNA metabarcoding and spatial modelling link diet diversification with distribution homogeneity in European bats.}, journal = {Nature communications}, volume = {11}, number = {1}, pages = {1154}, pmid = {32123172}, issn = {2041-1723}, mesh = {*Animal Nutritional Physiological Phenomena/genetics ; Animals ; Chiroptera/classification/*physiology ; DNA Barcoding, Taxonomic ; Diptera ; Ecosystem ; Europe ; Feces ; Lepidoptera ; Models, Biological ; Phylogeography ; *Predatory Behavior ; }, abstract = {Inferences of the interactions between species' ecological niches and spatial distribution have been historically based on simple metrics such as low-resolution dietary breadth and range size, which might have impeded the identification of meaningful links between niche features and spatial patterns. We analysed the relationship between dietary niche breadth and spatial distribution features of European bats, by combining continent-wide DNA metabarcoding of faecal samples with species distribution modelling. Our results show that while range size is not correlated with dietary features of bats, the homogeneity of the spatial distribution of species exhibits a strong correlation with dietary breadth. We also found that dietary breadth is correlated with bats' hunting flexibility. However, these two patterns only stand when the phylogenetic relations between prey are accounted for when measuring dietary breadth. Our results suggest that the capacity to exploit different prey types enables species to thrive in more distinct environments and therefore exhibit more homogeneous distributions within their ranges.}, }
@article {pmid32117798, year = {2020}, author = {Jablaoui, A and Kriaa, A and Mkaouar, H and Akermi, N and Soussou, S and Wysocka, M and Wołoszyn, D and Amouri, A and Gargouri, A and Maguin, E and Lesner, A and Rhimi, M}, title = {Fecal Serine Protease Profiling in Inflammatory Bowel Diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {21}, pmid = {32117798}, issn = {2235-2988}, mesh = {Feces ; Humans ; *Inflammatory Bowel Diseases ; Pancreatic Elastase ; *Serine Proteases ; }, abstract = {Serine proteases are extensively known to play key roles in many physiological processes. However, their dysregulation is often associated to several diseases including inflammatory bowel diseases (IBD). Here, we used specific substrates to monitor fecal protease activities in a large cohort of healthy and IBD patients. Of interest, serine protease activity was 10-fold higher in IBD fecal samples compared to healthy controls. Moreover, functional analysis of these fecal proteolytic activities revealed that the most increased activities are trypsin-like, elastase-like and cathepsin G-like. We also show for the first time, an increase of proteinase 3-like activity in these samples compared to controls. Results presented here will guide further investigations to better understand the relevance of these peptidases in IBD.}, }
@article {pmid32115438, year = {2020}, author = {Urayama, SI and Takaki, Y and Hagiwara, D and Nunoura, T}, title = {dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge.}, journal = {Microbes and environments}, volume = {35}, number = {2}, pages = {}, pmid = {32115438}, issn = {1347-4405}, mesh = {Animals ; Aquatic Organisms/virology ; *Genome, Viral ; Phylogeny ; Porifera/*virology ; RNA Viruses/*classification/isolation &amp; purification ; RNA, Double-Stranded/*genetics ; RNA, Viral/genetics ; RNA-Seq ; Sequence Analysis, DNA ; }, abstract = {Invertebrates are a source of previously unknown RNA viruses that fill gaps in the viral phylogenetic tree. Although limited information is currently available on RNA viral diversity in the marine sponge, a primordial multicellular animal that belongs to the phylum Porifera, the marine sponge is one of the well-studied holobiont systems. In the present study, we elucidated the putative complete genome sequences of five novel RNA viruses from Hymeniacidon sponge using a combination of double-stranded RNA sequencing, called fragmented and primer ligated dsRNA sequencing, and a conventional transcriptome method targeting single-stranded RNA. We identified highly diverged RNA-dependent RNA polymerase sequences, including a potential novel RNA viral lineage, in the sponge and three viruses presumed to infect sponge cells.}, }
@article {pmid32108224, year = {2020}, author = {Shoguchi, E and Yoshioka, Y and Shinzato, C and Arimoto, A and Bhattacharya, D and Satoh, N}, title = {Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera.}, journal = {Genome biology and evolution}, volume = {12}, number = {3}, pages = {203-209}, pmid = {32108224}, issn = {1759-6653}, mesh = {Animals ; *Anthozoa ; Dinoflagellida/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genome, Plastid ; Polymorphism, Single Nucleotide ; *RNA Editing ; }, abstract = {In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.}, }
@article {pmid32103386, year = {2020}, author = {Suárez, J}, title = {The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality.}, journal = {History and philosophy of the life sciences}, volume = {42}, number = {1}, pages = {11}, doi = {10.1007/s40656-020-00305-2}, pmid = {32103386}, issn = {1742-6316}, support = {FFU16/02570//Spanish Ministry of Education/ ; FFI2016-76799-P//Ministerio de Econom&#xed;a y Competitividad/ ; Bursary//Royal Institute of Philosophy/ ; }, mesh = {*Genome, Human ; Humans ; *Individuality ; *Phenotype ; }, abstract = {Bourrat and Griffiths (Hist Philos Life Sci 40(2):33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths' arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats (Nat Ecol Evol 2:659-668, 2018), I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics.}, }
@article {pmid32097591, year = {2020}, author = {Greyson-Gaito, CJ and Bartley, TJ and Cottenie, K and Jarvis, WMC and Newman, AEM and Stothart, MR}, title = {Into the wild: microbiome transplant studies need broader ecological reality.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1921}, pages = {20192834}, pmid = {32097591}, issn = {1471-2954}, mesh = {Ecology ; Gastrointestinal Microbiome ; *Microbiota ; *Symbiosis ; }, abstract = {Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host-microbiome interactions may be obscured by the current convention of highly controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host-microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized nine key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.}, }
@article {pmid32093216, year = {2020}, author = {Saurav, K and Borbone, N and Burgsdorf, I and Teta, R and Caso, A and Bar-Shalom, R and Esposito, G and Britstein, M and Steindler, L and Costantino, V}, title = {Identification of Quorum Sensing Activators and Inhibitors in The Marine Sponge Sarcotragus spinosulus.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32093216}, issn = {1660-3397}, support = {1243/16//Israel Science Foundation/ ; B61G18000470007//Regione Campania/ ; 2015-2018//Planning and Budgeting Committee of the Council for Higher Education of Israel/ ; }, mesh = {Animals ; Escherichia coli/*drug effects/physiology ; Luminescent Measurements ; Peptide Hydrolases/chemistry/pharmacology ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; Pyocyanine/chemistry/pharmacology ; Quorum Sensing/*drug effects ; Virulence Factors ; }, abstract = {Marine sponges, a well-documented prolific source of natural products, harbor highly diverse microbial communities. Their extracts were previously shown to contain quorum sensing (QS) signal molecules of the N-acyl homoserine lactone (AHL) type, known to orchestrate bacterial gene regulation. Some bacteria and eukaryotic organisms are known to produce molecules that can interfere with QS signaling, thus affecting microbial genetic regulation and function. In the present study, we established the production of both QS signal molecules as well as QS inhibitory (QSI) molecules in the sponge species Sarcotragus spinosulus. A total of eighteen saturated acyl chain AHLs were identified along with six unsaturated acyl chain AHLs. Bioassay-guided purification led to the isolation of two brominated metabolites with QSI activity. The structures of these compounds were elucidated by comparative spectral analysis of [1]HNMR and HR-MS data and were identified as 3-bromo-4-methoxyphenethylamine (1) and 5,6-dibromo-N,N-dimethyltryptamine (2). The QSI activity of compounds 1 and 2 was evaluated using reporter gene assays for long- and short-chain AHL signals (Escherichia coli pSB1075 and E. coli pSB401, respectively). QSI activity was further confirmed by measuring dose-dependent inhibition of proteolytic activity and pyocyanin production in Pseudomonas aeruginosa PAO1. The obtained results show the coexistence of QS and QSI in S. spinosulus, a complex signal network that may mediate the orchestrated function of the microbiome within the sponge holobiont.}, }
@article {pmid32092934, year = {2020}, author = {Mohanty, I and Podell, S and Biggs, JS and Garg, N and Allen, EE and Agarwal, V}, title = {Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32092934}, issn = {1660-3397}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; R01-ES030316/NH/NIH HHS/United States ; R00-ES026620/NH/NIH HHS/United States ; OCE-1837116//National Science Foundation/ ; }, mesh = {Animals ; *Ecosystem ; *Metabolomics ; *Microbiota ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; }, abstract = {Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.}, }
@article {pmid32084687, year = {2020}, author = {Musella, M and Wathsala, R and Tavella, T and Rampelli, S and Barone, M and Palladino, G and Biagi, E and Brigidi, P and Turroni, S and Franzellitti, S and Candela, M}, title = {Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137209}, doi = {10.1016/j.scitotenv.2020.137209}, pmid = {32084687}, issn = {1879-1026}, mesh = {Animals ; Gills ; Hemolymph ; *Microbiota ; *Mytilus ; Seafood ; }, abstract = {In this study, we characterize the structural variation of the microbiota of Mytilus galloprovincialis at the tissue scale, also exploring the connection with the microbial ecosystem of the surrounding water. Mussels were sampled within a farm located in the North-Western Adriatic Sea and microbiota composition was analyzed in gills, hemolymph, digestive glands, stomach and foot by Next Generation Sequencing marker gene approach. Mussels showed a distinctive microbiota structure, with specific declinations at the tissue level. Indeed, each tissue is characterized by a distinct pattern of dominant families, reflecting a peculiar adaptation to the respective tissue niche. For instance, the microbiota of the digestive gland is characterized by Ruminococcaceae and Lachnospiraceae, being shaped to ferment complex polysaccharides of dietary origin into short-chain fatty acids, well matching the general asset of the animal gut microbiota. Conversely, the gill and hemolymph ecosystems are dominated by marine microorganisms with aerobic oxidative metabolism, consistent with the role played by these tissues as an interface with the external environment. Our findings highlight the putative importance of mussel microbiota for different aspects of host physiology, with ultimate repercussions on mussel health and productivity.}, }
@article {pmid32078802, year = {2020}, author = {Kim, EK and Lee, KA and Hyeon, DY and Kyung, M and Jun, KY and Seo, SH and Hwang, D and Kwon, Y and Lee, WJ}, title = {Bacterial Nucleoside Catabolism Controls Quorum Sensing and Commensal-to-Pathogen Transition in the Drosophila Gut.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {3}, pages = {345-357.e6}, doi = {10.1016/j.chom.2020.01.025}, pmid = {32078802}, issn = {1934-6069}, mesh = {Animals ; Bacteria/*metabolism/*pathogenicity ; Bacterial Proteins/metabolism ; Drosophila/*microbiology ; Dual Oxidases/metabolism ; N-Glycosyl Hydrolases/metabolism ; *Quorum Sensing ; Reactive Oxygen Species/metabolism ; Ribose/metabolism ; Symbiosis ; Uracil/*metabolism ; Uridine/metabolism ; *Virulence ; }, abstract = {Although the gut microbiome is generally symbiotic or commensal, some microbiome members become pathogenic under certain circumstances. However, the factors driving this pathogenic switch are largely unknown. Pathogenic bacteria can generate uracil that triggers host dual oxidase (DUOX) to produce antimicrobial reactive oxygen species (ROS). We show that pathogens generate uracil and ribose upon nucleoside catabolism of gut luminal uridine, which triggers not only host defenses but also inter-bacterial communication and pathogenesis in Drosophila. Uridine-derived uracil triggers DUOX-dependent ROS generation, whereas ribose induces bacterial quorum sensing (QS) and virulence gene expression. Genes implicated in nucleotide metabolism are found in pathogens but not commensal bacteria, and their genetic ablation blocks QS and the commensal-to-pathogen transition in vivo. Furthermore, commensal bacteria lack functional nucleoside catabolism, which is required to achieve gut-microbe symbiosis, but can become pathogenic by enabling nucleotide catabolism. These findings reveal molecular mechanisms governing the commensal-to-pathogen transition in different contexts of host-microbe interactions.}, }
@article {pmid32077981, year = {2020}, author = {Bartolomaeus, H and McParland, V and Wilck, N}, title = {[Gut-heart axis : How gut bacteria influence cardiovascular diseases].}, journal = {Herz}, volume = {45}, number = {2}, pages = {134-141}, pmid = {32077981}, issn = {1615-6692}, mesh = {Bacteria ; *Cardiovascular Diseases/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {The view of humans as holobionts consisting of eukaryotic host cells and associated prokaryotic organisms, has opened up a new perspective on cardiovascular pathophysiology. In particular, intestinal bacteria influence the cell and organ functions of the host. Intestinal bacteria represent a metabolically active community whose composition and function can influence cardiovascular health and disease. The interaction between the intestinal microbiota and the heart occurs via metabolites of bacterial origin, which are resorbed in the intestine and distributed via the circulation. Bacterial metabolites are produced from food components, which in turn emphasizes the importance of nutrition. Some of these metabolites, such as trimethylamine N‑oxide (TMAO), can exacerbate cardiovascular pathologies. Short-chain fatty acids (SCFA) in turn are considered to be protective metabolites. The host's immune system is an important target for these metabolites and explains much of their effects. In the future, the targeted manipulation of intestinal bacteria could help to prevent the development and progression of cardiovascular diseases.}, }
@article {pmid32075724, year = {2020}, author = {Lee, WJ}, title = {Delipidation Destresses Drosophila.}, journal = {Immunity}, volume = {52}, number = {2}, pages = {215-217}, doi = {10.1016/j.immuni.2020.01.009}, pmid = {32075724}, issn = {1097-4180}, mesh = {Animals ; *Drosophila ; *Drosophila Proteins ; Immunity ; Lipids ; Reactive Oxygen Species ; }, abstract = {Stress responses at an organism level are complex and poorly understood. In this issue of Immunity, Li et al. demonstrate that Drosophila kidney excretes blood lipids to minimize damage by reactive oxygen species and that this function is essential for animal survival.}, }
@article {pmid32075325, year = {2020}, author = {Lewandowska, M and Hazan, Y and Moran, Y}, title = {Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis.}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, pmid = {32075325}, issn = {1999-4915}, mesh = {Animals ; Female ; Life Cycle Stages ; Phylogeny ; RNA-Seq ; Sea Anemones/*virology ; *Transcriptome ; Viral Load ; *Virome ; Viruses/*classification ; }, abstract = {The role of viruses in forming a stable holobiont has been the subject of extensive research in recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed an almost complete lack of viruses in the samples from the early developmental stages, which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for the functional studies of viruses and antiviral systems in this lab model cnidarian.}, }
@article {pmid32051527, year = {2020}, author = {Miyazaki, J and Ikuta, T and Watsuji, TO and Abe, M and Yamamoto, M and Nakagawa, S and Takaki, Y and Nakamura, K and Takai, K}, title = {Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica.}, journal = {The ISME journal}, volume = {14}, number = {5}, pages = {1273-1289}, pmid = {32051527}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics ; Campylobacter/*physiology ; Energy Metabolism ; Gills/microbiology ; In Situ Hybridization, Fluorescence ; Indian Ocean ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*microbiology/physiology ; *Symbiosis ; }, abstract = {Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.}, }
@article {pmid32048447, year = {2020}, author = {Howe-Kerr, LI and Bachelot, B and Wright, RM and Kenkel, CD and Bay, LK and Correa, AMS}, title = {Symbiont community diversity is more variable in corals that respond poorly to stress.}, journal = {Global change biology}, volume = {26}, number = {4}, pages = {2220-2234}, doi = {10.1111/gcb.14999}, pmid = {32048447}, issn = {1365-2486}, support = {G2016100191023671//Sigma Xi Grant-in-Aid of Research/ ; G11/34671.1//Australian Institute of Marine Science/ ; G14/37318.1//Australian Institute of Marine Science/ ; 1635798//US National Science Foundation/ ; 1800914//US National Science Foundation/ ; 1928609//US National Science Foundation/ ; 1401165//US National Science Foundation/ ; 2000009651//National Academies of Sciences, Engineering, and Medicine/ ; }, abstract = {Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts-the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four 'best performer' coral genets were analyzed at the end of the experiment because they survived high temperature, high pCO2 , bacterial exposure, or combined stressors, whereas four 'worst performer' genets were characterized because they experienced substantial mortality under these stressors. At the end of the experiment, seven of eight coral genets mainly hosted Cladocopium symbionts, whereas the eighth genet was dominated by both Cladocopium and Durusdinium symbionts. Symbiodiniaceae alpha and beta diversity were higher in worst performing genets than in best performing genets. Symbiont communities in worst performers also differed more after stress exposure relative to their controls (based on normalized proportional differences in beta diversity), than did best performers. A generalized joint attribute model estimated the influence of host genet and treatment on Symbiodiniaceae community composition and identified strong associations among particular symbionts and host genet performance, as well as weaker associations with treatment. Although dominant symbiont physiology and function contribute to host performance, these findings emphasize the importance of symbiont community diversity and stochasticity as components of host performance. Our findings also suggest that symbiont community diversity metrics may function as indicators of resilience and have potential applications in diverse disciplines from climate change adaptation to agriculture and medicine.}, }
@article {pmid32040614, year = {2020}, author = {Brodin, P}, title = {New approaches to the study of immune responses in humans.}, journal = {Human genetics}, volume = {139}, number = {6-7}, pages = {795-799}, pmid = {32040614}, issn = {1432-1203}, support = {Born-Immune//H2020 European Research Council/ ; }, mesh = {Animals ; *Cell Communication ; *Homeostasis ; Humans ; Immune System/*immunology ; Infections/*etiology ; Signal Transduction ; }, abstract = {The human immune system consists of multiple, layered mechanisms of sensing and responding to cellular stress, infection and tissue damage to ensure defense from pathogens, maintenance of tissue homeostasis, and the integrity of the holobiont. Every single cell in the body has a role to play, but a few dozen, specialized white blood cells are particularly important in this respect. Understanding the overall state of this multifaceted system in a single individual is challenging, and we are only beginning to do this across populations of individuals, to understand the vast range of inter-individual variation, and the influences of genes and environmental factors that collectively shape the immune system in a given individual. We are also only beginning to understand the changes occurring within this system over time, and how this relates to health and disease susceptibility. Several technological breakthroughs in recent years have enabled these developments and the emergence of a new, complementary approach to studying human immune systems, namely systems immunology. In this paradigm, the focus is shifted from the understanding of individual immune system components and their mechanisms of action, towards analyses of cell-cell interactions, and mechanisms of coordination and regulation within the human immune system.}, }
@article {pmid32039567, year = {2020}, author = {Baedke, J and Fábregas-Tejeda, A and Nieves Delgado, A}, title = {The holobiont concept before Margulis.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {334}, number = {3}, pages = {149-155}, doi = {10.1002/jez.b.22931}, pmid = {32039567}, issn = {1552-5015}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*cytology/*genetics ; History, 20th Century ; *Host Microbial Interactions ; Microbiota ; Selection, Genetic ; Symbiosis/*genetics/*physiology ; }, abstract = {In recent years, Lynn Margulis has been credited in various articles as the person who introduced the concept of holobiont into biology in the early 1990s. Today, the origin of evolutionary studies on holobionts is closely linked to her name. However, Margulis was not the first person to use this concept in its current context. That honor goes to the German theoretical biologist Adolf Meyer-Abich, who introduced the holobiont concept nearly 50 years before her (in 1943). Although nearly completely forgotten today, in the 1940-60s he developed a comprehensive theory of evolutionary change through "holobiosis." It had a surprisingly modern outlook, as it not only addressed tenets of today's evolutionary developmental biology (evo-devo), like the origin of form and production of variation, but also anticipated key elements of Margulis' later endosymbiotic theory. As the holobiont concept has become an important guiding concept for organizing research, labeling conferences, and publishing articles on host-microbiota collectives and hologenomes, the field should become aware of the independent origin of this concept in the context of holistic biology of the 1940s.}, }
@article {pmid32038589, year = {2019}, author = {Araya, JP and González, M and Cardinale, M and Schnell, S and Stoll, A}, title = {Microbiome Dynamics Associated With the Atacama Flowering Desert.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3160}, pmid = {32038589}, issn = {1664-302X}, abstract = {In a desert, plants as holobionts quickly respond to resource pulses like precipitation. However, little is known on how environment and plants modulate the rhizosphere-associated microbiome. As a model species to represent the Atacama Desert bloom, Cistanthe longiscapa (Montiaceae family) was selected to study the influence of abiotic and biotic environment on the diversity and structure of the microbiota associated to its rhizosphere. We analyzed the rhizosphere and soil microbiome along a North-South precipitation gradient and between a dry and rainy year by using Illumina high-throughput sequencing of 16S rRNA gene fragments and ITS2 regions for prokaryotes and fungi, respectively. In the rhizosphere of C. longiscapa the microbiota clearly differs in composition and structure from the surrounding bulk soil. The fungal and bacterial communities respond differently to environmental conditions. The diversity and richness of fungal OTUs were negatively correlated with aridity, as predicted. The community structure was predominantly influenced by other soil characteristics (pH, organic matter content) but not by aridity. In contrast, diversity, composition, and structure of the bacterial community were not influenced by aridity or any other evaluated soil parameter. These findings coincide with the identification of mainly site-specific microbial communities, not shared along the sites. These local communities contain a group of OTUs, which are exclusive to the rhizosphere of each site and presumably vertically inherited as seed endophytes. Their ecological functions and dispersal mechanisms remain unclear. The analysis of co-occurrence patterns highlights the strong effect of the desert habitat over the soil- and rhizosphere-microbiome. The site-independent enrichment of only a small bacterial cluster consistently associated with the rhizosphere of C. longiscapa further supports this conclusion. In a rainy year, the rhizosphere microbiota significantly differed from bulk and bare soil, whereas in a dry year, the community structure of the former rhizosphere approximates to the one found in the bulk. In the context of plant-microbe interactions in desert environments, our study contributes new insights into the importance of aridity in microbial community structure and composition, discovering the influence of other soil parameters in this complex dynamic network, which needs further to be investigated.}, }
@article {pmid32023487, year = {2020}, author = {Wang, GH and Berdy, BM and Velasquez, O and Jovanovic, N and Alkhalifa, S and Minbiole, KPC and Brucker, RM}, title = {Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {2}, pages = {213-224.e7}, doi = {10.1016/j.chom.2020.01.009}, pmid = {32023487}, issn = {1934-6069}, mesh = {Animals ; Atrazine/metabolism/toxicity ; Bacteria/genetics/isolation &amp; purification/metabolism ; Directed Molecular Evolution ; Drug Resistance/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; Genes, Bacterial ; Maternal Inheritance ; Metagenomics ; Pesticides/metabolism/*toxicity ; Pseudomonas/genetics/isolation &amp; purification/metabolism ; Serratia marcescens/genetics/isolation &amp; purification/metabolism ; Wasps/drug effects/*microbiology ; Xenobiotics/metabolism/toxicity ; }, abstract = {The gut is a first point of contact with ingested xenobiotics, where chemicals are metabolized directly by the host or microbiota. Atrazine is a widely used pesticide, but the role of the microbiome metabolism of this xenobiotic and the impact on host responses is unclear. We exposed successive generations of the wasp Nasonia vitripennis to subtoxic levels of atrazine and observed changes in the structure and function of the gut microbiome that conveyed atrazine resistance. This microbiome-mediated resistance was maternally inherited and increased over successive generations, while also heightening the rate of host genome selection. The rare gut bacteria Serratia marcescens and Pseudomonas protegens contributed to atrazine metabolism. Both of these bacteria contain genes that are linked to atrazine degradation and were sufficient to confer resistance in experimental wasp populations. Thus, pesticide exposure causes functional, inherited changes in the microbiome that should be considered when assessing xenobiotic exposure and as potential countermeasures to toxicity.}, }
@article {pmid32021942, year = {2020}, author = {Mondo, E and Barone, M and Soverini, M and D'Amico, F and Cocchi, M and Petrulli, C and Mattioli, M and Marliani, G and Candela, M and Accorsi, PA}, title = {Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders.}, journal = {Heliyon}, volume = {6}, number = {1}, pages = {e03311}, pmid = {32021942}, issn = {2405-8440}, abstract = {Accompanying human beings since the Paleolithic period, dogs has been recently regarded as a reliable model for the study of the gut microbiome connections with health and disease. In order to provide some glimpses on the connections between the gut microbiome layout and host behavior, we profiled the phylogenetic composition and structure of the canine gut microbiome of dogs with aggressive (n = 11), phobic (n = 13) and normal behavior (n = 18). Hormones' determination was made through Radio Immuno-Assay (RIA), and next generation sequencing of the V3-V4 gene region of the bacterial 16S rRNA was employed to determine gut microbiome composition. Our results did not evidence any significant differences of hormonal levels between the three groups. According to our findings, aggressive behavioral disorder was found to be characterized by a peculiar gut microbiome structure, with high biodiversity and enrichment in generally subdominant bacterial genera (i.e. Catenibacterium and Megamonas). On the other hand, phobic dogs were enriched in Lactobacillus, a bacterial genus with known probiotic and psychobiotic properties. Although further studies are needed to validate our findings, our work supports the intriguing opportunity that different behavioral phenotypes in dogs may be associated with peculiar gut microbiome layouts, suggesting possible connections between the gut microbiome and the central nervous system and indicating the possible adoption of probiotic interventions aimed at restoring a balanced host-symbiont interplay for mitigating behavioral disorders.}, }
@article {pmid32011756, year = {2020}, author = {Kennedy, SR and Tsau, S and Gillespie, R and Krehenwinkel, H}, title = {Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua.}, journal = {Molecular ecology}, volume = {29}, number = {5}, pages = {1001-1015}, doi = {10.1111/mec.15370}, pmid = {32011756}, issn = {1365-294X}, mesh = {Animals ; Bacteria/*classification ; Bacterial Load ; California ; *Diet ; *Gastrointestinal Microbiome ; Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Spiders/*microbiology ; }, abstract = {Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven. This assumption is supported by a feeding experiment, in which two types of prey-crickets and fruit flies-both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.}, }
@article {pmid32010100, year = {2019}, author = {Flores-Núñez, VM and Fonseca-García, C and Desgarennes, D and Eloe-Fadrosh, E and Woyke, T and Partida-Martínez, LP}, title = {Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3044}, pmid = {32010100}, issn = {1664-302X}, abstract = {Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.}, }
@article {pmid32008576, year = {2020}, author = {Osman, EO and Suggett, DJ and Voolstra, CR and Pettay, DT and Clark, DR and Pogoreutz, C and Sampayo, EM and Warner, ME and Smith, DJ}, title = {Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {8}, pmid = {32008576}, issn = {2049-2618}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology ; Bacteria/*classification ; Coral Reefs ; Dinoflagellida/classification/*physiology ; *Host Specificity ; Hot Temperature ; Indian Ocean ; *Microbiota ; *Symbiosis ; }, abstract = {BACKGROUND: The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.<br><br>RESULTS: We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4&#xb0; of latitude&#xa0;and summer mean temperature ranges from 26.6&#x2009;&#xb0;C to 29.3&#x2009;&#xb0;C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.<br><br>CONCLUSION: The conserved endosymbiotic community&#xa0;suggests high physiological plasticity to support holobiont productivity&#xa0;across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated&#xa0;with&#xa0;the SML across sites may contribute to&#xa0;holobiont&#xa0;function and broaden the ecological&#xa0;niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.}, }
@article {pmid31983620, year = {2020}, author = {Bettenfeld, P and Fontaine, F and Trouvelot, S and Fernandez, O and Courty, PE}, title = {Woody Plant Declines. What's Wrong with the Microbiome?.}, journal = {Trends in plant science}, volume = {25}, number = {4}, pages = {381-394}, doi = {10.1016/j.tplants.2019.12.024}, pmid = {31983620}, issn = {1878-4372}, mesh = {Carbon ; *Microbiota ; Nitrogen ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {Woody plant (WP) declines have multifactorial determinants as well as a biological and economic reality. The vascular system of WPs involved in the transport of carbon, nitrogen, and water from sources to sinks has a seasonal activity, which places it at a central position for mediating plant-environment interactions from nutrient cycling to community assembly and for regulating a variety of processes. To limit effects and to fight against declines, we propose: (i) to consider the WP and its associated microbiota as an holobiont and as a set of functions; (ii) to consider simultaneously, without looking at what comes first, the physiological or pathogenic disorders; and (iii) to define pragmatic strategies, including preventive and curative agronomical practices based on microbiota engineering.}, }
@article {pmid31971565, year = {2020}, author = {Xing, H and Kembel, SW and Makarenkov, V}, title = {Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {9}, pages = {2740-2749}, doi = {10.1093/bioinformatics/btaa043}, pmid = {31971565}, issn = {1367-4811}, mesh = {*Evolution, Molecular ; Gene Transfer, Horizontal ; Genome ; Phylogeny ; *Software ; }, abstract = {MOTIVATION: Phylogenetic trees and the methods for their analysis have played a key role in many evolutionary, ecological and bioinformatics studies. Alternatively, phylogenetic networks have been widely used to analyze and represent complex reticulate evolutionary processes which cannot be adequately studied using traditional phylogenetic methods. These processes include, among others, hybridization, horizontal gene transfer, and genetic recombination. Nowadays, sequence similarity and genome similarity networks have become an efficient tool for community analysis of large molecular datasets in comparative studies. These networks can be used for tackling a variety of complex evolutionary problems such as the identification of horizontal gene transfer events, the recovery of mosaic genes and genomes, and the study of holobionts.<br><br>RESULTS: The shortest path in a phylogenetic tree is used to estimate evolutionary distances between species. We show how the shortest path concept can be extended to sequence similarity networks by defining five new distances, NetUniFrac, Spp, Spep, Spelp and Spinp, and the Transfer index, between species communities present in the network. These new distances can be seen as network analogs of the traditional UniFrac distance used to assess dissimilarity between species communities in a phylogenetic tree, whereas the Transfer index is intended for estimating the rate and direction of gene transfers, or species dispersal, between different phylogenetic, or ecological, species communities. Moreover, NetUniFrac and the Transfer index can be computed in linear time with respect to the number of edges in the network. We show how these new measures can be used to analyze microbiota and antibiotic resistance gene similarity networks.<br><br>Our NetFrac program, implemented in R and C, along with its source code, is freely available on Github at the following URL address: https://github.com/XPHenry/Netfrac.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31969889, year = {2019}, author = {Vincent, D and Rafiqi, M and Job, D}, title = {The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1626}, pmid = {31969889}, issn = {1664-462X}, abstract = {The plant secretome is usually considered in the frame of proteomics, aiming at characterizing extracellular proteins, their biological roles and the mechanisms accounting for their secretion in the extracellular space. In this review, we aim to highlight recent results pertaining to secretion through the conventional and unconventional protein secretion pathways notably those involving plant exosomes or extracellular vesicles. Furthermore, plants are well known to actively secrete a large array of different molecules from polymers (e.g. extracellular RNA and DNA) to small compounds (e.g. ATP, phytochemicals, secondary metabolites, phytohormones). All of these play pivotal roles in plant-fungi (or oomycetes) interactions, both for beneficial (mycorrhizal fungi) and deleterious outcomes (pathogens) for the plant. For instance, recent work reveals that such secretion of small molecules by roots is of paramount importance to sculpt the rhizospheric microbiota. Our aim in this review is to extend the definition of the plant and fungal secretomes to a broader sense to better understand the functioning of the plant/microorganisms holobiont. Fundamental perspectives will be brought to light along with the novel tools that should support establishing an environment-friendly and sustainable agriculture.}, }
@article {pmid31964724, year = {2020}, author = {Motone, K and Takagi, T and Aburaya, S and Miura, N and Aoki, W and Ueda, M}, title = {A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964724}, issn = {2150-7511}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Microbiota ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Zeaxanthins/*biosynthesis ; }, abstract = {Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [Fv/Fm]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the Fv/Fm and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the Fv/Fm and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.IMPORTANCE Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions.}, }
@article {pmid31960895, year = {2019}, author = {Bovio, E and Sfecci, E and Poli, A and Gnavi, G and Prigione, V and Lacour, T and Mehiri, M and Varese, GC}, title = {The culturable mycobiota associated with the Mediterranean sponges Aplysina cavernicola, Crambe crambe and Phorbas tenacior.}, journal = {FEMS microbiology letters}, volume = {366}, number = {24}, pages = {}, doi = {10.1093/femsle/fnaa014}, pmid = {31960895}, issn = {1574-6968}, mesh = {Animals ; Biodiversity ; Crambe Sponge/*microbiology ; Fungi/isolation &amp; purification ; Mediterranean Sea ; *Microbiota ; Phylogeny ; Porifera/microbiology ; Seawater/microbiology ; }, abstract = {Marine fungi are part of the huge and understudied biodiversity hosted in the sea. To broaden the knowledge on fungi inhabiting the Mediterranean Sea and their role in sponge holobiont, three sponges namely Aplysina cavernicola, Crambe crambe and Phorbas tenacior were collected in Villefranche sur Mer, (France) at about 25 m depth. The fungal communities associated with the sponges were isolated using different techniques to increase the numbers of fungi isolated. All fungi were identified to species level giving rise to 19, 13 and 3 species for P. tenacior, A. cavernicola and C. crambe, respectively. Of note, 35.7% and 50.0% of the species detected were either reported for the first time in the marine environment or in association with sponges. The mini-satellite analysis confirmed the uniqueness of the mycobiota of each sponge, leading to think that the sponge, with its metabolome, may shape the microbial community.}, }
@article {pmid31959785, year = {2020}, author = {Moreno-Pino, M and Cristi, A and Gillooly, JF and Trefault, N}, title = {Characterizing the microbiomes of Antarctic sponges: a functional metagenomic approach.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {645}, pmid = {31959785}, issn = {2045-2322}, mesh = {Animals ; Antarctic Regions ; Carbon/metabolism ; Carbon Dioxide/metabolism ; Chemoautotrophic Growth ; Light ; Marine Biology/*methods ; Metagenomics/*methods ; *Microbiota/genetics/physiology ; Nitrogen/metabolism ; Nutrients/metabolism ; Porifera/*genetics/metabolism/*microbiology/physiology ; Seawater/microbiology ; Symbiosis ; }, abstract = {Relatively little is known about the role of sponge microbiomes in the Antarctic marine environment, where sponges may dominate the benthic landscape. Specifically, we understand little about how taxonomic and functional diversity contributes to the symbiotic lifestyle and aids in nutrient cycling. Here we use functional metagenomics to investigate the community composition and metabolic potential of microbiomes from two abundant Antarctic sponges, Leucetta antarctica and Myxilla sp. Genomic and taxonomic analyses show that both sponges harbor a distinct microbial community with high fungal abundance, which differs from the surrounding seawater. Functional analyses reveal both sponge-associated microbial communities are enriched in functions related to the symbiotic lifestyle (e.g., CRISPR system, Eukaryotic-like proteins, and transposases), and in functions important for nutrient cycling. Both sponge microbiomes possessed genes necessary to perform processes important to nitrogen cycling (i.e., ammonia oxidation, nitrite oxidation, and denitrification), and carbon fixation. The latter indicates that Antarctic sponge microorganisms prefer light-independent pathways for CO2 fixation mediated by chemoautotrophic microorganisms. Together, these results show how the unique metabolic potential of two Antarctic sponge microbiomes help these sponge holobionts survive in these inhospitable environments, and contribute to major nutrient cycles of these ecosystems.}, }
@article {pmid31945519, year = {2020}, author = {Meenatchi, R and Thinesh, T and Brindangnanam, P and Hassan, S and Kiran, GS and Selvin, J}, title = {Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis.}, journal = {Microbiological research}, volume = {233}, number = {}, pages = {126408}, doi = {10.1016/j.micres.2019.126408}, pmid = {31945519}, issn = {1618-0623}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification ; Coral Reefs ; *Heat-Shock Response ; High-Throughput Nucleotide Sequencing ; India ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Coral bleaching, a phenomenon by which the expulsion of corals' alveolate endosymbiont (zooxanthellae) occurs when experiencing thermal stress is the major cause for devastation of corals. However, apart from this obligate symbiont of Scleractinian corals, there are different kinds of microbes that exist as stable, transient or sporadic members of the holobiont which reside within various microhabitats in the coral structures. Thus, this study aims to profile the coral bacterial community composition among different coral genera (thermally-sensitive (Acropora digetifera and A. noblis) and thermally resistant (Favites abdita) coral genera analyzed by field monitoring surveys) and also in a particular coral genus (thermally sensitive coral-A. digetifera) at two different sampling times (March 2016 and January 2017). A total of about 608695 paired end reads were obtained through Illumina MiSeq Sequencing platform. The alpha diversity indices (ACE, Chao1 and Shannon) were found to be higher in A. nobilis, followed by A. digetifera and Favites abdita, and the corresponding Simpson values were also found to follow the same trend, indicating that the samples are both rich in species diversity and species evenness. Proteobacteria was found to be the most dominant phylum and Gammaproteobacteria was the predominant class present in all the coral genera studied as also during different sampling time periods. As Vibrionaceae was previously reported to increase its abundance during bleaching stress conditions, bacterial profiling among different coral genera showed the presence of 86 % Vibrionaceae in A. digetifera colonies, and it was 93 % in A. digetifera samples collected during March 2016 whereas, it was found to decrease significantly (7 %) in same tagged colonies collected during January 2017. Thus, profiling of microbiome is of prime importance while studying the holobiont organism like the corals. Stress levels experienced by Palk Bay are even depicted in this microbiome study showing high alpha diversity indices that should alarm reef managers to pay attention to this precious stress tolerant reef community.}, }
@article {pmid31943674, year = {2020}, author = {Matthews, JL and Raina, JB and Kahlke, T and Seymour, JR and van Oppen, MJH and Suggett, DJ}, title = {Symbiodiniaceae-bacteria interactions: rethinking metabolite exchange in reef-building corals as multi-partner metabolic networks.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1675-1687}, doi = {10.1111/1462-2920.14918}, pmid = {31943674}, issn = {1462-2920}, support = {DP180100074//Australian Research Council/International ; DP180100838//Australian Research Council/International ; FL180100036//Australian Research Council/International ; LT000625/2018&#x2010;L//Human Frontier Science Program/International ; }, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*metabolism ; Bacteria/genetics/*metabolism ; Coral Reefs ; Dinoflagellida/*microbiology ; Ecosystem ; Fungi/genetics/*metabolism ; Metabolic Networks and Pathways ; Symbiosis/*physiology ; }, abstract = {The intimate relationship between scleractinian corals and their associated microorganisms is fundamental to healthy coral reef ecosystems. Coral-associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi and viruses) support coral health and resilience through metabolite transfer, inter-partner signalling, and genetic exchange. However, much of our understanding of the coral holobiont relationship has come from studies that have investigated either coral-Symbiodiniaceae or coral-bacteria interactions in isolation, while relatively little research has focused on other ecological and metabolic interactions potentially occurring within the coral multi-partner symbiotic network. Recent evidences of intimate coupling between phytoplankton and bacteria have demonstrated that obligate resource exchange between partners fundamentally drives their ecological success. Here, we posit that similar associations with bacterial consortia regulate Symbiodiniaceae productivity and are in turn central to the health of corals. Indeed, we propose that this bacteria-Symbiodiniaceae-coral relationship underpins the coral holobiont's nutrition, stress tolerance and potentially influences the future survival of coral reef ecosystems under changing environmental conditions. Resolving Symbiodiniaceae-bacteria associations is therefore a logical next step towards understanding the complex multi-partner interactions occurring in the coral holobiont.}, }
@article {pmid31926407, year = {2020}, author = {Edge, TA and Baird, DJ and Bilodeau, G and Gagné, N and Greer, C and Konkin, D and Newton, G and Séguin, A and Beaudette, L and Bilkhu, S and Bush, A and Chen, W and Comte, J and Condie, J and Crevecoeur, S and El-Kayssi, N and Emilson, EJS and Fancy, DL and Kandalaft, I and Khan, IUH and King, I and Kreutzweiser, D and Lapen, D and Lawrence, J and Lowe, C and Lung, O and Martineau, C and Meier, M and Ogden, N and Paré, D and Phillips, L and Porter, TM and Sachs, J and Staley, Z and Steeves, R and Venier, L and Veres, T and Watson, C and Watson, S and Macklin, J}, title = {The Ecobiomics project: Advancing metagenomics assessment of soil health and freshwater quality in Canada.}, journal = {The Science of the total environment}, volume = {710}, number = {}, pages = {135906}, doi = {10.1016/j.scitotenv.2019.135906}, pmid = {31926407}, issn = {1879-1026}, mesh = {Animals ; Biodiversity ; Canada ; Fresh Water ; Humans ; *Metagenomics ; *Soil ; }, abstract = {Transformative advances in metagenomics are providing an unprecedented ability to characterize the enormous diversity of microorganisms and invertebrates sustaining soil health and water quality. These advances are enabling a better recognition of the ecological linkages between soil and water, and the biodiversity exchanges between these two reservoirs. They are also providing new perspectives for understanding microorganisms and invertebrates as part of interacting communities (i.e. microbiomes and zoobiomes), and considering plants, animals, and humans as holobionts comprised of their own cells as well as diverse microorganisms and invertebrates often acquired from soil and water. The Government of Canada's Genomics Research and Development Initiative (GRDI) launched the Ecobiomics Project to coordinate metagenomics capacity building across federal departments, and to apply metagenomics to better characterize microbial and invertebrate biodiversity for advancing environmental assessment, monitoring, and remediation activities. The Project has adopted standard methods for soil, water, and invertebrate sampling, collection and provenance of metadata, and nucleic acid extraction. High-throughput sequencing is located at a centralized sequencing facility. A centralized Bioinformatics Platform was established to enable a novel government-wide approach to harmonize metagenomics data collection, storage and bioinformatics analyses. Sixteen research projects were initiated under Soil Microbiome, Aquatic Microbiome, and Invertebrate Zoobiome Themes. Genomic observatories were established at long-term environmental monitoring sites for providing more comprehensive biodiversity reference points to assess environmental change.}, }
@article {pmid31925332, year = {2020}, author = {Gibbin, E and Banc-Prandi, G and Fine, M and Comment, A and Meibom, A}, title = {A method to disentangle and quantify host anabolic turnover in photosymbiotic holobionts with subcellular resolution.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {14}, pmid = {31925332}, issn = {2399-3642}, mesh = {Animals ; Anthozoa/metabolism/ultrastructure ; Carbohydrate Metabolism ; Microbiology ; *Photosynthesis ; Pyruvic Acid/metabolism ; *Symbiosis ; }, abstract = {A wide range of organisms host photosynthesizing symbionts. In these animals the metabolic exchange between host and symbionts has prevented in situ host anabolic turnover to be studied without the confounding effect of translocated photosynthates. Using the symbiotic coral Stylophora pistillata as a model organism and [1-[13]C]-pyruvate and [2,3-[13]C]-pyruvate in different incubation conditions (light, light + DCMU, and darkness), we employed NanoSIMS isotopic imaging to quantify host anabolism, with and without translocated metabolites from their photosynthesizing dinoflagellate symbionts. Under our experimental conditions, host de novo lipid synthesis accounted for ~40% of the total holobiont lipid reserve, and dinoflagellate recycling of metabolic [13]CO2 enhanced host tissue [13]C-enrichment by 13-22% in the epidermis, 40-58% in the gastrodermis, and 135-169% in host lipid bodies. Furthermore, we show that host anabolic turnover in different tissue structures differs, in a manner consistent with the localisation, function and cellular composition of these structures.}, }
@article {pmid31921931, year = {2020}, author = {Pontarollo, G and Kiouptsi, K and Reinhardt, C}, title = {A holobiont view on thrombosis: unravelling the microbiota's influence on arterial thrombus growth.}, journal = {Microbial cell (Graz, Austria)}, volume = {7}, number = {1}, pages = {28-31}, doi = {10.15698/mic2020.01.704}, pmid = {31921931}, issn = {2311-2638}, abstract = {The commensal microbiota has co-evolved with its host, colonizing all body surfaces. Therefore, this microbial ecosystem is intertwined with host physiology at multiple levels. While it is evident that microbes that reach the blood stream can trigger thrombus formation, it remains poorly explored if the wealth of microbes that colonize the body surfaces of the mammalian host can be regarded as a modifier of cardiovascular disease (CVD) development. To experimentally address the microbiota's role in the development of atherosclerotic lesions and arterial thrombosis, we generated a germ-free (GF) low-density lipoprotein receptor-deficient (Ldlr[-/-]) atherosclerosis mouse model (Kiouptsi et al., mBio, 2019) and explored the role of nutritional composition on arterial thrombogenesis.}, }
@article {pmid31905988, year = {2019}, author = {Ou, H and Li, M and Wu, S and Jia, L and Hill, RT and Zhao, J}, title = {Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas.}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {31905988}, issn = {2076-2607}, support = {17GYY008NF04//Scientific Research Project of Xiamen Southern Ocean Center, China/ ; 41876183//National Natural Science Foundation of China/ ; }, abstract = {Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. Massive polyP granules were observed under confocal microscopy in samples from very low DIP environments. The composition of sponge symbiotic microbes was analyzed by high-throughput sequencing and the corresponding polyphosphate kinase (ppk) genes were detected. Sequence analysis revealed that in the low DIP environment, those sponges with higher polyP content and enrichment rates had relatively higher abundances of cyanobacteria. Mantel tests and canonical correspondence analysis (CCA) examined that the polyP enrichment rate was most strongly correlated with the structure of microbial communities, including genera Synechococcus, Rhodopirellula, Blastopirellula, and Rubripirellula. About 50% of ppk genes obtained from the total DNA of sponge holobionts, had above 80% amino acid sequence similarities to those sequences from Synechococcus. In general, it suggested that sponges employed differentiated strategies towards the use of phosphorus in different nutrient environments and the symbiotic Synechococcus could play a key role in accumulating polyP.}, }
@article {pmid31900444, year = {2020}, author = {Wall, CB and Kaluhiokalani, M and Popp, BN and Donahue, MJ and Gates, RD}, title = {Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient.}, journal = {The ISME journal}, volume = {14}, number = {4}, pages = {945-958}, pmid = {31900444}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; Autotrophic Processes ; Carbon ; *Coral Reefs ; Dinoflagellida ; Heterotrophic Processes ; Photosynthesis ; Seasons ; Species Specificity ; *Sunlight ; Symbiosis/*physiology ; }, abstract = {Reef corals are mixotrophic organisms relying on symbiont-derived photoautotrophy and water column heterotrophy. Coral endosymbionts (Family: Symbiodiniaceae), while typically considered mutualists, display a range of species-specific and environmentally mediated opportunism in their interactions with coral hosts, potentially requiring corals to rely more on heterotrophy to avoid declines in performance. To test the influence of symbiont communities on coral physiology (tissue biomass, symbiont density, photopigmentation) and nutrition (δ[13]C, δ[15]N), we sampled Montipora capitata colonies dominated by a specialist symbiont Cladocopium spp. or a putative opportunist Durusdinium glynnii (hereafter, C- or D-colonies) from Kāne'ohe Bay, Hawai'i, across gradients in photosynthetically active radiation (PAR) during summer and winter. We report for the first time that isotope values of reef corals are influenced by Symbiodiniaceae communities, indicative of different autotrophic capacities among symbiont species. D-colonies had on average 56% higher symbiont densities, but lower photopigments per symbiont cell and consistently lower δ[13]C values in host and symbiont tissues; this pattern in isotope values is consistent with lower symbiont carbon assimilation and translocation to the host. Neither C- nor D-colonies showed signs of greater heterotrophy or nutritional plasticity; instead changes in δ[13]C values were driven by PAR availability and photoacclimation attributes that differed between symbiont communities. Together, these results reveal Symbiodiniaceae functional diversity produces distinct holobionts with different capacities for autotrophic nutrition, and energy tradeoffs from associating with opportunist symbionts are not met with increased heterotrophy.}, }
@article {pmid31878183, year = {2019}, author = {Chialva, M and Ghignone, S and Novero, M and Hozzein, WN and Lanfranco, L and Bonfante, P}, title = {Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota.}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {31878183}, issn = {2076-2607}, support = {TO_call03_2012_0039//Compagnia di San Paolo/ ; 727929//Horizon 2020 Framework Programme/ ; RSP-2019/53//King Saud University/ ; }, abstract = {Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early "omics" experiments focused mainly on the species composition of microbial communities, new "meta-omics" approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research.}, }
@article {pmid31866971, year = {2019}, author = {Pausan, MR and Csorba, C and Singer, G and Till, H and Schöpf, V and Santigli, E and Klug, B and Högenauer, C and Blohs, M and Moissl-Eichinger, C}, title = {Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2796}, pmid = {31866971}, issn = {1664-302X}, support = {P 32697/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) to 81 RSVs in a representative sample set. The results from this extensive primer-evaluation led to the identification of the primer pair combination 344f-1041R/519F-806R which performed superior for the analysis of the archaeome of gastrointestinal tract, oral cavity and skin. The proposed protocol might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobiont samples.}, }
@article {pmid31857601, year = {2019}, author = {Tilstra, A and El-Khaled, YC and Roth, F and Rädecker, N and Pogoreutz, C and Voolstra, CR and Wild, C}, title = {Denitrification Aligns with N2 Fixation in Red Sea Corals.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19460}, pmid = {31857601}, issn = {2045-2322}, support = {Wi 2677/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, mesh = {Animals ; Anthozoa/genetics/*metabolism ; Denitrification/*physiology ; Dinoflagellida/*metabolism ; Gene Dosage ; Indian Ocean ; Nitrogen/metabolism ; Nitrogen Fixation/*physiology ; Photosynthesis ; Symbiosis ; }, abstract = {Denitrification may potentially alleviate excess nitrogen (N) availability in coral holobionts to maintain a favourable N to phosphorous ratio in the coral tissue. However, little is known about the abundance and activity of denitrifiers in the coral holobiont. The present study used the nirS marker gene as a proxy for denitrification potential along with measurements of denitrification rates in a comparative coral taxonomic framework from the Red Sea: Acropora hemprichii, Millepora dichotoma, and Pleuractis granulosa. Relative nirS gene copy numbers associated with the tissues of these common corals were assessed and compared with denitrification rates on the holobiont level. In addition, dinitrogen (N2) fixation rates, Symbiodiniaceae cell density, and oxygen evolution were assessed to provide an environmental context for denitrification. We found that relative abundances of the nirS gene were 16- and 17-fold higher in A. hemprichii compared to M. dichotoma and P. granulosa, respectively. In concordance, highest denitrification rates were measured in A. hemprichii, followed by M. dichotoma and P. granulosa. Denitrification rates were positively correlated with N2 fixation rates and Symbiodiniaceae cell densities. Our results suggest that denitrification may counterbalance the N input from N2 fixation in the coral holobiont, and we hypothesize that these processes may be limited by photosynthates released by the Symbiodiniaceae.}, }
@article {pmid31849163, year = {2020}, author = {Singh, BK and Liu, H and Trivedi, P}, title = {Eco-holobiont: A new concept to identify drivers of host-associated microorganisms.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {564-567}, doi = {10.1111/1462-2920.14900}, pmid = {31849163}, issn = {1462-2920}, support = {DP170104634//Australian Research Council/International ; DP190103714//Australian Research Council/International ; }, mesh = {Animals ; Biological Evolution ; Humans ; Microbiota/*physiology ; Plants ; Symbiosis/*physiology ; }, abstract = {Host microbiomes play a critical role in host fitness and health. Whilst the current 'holobiont' concept framework has greatly expanded eco-evolutionary and functional understanding of host-microbiome interactions, the important role of biotic interactions and microbial loop (compositional linkage between soil, plant and animal) in shaping host-microbiome are poorly understood. We proposed an 'eco-holobiont' concept to fill the knowledge gap.}, }
@article {pmid31848270, year = {2019}, author = {Hinzke, T and Kleiner, M and Breusing, C and Felbeck, H and Häsler, R and Sievert, SM and Schlüter, R and Rosenstiel, P and Reusch, TBH and Schweder, T and Markert, S}, title = {Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31848270}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animal Nutritional Physiological Phenomena ; Animals ; Aquatic Organisms ; Energy Metabolism ; Metabolic Networks and Pathways ; Metabolome ; *Microbiota ; Oxidation-Reduction ; Polychaeta/*metabolism/*microbiology/ultrastructure ; Proteome ; Proteomics/methods ; Seawater ; *Symbiosis ; }, abstract = {The deep-sea tubeworm Riftia pachyptila lacks a digestive system but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which served as a basis for comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. Our results suggest that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion and substrate transfer to the symbiont by abundant host proteins. We furthermore propose that Riftia maintains its symbiont by protecting the bacteria from oxidative damage while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.IMPORTANCE All animals are associated with microorganisms; hence, host-microbe interactions are of fundamental importance for life on earth. However, we know little about the molecular basis of these interactions. Therefore, we studied the deep-sea Riftia pachyptila symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition. Using a metaproteomics approach, we identified both metabolic interaction processes, such as substrate transfer between the two partners, and interactions that serve to maintain the symbiotic balance, e.g., host efforts to control the symbiont population or symbiont strategies to modulate these host efforts. We suggest that these interactions are essential principles of mutualistic animal-microbe associations.}, }
@article {pmid31844749, year = {2019}, author = {Hussien, E and Juhmani, AS and AlMasri, R and Al-Horani, F and Al-Saghir, M}, title = {Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba.}, journal = {Heliyon}, volume = {5}, number = {11}, pages = {e02876}, pmid = {31844749}, issn = {2405-8440}, abstract = {Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.}, }
@article {pmid31843471, year = {2020}, author = {Edwards, JM and Roy, S and Tomcho, JC and Schreckenberger, ZJ and Chakraborty, S and Bearss, NR and Saha, P and McCarthy, CG and Vijay-Kumar, M and Joe, B and Wenceslau, CF}, title = {Microbiota are critical for vascular physiology: Germ-free status weakens contractility and induces sex-specific vascular remodeling in mice.}, journal = {Vascular pharmacology}, volume = {125-126}, number = {}, pages = {106633}, pmid = {31843471}, issn = {1879-3649}, support = {R00 GM118885/GM/NIGMS NIH HHS/United States ; R01 CA219144/CA/NCI NIH HHS/United States ; R01 HL143082/HL/NHLBI NIH HHS/United States ; R01 HL149762/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Elastic Modulus ; Female ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Host Microbial Interactions ; Male ; Mesenteric Arteries/metabolism/*physiology ; Mice, Inbred C57BL ; Neutrophils/metabolism ; Reactive Oxygen Species/metabolism ; Sex Factors ; *Vascular Remodeling ; Vascular Resistance ; Vascular Stiffness ; *Vasoconstriction ; }, abstract = {Commensal microbiota within a holobiont contribute to the overall health of the host via mutualistic symbiosis. Disturbances in such symbiosis is prominently correlated with a variety of diseases affecting the modern society of humans including cardiovascular diseases, which are the number one contributors to human mortality. Given that a hallmark of all cardiovascular diseases is changes in vascular function, we hypothesized that depleting microbiota from a holobiont would induce vascular dysfunction. To test this hypothesis, young mice of both sexes raised in germ-free conditions were examined vascular contractility and structure. Here we observed that male and female germ-free mice presented a decrease in contraction of resistance arteries. These changes were more pronounced in germ-free males than in germ-free females mice. Furthermore, there was a distinct change in vascular remodeling between males and females germ-free mice. Resistance arteries from male germ-free mice demonstrated increased vascular stiffness, as shown by the leftward shift in the stress-strain curve and inward hypotrophic remodeling, a characteristic of chronic reduction in blood flow. On the other hand, resistance arteries from germ-free female mice were similar in the stress-strain curves to that of conventionally raised mice, but were distinctly different and showed outward hypertrophic remodeling, a characteristic seen in aging. Interestingly, we observed that reactive oxygen species (ROS) generation from bone marrow derived neutrophils is blunted in female germ-free mice, but it is exacerbated in male germ-free mice. In conclusion, these observations indicate that commensal microbiota of a holobiont are central to maintain proper vascular function and structure homeostasis, especially in males.}, }
@article {pmid31841144, year = {2020}, author = {Martin, BC and Alarcon, MS and Gleeson, D and Middleton, JA and Fraser, MW and Ryan, MH and Holmer, M and Kendrick, GA and Kilminster, K}, title = {Root microbiomes as indicators of seagrass health.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz201}, pmid = {31841144}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Biomass ; Environmental Biomarkers/*genetics ; Estuaries ; Hydrocharitaceae/growth &amp; development/metabolism/*microbiology/*physiology ; Microbiota/*genetics ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; South Australia ; Sulfides/metabolism ; }, abstract = {The development of early warning indicators that identify ecosystem stress is a priority for improving ecosystem management. As microbial communities respond rapidly to environmental disturbance, monitoring their composition could prove one such early indicator of environmental stress. We combined 16S rRNA gene sequencing of the seagrass root microbiome of Halophila ovalis with seagrass health metrics (biomass, productivity and Fsulphide) to develop microbial indicators for seagrass condition across the Swan-Canning Estuary and the Leschenault Estuary (south-west Western Australia); the former had experienced an unseasonal rainfall event leading to declines in seagrass health. Microbial indicators detected sites of potential stress that other seagrass health metrics failed to detect. Genera that were more abundant in 'healthy' seagrasses included putative methylotrophic bacteria (e.g. Methylotenera and Methylophaga), iron cycling bacteria (e.g. Deferrisoma and Geothermobacter) and N2 fixing bacteria (e.g. Rhizobium). Conversely, genera that were more abundant in 'stressed' seagrasses were dominated by putative sulphur-cycling bacteria, both sulphide-oxidising (e.g. Candidatus Thiodiazotropha and Candidatus Electrothrix) and sulphate-reducing (e.g. SEEP-SRB1, Desulfomonile and Desulfonema). The sensitivity of the microbial indicators developed here highlights their potential to be further developed for use in adaptive seagrass management, and emphasises their capacity to be effective early warning indicators of stress.}, }
@article {pmid31841132, year = {2020}, author = {Karimi, E and Geslain, E and KleinJan, H and Tanguy, G and Legeay, E and Corre, E and Dittami, SM}, title = {Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.}, journal = {Genome biology and evolution}, volume = {12}, number = {1}, pages = {3647-3655}, pmid = {31841132}, issn = {1759-6653}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; *Genome, Bacterial ; Phaeophyceae/*microbiology ; Phylogeny ; Secondary Metabolism/genetics ; Symbiosis ; Vitamins/biosynthesis ; }, abstract = {Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host-microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.}, }
@article {pmid31831078, year = {2019}, author = {Ricci, F and Rossetto Marcelino, V and Blackall, LL and Kühl, M and Medina, M and Verbruggen, H}, title = {Beneath the surface: community assembly and functions of the coral skeleton microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {159}, pmid = {31831078}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification ; Bacteria/classification ; Biodiversity ; *Coral Reefs ; Microbiota/*physiology ; }, abstract = {Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.}, }
@article {pmid31824548, year = {2019}, author = {Maréchal, E}, title = {Marine and Freshwater Plants: Challenges and Expectations.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1545}, pmid = {31824548}, issn = {1664-462X}, abstract = {The past decades have seen an increasing interest on the biology of photosynthetic species living in aquatic environments, including diverse organisms collectively called "algae." If we consider the relative size of scientific communities, marine and freshwater plants have been overall less studied than terrestrial ones. The efforts put on land plants were motivated by agriculture and forestry, applications for human industry, easy access to terrestrial ecosystems, and convenient cultivation methods in fields or growth chambers. By contrast, the fragmentary knowledge on the biology of algae, the hope to find in this biodiversity inspiration for biotechnologies, and the emergency created by the environmental crisis affecting oceans, lakes, rivers, or melting glaciers, have stressed the importance to make up for lost time. Needed efforts embrace a broad spectrum of disciplines, from environmental and evolutionary sciences, to molecular and cell biology. In this multiscale view, functional genomics and ecophysiology occupy a pivotal position linking molecular and cellular analyses and ecosystem-level studies. Without pretending to be exhaustive and with few selected references, six grand challenges, requiring multidisciplinary approaches, are introduced below.}, }
@article {pmid31822603, year = {2019}, author = {Luter, HM and Whalan, S and Andreakis, N and Abdul Wahab, M and Botté, ES and Negri, AP and Webster, NS}, title = {The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31822603}, issn = {2379-5077}, abstract = {Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter[-1] polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter[-1] PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter[-1] PAH) and 1.6% (38 mg liter[-1] Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter[-1] PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants.IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.}, }
@article {pmid31802185, year = {2020}, author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP}, title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {985-997}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, mesh = {Animal Distribution ; Animals ; Bacteria/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Mycobiome ; Skin/*microbiology ; Southeastern United States ; Spatial Analysis ; Tennessee ; Caudata/*microbiology ; }, abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.}, }
@article {pmid31801294, year = {2019}, author = {Alex, A and Antunes, A}, title = {Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31801294}, issn = {2076-2607}, support = {PTDC/BIA-BMA/29985/2017 (POCI-01-0145-FEDER-029985)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017).//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; UID/Multi/04423/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/International ; }, abstract = {The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.}, }
@article {pmid31795848, year = {2019}, author = {Achlatis, M and Pernice, M and Green, K and de Goeij, JM and Guagliardo, P and Kilburn, MR and Hoegh-Guldberg, O and Dove, S}, title = {Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1916}, pages = {20192153}, pmid = {31795848}, issn = {1471-2954}, mesh = {Animals ; Coral Reefs ; Dinoflagellida/physiology ; Nitrogen/metabolism ; Porifera/*physiology ; *Symbiosis ; }, abstract = {Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track [15]N- and [13]C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.}, }
@article {pmid31788212, year = {2019}, author = {McIlroy, SE and Cunning, R and Baker, AC and Coffroth, MA}, title = {Competition and succession among coral endosymbionts.}, journal = {Ecology and evolution}, volume = {9}, number = {22}, pages = {12767-12778}, pmid = {31788212}, issn = {2045-7758}, abstract = {Host species often support a genetically diverse guild of symbionts, the identity and performance of which can determine holobiont fitness under particular environmental conditions. These symbiont communities are structured by a complex set of potential interactions, both positive and negative, between the host and symbionts and among symbionts. In reef-building corals, stable associations with specific symbiont species are common, and we hypothesize that this is partly due to ecological mechanisms, such as succession and competition, which drive patterns of symbiont winnowing in the initial colonization of new generations of coral recruits. We tested this hypothesis using the experimental framework of the de Wit replacement series and found that competitive interactions occurred among symbionts which were characterized by unique ecological strategies. Aposymbiotic octocoral recruits within high- and low-light environments were inoculated with one of three Symbiodiniaceae species as monocultures or with cross-paired mixtures, and we tracked symbiont uptake using quantitative genetic assays. Priority effects, in which early colonizers excluded competitive dominants, were evidenced under low light, but these early opportunistic species were later succeeded by competitive dominants. Under high light, a more consistent competitive hierarchy was established in which competitive dominants outgrew and limited the abundance of others. These findings provide insight into mechanisms of microbial community organization and symbiosis breakdown and recovery. Furthermore, transitions in competitive outcomes across spatial and temporal environmental variation may improve lifetime host fitness.}, }
@article {pmid31780680, year = {2019}, author = {Vivero, RJ and Villegas-Plazas, M and Cadavid-Restrepo, GE and Herrera, CXM and Uribe, SI and Junca, H}, title = {Wild specimens of sand fly phlebotomine Lutzomyia evansi, vector of leishmaniasis, show high abundance of Methylobacterium and natural carriage of Wolbachia and Cardinium types in the midgut microbiome.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17746}, pmid = {31780680}, issn = {2045-2322}, mesh = {Animals ; Bacteroidetes/genetics/*isolation &amp; purification ; Female ; Gastrointestinal Microbiome ; Humans ; Insect Vectors/*microbiology ; Leishmaniasis/*transmission ; Male ; Methylobacterium/genetics/*isolation &amp; purification ; Psychodidae/*microbiology ; RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/*isolation &amp; purification ; }, abstract = {Phlebotomine sand flies are remarkable vectors of several etiologic agents (virus, bacterial, trypanosomatid Leishmania), posing a heavy health burden for human populations mainly located at developing countries. Their intestinal microbiota is involved in a wide range of biological and physiological processes, and could exclude or facilitate such transmission of pathogens. In this study, we investigated the Eubacterial microbiome from digestive tracts of Lu. evansi adults structure using 16S rRNA gene sequence amplicon high throughput sequencing (Illumina MiSeq) obtained from digestive tracts of Lu. evansi adults. The samples were collected at two locations with high incidence of the disease in humans: peri-urban and forest ecosystems from the department of Sucre, Colombia. 289,068 quality-filtered reads of V4 region of 16S rRNA gene were obtained and clustered into 1,762 operational taxonomic units (OTUs) with 97% similarity. Regarding eubacterial diversity, 14 bacterial phyla and 2 new candidate phyla were found to be consistently associated with the gut microbiome content. Proteobacteria, Firmicutes, and Bacteroidetes were the most abundant phyla in all the samples and the core microbiome was particularly dominated by Methylobacterium genus. Methylobacterium species, are known to have mutualistic relationships with some plants and are involved in shaping the microbial community in the phyllosphere. As a remarkable feature, OTUs classified as Wolbachia spp. were found abundant on peri-urban ecosystem samples, in adult male (OTUs n = 776) and unfed female (OTUs n = 324). Furthermore, our results provide evidence of OTUs classified as Cardinium endosymbiont in relative abundance, notably higher with respect to Wolbachia. The variation in insect gut microbiota may be determined by the environment as also for the type of feeding. Our findings increase the richness of the microbiota associated with Lu. evansi. In this study, OTUs of Methylobacterium found in Lu. evansi was higher in engorged females, suggesting that there are interactions between microbes from plant sources, blood nutrients and the parasites they transmit during the blood intake.}, }
@article {pmid31772223, year = {2019}, author = {Kamm, K and Osigus, HJ and Stadler, PF and DeSalle, R and Schierwater, B}, title = {Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17561}, pmid = {31772223}, issn = {2045-2322}, mesh = {Amino Acids/biosynthesis ; Animals ; Evolution, Molecular ; Genome/genetics ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Placozoa/*genetics/microbiology/physiology ; Rickettsia/*genetics/physiology ; Symbiosis/*genetics ; }, abstract = {Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain "Panama"). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.}, }
@article {pmid31767877, year = {2019}, author = {Heo, K and Park, YH and Lee, KA and Kim, J and Ham, HI and Kim, BG and Lee, WJ and Seok, YJ}, title = {Sugar-mediated regulation of a c-di-GMP phosphodiesterase in Vibrio cholerae.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {5358}, pmid = {31767877}, issn = {2041-1723}, mesh = {3',5'-Cyclic-GMP Phosphodiesterases/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biofilms/growth &amp; development ; Cyclic GMP/*analogs &amp; derivatives/metabolism ; Gene Expression Regulation, Bacterial ; Glucose/metabolism ; Phosphoenolpyruvate Sugar Phosphotransferase System/genetics/metabolism ; Sugars/*metabolism ; Vibrio cholerae/*enzymology/genetics/physiology ; }, abstract = {Biofilm formation protects bacteria from stresses including antibiotics and host immune responses. Carbon sources can modulate biofilm formation and host colonization in Vibrio cholerae, but the underlying mechanisms remain unclear. Here, we show that EIIA[Glc], a component of the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS), regulates the intracellular concentration of the cyclic dinucleotide c-di-GMP, and thus biofilm formation. The availability of preferred sugars such as glucose affects EIIA[Glc] phosphorylation state, which in turn modulates the interaction of EIIA[Glc] with a c-di-GMP phosphodiesterase (hereafter referred to as PdeS). In a Drosophila model of V. cholerae infection, sugars in the host diet regulate gut colonization in a manner dependent on the PdeS-EIIA[Glc] interaction. Our results shed light into the mechanisms by which some nutrients regulate biofilm formation and host colonization.}, }
@article {pmid31762410, year = {2020}, author = {Zhang, Y and Kumarasamy, S and Mell, B and Cheng, X and Morgan, EE and Britton, SL and Vijay-Kumar, M and Koch, LG and Joe, B}, title = {Vertical selection for nuclear and mitochondrial genomes shapes gut microbiota and modifies risks for complex diseases.}, journal = {Physiological genomics}, volume = {52}, number = {1}, pages = {1-14}, pmid = {31762410}, issn = {1531-2267}, support = {P40 OD021331/OD/NIH HHS/United States ; }, mesh = {Adiposity/genetics ; Animals ; Behavior, Animal ; Blood Pressure/genetics ; Body Weight/genetics ; Cardiovascular Diseases/genetics ; Cell Nucleus/*genetics ; Cognition ; DNA, Mitochondrial/genetics ; Gastrointestinal Microbiome/*genetics ; *Genetic Predisposition to Disease ; *Genome, Mitochondrial ; Physical Conditioning, Animal ; Rats ; Risk Factors ; Selection, Genetic ; Ventricular Remodeling/genetics ; }, abstract = {Here we postulate that the heritability of complex disease traits previously ascribed solely to the inheritance of the nuclear and mitochondrial genomes is broadened to encompass a third component of the holobiome, the microbiome. To test this, we expanded on the selectively bred low capacity runner/high capacity runner (LCR/HCR) rat exercise model system into four distinct rat holobiont model frameworks including matched and mismatched host nuclear and mitochondrial genomes. Vertical selection of varying nuclear and mitochondrial genomes resulted in differential acquisition of the microbiome within each of these holobiont models. Polygenic disease risk of these novel models were assessed and subsequently correlated with patterns of acquisition and contributions of their microbiomes in controlled laboratory settings. Nuclear-mitochondrial-microbiotal interactions were not for exercise as a reporter of health, but significantly noted for increased adiposity, increased blood pressure, compromised cardiac function, and loss of long-term memory as reporters of disease susceptibility. These findings provide evidence for coselection of the microbiome with nuclear and mitochondrial genomes as an important feature impacting the heritability of complex diseases.}, }
@article {pmid31759226, year = {2019}, author = {Cooke, I and Mead, O and Whalen, C and Boote, C and Moya, A and Ying, H and Robbins, S and Strugnell, JM and Darling, A and Miller, D and Voolstra, CR and Adamska, M and , }, title = {Molecular techniques and their limitations shape our view of the holobiont.}, journal = {Zoology (Jena, Germany)}, volume = {137}, number = {}, pages = {125695}, doi = {10.1016/j.zool.2019.125695}, pmid = {31759226}, issn = {1873-2720}, mesh = {*Environmental Microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.}, }
@article {pmid31753537, year = {2020}, author = {Monteil, CL and Lefevre, CT}, title = {Magnetoreception in Microorganisms.}, journal = {Trends in microbiology}, volume = {28}, number = {4}, pages = {266-275}, doi = {10.1016/j.tim.2019.10.012}, pmid = {31753537}, issn = {1878-4380}, mesh = {Biomineralization/physiology ; Eukaryota/chemistry/*metabolism/ultrastructure ; *Magnetic Phenomena ; *Magnetics ; Magnetosomes/chemistry/*metabolism/ultrastructure ; Prokaryotic Cells/classification/*metabolism/ultrastructure ; Symbiosis ; }, abstract = {Magnetoreception is the sense whereby organisms geolocate and navigate in response to the Earth's magnetic field lines. For decades, magnetotactic bacteria have been the only known magnetoreceptive microorganisms. The magnetotactic behaviour of these aquatic prokaryotes is due to the biomineralization of magnetic crystals. While an old report alleged the existence of microbial algae with similar behaviour, recent discoveries have demonstrated the existence of unicellular eukaryotes able to sense the geomagnetic field, and have revealed different mechanisms and strategies involved in such a sensing. Some ciliates can be magnetically guided after predation of magnetotactic bacteria, while some flagellates acquired this sense through symbiosis with magnetic bacteria. A report has even suggested that some magnetotactic protists could biomineralize magnetic crystals.}, }
@article {pmid31752998, year = {2019}, author = {Sweet, M and Burian, A and Fifer, J and Bulling, M and Elliott, D and Raymundo, L}, title = {Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {139}, pmid = {31752998}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/*pathogenicity ; *Coral Reefs ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Micronesia ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.<br><br>RESULTS: Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.<br><br>CONCLUSIONS: Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase &#x3b2;-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.}, }
@article {pmid31739792, year = {2019}, author = {Li, Y and Tassia, MG and Waits, DS and Bogantes, VE and David, KT and Halanych, KM}, title = {Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {91}, pmid = {31739792}, issn = {1741-7007}, mesh = {Animals ; *Chemoautotrophic Growth ; Genome/*physiology ; Hydrothermal Vents ; Polychaeta/*genetics/*microbiology ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored.<br><br>RESULTS: Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary&#xa0;invertebrates. We sequenced the worm's ~&#x2009;688-Mb haploid genome with an overall completeness of ~&#x2009;95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267&#xa0;mya (&#xb1;&#x2009;70&#xa0;my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126&#xa0;mya for vestimentiferans.<br><br>CONCLUSIONS: Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.}, }
@article {pmid31731227, year = {2019}, author = {Mitter, B and Brader, G and Pfaffenbichler, N and Sessitsch, A}, title = {Next generation microbiome applications for crop production - limitations and the need of knowledge-based solutions.}, journal = {Current opinion in microbiology}, volume = {49}, number = {}, pages = {59-65}, doi = {10.1016/j.mib.2019.10.006}, pmid = {31731227}, issn = {1879-0364}, mesh = {Agricultural Inoculants ; Crop Production/*methods/*trends ; Crops, Agricultural/growth &amp; development/*microbiology ; Knowledge Bases ; *Microbiota ; }, abstract = {Plants are associated with highly diverse microbiota, which are crucial partners for their host carrying out important functions. Essentially, they are involved in nutrient supply, pathogen antagonism and protection of their host against different types of stress. The potential of microbial inoculants has been demonstrated in numerous studies, primarily under greenhouse conditions. However, field application, for example, as biofertilizer or biocontrol agent, is still a challenge as the applied microorganisms often are not provided in sufficiently high cell numbers, are rapidly outcompeted and cannot establish or require specific conditions to mediate the desired effects. We still have limited understanding on the fate of inoculants and on holobiont interactions, that is, interactions between plants, micro-biota and macro-biota and the environment, under field conditions. A better understanding will provide the basis for establishing models predicting the behaviour of strains or consortia and will help identifying microbiome members being able to establish and to mediate desired effects under certain conditions. Such models may also inform about the best management practices modulating microbiota in a desired way. Also, smart delivery approaches of microbial inoculants as well as the selection or breeding of plant genotypes better able to interact with microbiota may represent promising avenues.}, }
@article {pmid31722669, year = {2019}, author = {Sauvage, T and Schmidt, WE and Yoon, HS and Paul, VJ and Fredericq, S}, title = {Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {850}, pmid = {31722669}, issn = {1471-2164}, support = {GIAR 2013&amp;2014//Phycological Society of America/ ; }, mesh = {Caulerpa/*genetics ; Genome, Bacterial ; *Genome, Chloroplast ; Genome, Mitochondrial ; Genomics/methods ; Nanopore Sequencing/*methods ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The MinION Access Program (MAP, 2014-2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches.<br><br>RESULTS: The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii's nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope's estimate (>&#x2009;26.3 Mbp, including 4.8 Mbp in repeat).<br><br>CONCLUSION: Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic 'chlorotypes' in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii's nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.}, }
@article {pmid31709760, year = {2019}, author = {Collens, A and Kelley, E and Katz, LA}, title = {The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {332}, number = {8}, pages = {349-355}, pmid = {31709760}, issn = {1552-5015}, support = {R15 GM113177/GM/NIGMS NIH HHS/United States ; R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological ; *Biological Evolution ; *Epigenesis, Genetic ; Genome ; Microbiota ; Symbiosis/*genetics ; }, abstract = {John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.}, }
@article {pmid31708944, year = {2019}, author = {Lucaciu, R and Pelikan, C and Gerner, SM and Zioutis, C and Köstlbacher, S and Marx, H and Herbold, CW and Schmidt, H and Rattei, T}, title = {A Bioinformatics Guide to Plant Microbiome Analysis.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1313}, pmid = {31708944}, issn = {1664-462X}, abstract = {Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.}, }
@article {pmid31701649, year = {2020}, author = {Staples, R and LaDuca, RL and Roze, LV and Laivenieks, M and Linz, JE and Beaudry, R and Fryday, A and Schilmiller, AL and Koptina, AV and Smith, B and Trail, F}, title = {Structure and Chemical Analysis of Major Specialized Metabolites Produced by the Lichen Evernia prunastri.}, journal = {Chemistry &amp; biodiversity}, volume = {17}, number = {1}, pages = {e1900465}, doi = {10.1002/cbdv.201900465}, pmid = {31701649}, issn = {1612-1880}, support = {//MSU Office of the Vice President of Research and Graduate Studies/ ; //AgBioResearch and the College of Natural Sciences/ ; }, mesh = {Benzofurans/*analysis/metabolism ; Hydroxybenzoates/*analysis/metabolism ; Lichens/*chemistry/metabolism ; Models, Molecular ; Salicylates/*analysis/metabolism ; }, abstract = {We performed comparative profiling of four specialized metabolites in the lichen Evernia prunastri, collected at three different geographic locations, California and Maine, USA, and Yoshkar Ola, Mari El, Russia. Among the compounds produced at high concentrations that were identified in all three specimens, evernic acid, usnic acid, lecanoric acid and chloroatranorin, evernic acid was the most abundant. Two depsidones, salazinic acid and physodic acid, were detected in the Yoshkar-Ola collection only. The crystalline structure of evernic acid (2-hydroxy-4-[(2-hydroxy-4-methoxy-6-methylbenzoyl)oxy]-6-methylbenzoate) (hmb) revealed two crystallographically and conformationally distinct hmb anions, along with two monovalent sodium atoms. One hmb moiety contained an exotetradentate binding mode to sodium, whereas the other exhibited an exohexadentate binding mode to sodium. Embedded edge-sharing {Na2 O8 }n sodium-oxygen chains connected the hmb anions into the full three-dimensional crystal structure of the title compound. The crystal used for single-crystal X-ray diffraction exhibited non-merohedral twinning. The data suggest the importance of the acetyl-polymalonyl pathway products to processes of maintaining integrity of the lichen holobiont community.}, }
@article {pmid31701578, year = {2020}, author = {Weishaar, R and Wellmann, R and Camarinha-Silva, A and Rodehutscord, M and Bennewitz, J}, title = {Selecting the hologenome to breed for an improved feed efficiency in pigs-A novel selection index.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {137}, number = {1}, pages = {14-22}, doi = {10.1111/jbg.12447}, pmid = {31701578}, issn = {1439-0388}, mesh = {Animals ; Breeding/*methods ; Female ; *Genomics ; Male ; Microbiota ; Models, Genetic ; Swine/*genetics/microbiology ; }, abstract = {Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect m i of the microbiota composition on the breeding value g i of an animal i is the conditional expectation of its breeding value, given the vector φ i with microbiota frequencies, that is m i = E g i | φ i . The breeding value g i of an animal can therefore be decomposed into a heritable contribution m i that arises from an altered microbiota composition and a heritable contribution p i that arises from altered metabolic pathways within the animal, so g i = m i + p i . Instead of selecting for breeding value g ^ i , an index comprising the two components m ^ i and p ^ i with appropriate weights, that is I i = λ 1 m ^ i + λ 2 p ^ i , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.}, }
@article {pmid31699041, year = {2019}, author = {Yuen, B and Polzin, J and Petersen, JM}, title = {Organ transcriptomes of the lucinid clam Loripes orbiculatus (Poli, 1791) provide insights into their specialised roles in the biology of a chemosymbiotic bivalve.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {820}, pmid = {31699041}, issn = {1471-2164}, support = {VRG14-021//Vienna Science and Technology Fund/ ; }, mesh = {Animals ; Apoptosis/genetics ; Bacterial Physiological Phenomena ; Bivalvia/cytology/*genetics/immunology/microbiology ; Environment ; Foot/physiology ; *Gene Expression Profiling ; Immunity, Innate/genetics ; Nutrients/metabolism ; *Symbiosis ; }, abstract = {BACKGROUND: The lucinid clam Loripes orbiculatus lives in a nutritional symbiosis with sulphur-oxidizing bacteria housed in its gills. Although our understanding of the lucinid endosymbiont physiology and metabolism has made significant progress, relatively little is known about how the host regulates the symbiosis at the genetic and molecular levels. We generated transcriptomes from four L. orbiculatus organs (gills, foot, visceral mass, and mantle) for differential expression analyses, to better understand this clam's physiological adaptations to a chemosymbiotic lifestyle, and how it regulates nutritional and immune interactions with its symbionts.<br><br>RESULTS: The transcriptome profile of the symbiont-housing gill suggests the regulation of apoptosis and innate immunity are important processes in this organ. We also identified many transcripts encoding ion transporters from the solute carrier family that possibly allow metabolite exchange between host and symbiont. Despite the clam holobiont's clear reliance on chemosynthesis, the clam's visceral mass, which contains the digestive tract, is characterised by enzymes involved in digestion, carbohydrate recognition and metabolism, suggesting that L. orbiculatus has a mixotrophic diet. The foot transcriptome is dominated by the biosynthesis of glycoproteins for the construction of mucus tubes, and receptors that mediate the detection of chemical cues in the environment.<br><br>CONCLUSIONS: The transcriptome profiles of gills, mantle, foot and visceral mass provide insights into the molecular basis underlying the functional specialisation of bivalve organs adapted to a chemosymbiotic lifestyle.}, }
@article {pmid31692275, year = {2020}, author = {Thomas, F and Dittami, SM and Brunet, M and Le Duff, N and Tanguy, G and Leblanc, C and Gobet, A}, title = {Evaluation of a new primer combination to minimize plastid contamination in 16S rDNA metabarcoding analyses of alga-associated bacterial communities.}, journal = {Environmental microbiology reports}, volume = {12}, number = {1}, pages = {30-37}, doi = {10.1111/1758-2229.12806}, pmid = {31692275}, issn = {1758-2229}, support = {ANR-10-BTBR-04//Agence Nationale de la Recherche/International ; //Institut Fran&#xe7;ais de Recherche pour l'Exploitation de la Mer/International ; //Centre National de la Recherche Scientifique/International ; }, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA Primers/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/*genetics ; Genome, Bacterial ; *Microbiota ; Phylogeny ; Plastids/*genetics ; RNA, Ribosomal, 16S/genetics ; Seaweed/*microbiology ; }, abstract = {Plant- and alga-associated bacterial communities are generally described via 16S rDNA metabarcoding using universal primers. As plastid genomes encode 16S rDNA related to cyanobacteria, these data sets frequently contain >90% plastidial sequences, and the bacterial diversity may be under-sampled. To overcome this limitation we evaluated in silico the taxonomic coverage for four primer combinations targeting the 16S rDNA V3-V4 region. They included a forward primer universal to Bacteria (S-D-Bact-0341-b-S-17) and four reverse primers designed to avoid plastid DNA amplification. The best primer combination (NOCHL) was compared to the universal primer set in the wet lab using a synthetic community and samples from three macroalgal species. The proportion of plastid sequences was reduced by 99%-100% with the NOCHL primers compared to the universal primers, irrespective of algal hosts, sample collection and extraction protocols. Additionally, the NOCHL primers yielded a higher richness while maintaining the community structure. As Planctomycetes, Verrucomicrobia and Cyanobacteria were underrepresented (70%-90%) compared to universal primers, combining the NOCHL set with taxon-specific primers may be useful for a complete description of the alga-associated bacterial diversity. The NOCHL primers represent an innovation to study algal holobionts without amplifying host plastid sequences and may further be applied to other photosynthetic hosts.}, }
@article {pmid31692206, year = {2020}, author = {Alves Monteiro, HJ and Brahmi, C and Mayfield, AB and Vidal-Dupiol, J and Lapeyre, B and Le Luyer, J}, title = {Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses.}, journal = {Global change biology}, volume = {26}, number = {3}, pages = {1271-1284}, doi = {10.1111/gcb.14907}, pmid = {31692206}, issn = {1365-2486}, support = {//Labex CORAIL/International ; //IFREMER/International ; }, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Polynesia ; Symbiosis ; Temperature ; }, abstract = {Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermotolerant from thermosensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.}, }
@article {pmid31655460, year = {2019}, author = {Newbold, LK and Robinson, A and Rasnaca, I and Lahive, E and Soon, GH and Lapied, E and Oughton, D and Gashchak, S and Beresford, NA and Spurgeon, DJ}, title = {Genetic, epigenetic and microbiome characterisation of an earthworm species (Octolasion lacteum) along a radiation exposure gradient at Chernobyl.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {255}, number = {Pt 1}, pages = {113238}, doi = {10.1016/j.envpol.2019.113238}, pmid = {31655460}, issn = {1873-6424}, mesh = {Amplified Fragment Length Polymorphism Analysis ; Animals ; Bacteria/drug effects ; *Chernobyl Nuclear Accident ; Epigenesis, Genetic ; Gastrointestinal Microbiome ; Microbiota/*radiation effects ; Oligochaeta/drug effects/microbiology/*physiology/radiation effects ; Radiation Exposure ; Radiation Monitoring ; Radioisotopes ; Soil/chemistry ; }, abstract = {The effects of exposure to different levels of ionising radiation were assessed on the genetic, epigenetic and microbiome characteristics of the "hologenome" of earthworms collected at sites within the Chernobyl exclusion zone (CEZ). The earthworms Aporrectodea caliginosa (Savigny, 1826) and Octolasion lacteum (Örley, 1881) were the two species that were most frequently found at visited sites, however, only O. lacteum was present at sufficient number across different exposure levels to enable comparative hologenome analysis. The identification of morphotype O. lacteum as a probable single clade was established using a combination of mitochondrial (cytochrome oxidase I) and nuclear genome (Amplified Fragment Length Polymorphism (AFLP) using MspI loci). No clear site associated differences in population genetic structure was found between populations using the AFLP marker loci. Further, no relationship between ionising radiation exposure levels and the percentage of methylated loci or pattern of distribution of DNA methylation marks was found. Microbiome structure was clearly site dependent, with gut microbiome community structure and diversity being systematically associated with calculated site-specific earthworm dose rates. There was, however, also co-correlation between earthworm dose rates and other soil properties, notably soil pH; a property known to affect soil bacterial community structure. Such co-correlation means that it is not possible to attribute microbiome changes unequivocally to radionuclide exposure. A better understanding of the relationship between radionuclide exposure soil properties and their interactions on bacterial microbiome community response is, therefore, needed to establish whether these the observed microbiome changes are attributed directly to radiation exposure, other soil properties or to an interaction between multiple variables at sites within the CEZ.}, }
@article {pmid31650344, year = {2019}, author = {Le Pennec, G and Gall, EA}, title = {The microbiome of Codium tomentosum: original state and in the presence of copper.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {35}, number = {11}, pages = {167}, pmid = {31650344}, issn = {1573-0972}, mesh = {Bacteria/*classification/*drug effects/isolation &amp; purification/metabolism ; Biodiversity ; Chlorophyta/*microbiology ; Copper/*toxicity ; Microbiota/*drug effects/physiology ; Seawater/chemistry/microbiology ; Seaweed/microbiology ; Trace Elements ; Water Pollutants ; }, abstract = {Codium tomentosum, as all organisms, hosts transiently and permanently numerous microorganisms. These holobionts can undergo environmental pressures influencing both partners creating modifications/imbalances within the associations, which may directly influence their physiological status by selecting tolerant bacteria. Furthermore, the capability of remediation of the associated bacterioflora, in particular of metallic trace elements, may provide the host with survival potential in polluted environments. In this context, we incubated C. tomentosum thalli in the presence of copper and studied its influence on the reference bacteriome. Whatever the concentration of copper, no shift was evidenced on the bacteriome at the phylum level. However, a high copper concentration enriched the bacteriome of C. tomentosum in both the genera Clostridium and Pseudolteromonas.}, }
@article {pmid31640519, year = {2019}, author = {Stothart, MR and Palme, R and Newman, AEM}, title = {It's what's on the inside that counts: stress physiology and the bacterial microbiome of a wild urban mammal.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1913}, pages = {20192111}, pmid = {31640519}, issn = {1471-2954}, mesh = {Animals ; Feces/microbiology ; Mammals ; Microbiota ; Pituitary-Adrenal System ; Sciuridae/*microbiology/physiology ; Stress, Physiological/*physiology ; Urbanization ; }, abstract = {The microbiome's capacity to shape the host phenotype and its mutability underlie theorization that the microbiome might facilitate host acclimation to rapid environmental change. However, when environmental change occurs, it is unclear whether resultant microbiome restructuring is proximately driven by this changing external environment or by the host's physiological response to this change. We leveraged urbanization to compare the ability of host environment (urban or forest) versus multi-scale biological measures of host hypothalamic-pituitary-adrenal (HPA) axis physiology (neutrophil : lymphocyte ratio, faecal glucocorticoid metabolites, hair cortisol) to explain variation in the eastern grey squirrel (Sciurus carolinensis) faecal microbiome. Urban and forest squirrels differed across all three of the interpretations of HPA axis activity we measured. Direct consideration of these physiological measures better explained greater phylogenetic turnover between squirrels than environment. This pattern was strongly driven by trade-offs between bacteria which specialize on metabolizing digesta versus host-derived nutrient sources. Drawing on ecological theory to explain patterns in intestinal bacterial communities, we conclude that although environmental change can affect the microbiome, it might primarily do so indirectly by altering host physiology. We demonstrate that the inclusion and careful consideration of dynamic, rather than fixed (e.g. sex), dimensions of host physiology are essential for the study of host-microbe symbioses at the micro-evolutionary scale.}, }
@article {pmid31636428, year = {2019}, author = {Trevathan-Tackett, SM and Sherman, CDH and Huggett, MJ and Campbell, AH and Laverock, B and Hurtado-McCormick, V and Seymour, JR and Firl, A and Messer, LF and Ainsworth, TD and Negandhi, KL and Daffonchio, D and Egan, S and Engelen, AH and Fusi, M and Thomas, T and Vann, L and Hernandez-Agreda, A and Gan, HM and Marzinelli, EM and Steinberg, PD and Hardtke, L and Macreadie, PI}, title = {A horizon scan of priorities for coastal marine microbiome research.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {11}, pages = {1509-1520}, doi = {10.1038/s41559-019-0999-7}, pmid = {31636428}, issn = {2397-334X}, mesh = {Climate ; Fisheries ; Humans ; *Microbiota ; }, abstract = {Research into the microbiomes of natural environments is changing the way ecologists and evolutionary biologists view the importance of microorganisms in ecosystem function. This is particularly relevant in ocean environments, where microorganisms constitute the majority of biomass and control most of the major biogeochemical cycles, including those that regulate Earth's climate. Coastal marine environments provide goods and services that are imperative to human survival and well-being (for example, fisheries and water purification), and emerging evidence indicates that these ecosystem services often depend on complex relationships between communities of microorganisms (the 'microbiome') and the environment or their hosts - termed the 'holobiont'. Understanding of coastal ecosystem function must therefore be framed under the holobiont concept, whereby macroorganisms and their associated microbiomes are considered as a synergistic ecological unit. Here, we evaluate the current state of knowledge on coastal marine microbiome research and identify key questions within this growing research area. Although the list of questions is broad and ambitious, progress in the field is increasing exponentially, and the emergence of large, international collaborative networks and well-executed manipulative experiments are rapidly advancing the field of coastal marine microbiome research.}, }
@article {pmid31634977, year = {2020}, author = {Liu, C and Cheng, SH and Lin, S}, title = {Illuminating the dark depths inside coral.}, journal = {Cellular microbiology}, volume = {22}, number = {1}, pages = {e13122}, doi = {10.1111/cmi.13122}, pmid = {31634977}, issn = {1462-5822}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; Dinoflagellida/physiology ; Microscopy, Fluorescence/methods ; *Symbiosis ; }, abstract = {The ability to observe in situ 3D distribution and dynamics of endosymbionts in corals is crucial for gaining a mechanistic understanding of coral bleaching and reef degradation. Here, we report the development of a tissue clearing (TC) coupled with light sheet fluorescence microscopy (LSFM) method for 3D imaging of the coral holobiont at single-cell resolution. The initial applications have demonstrated the ability of this technique to provide high spatial resolution quantitative information of endosymbiont abundance and distribution within corals. With specific fluorescent probes or assays, TC-LSFM also revealed spatial distribution and dynamics of physiological conditions (such as cell proliferation, apoptosis, and hypoxia response) in both corals and their endosymbionts. This tool is highly promising for in situ and in-depth data acquisition to illuminate coral symbiosis and health conditions in the changing marine environment, providing fundamental information for coral reef conservation and restoration.}, }
@article {pmid31618499, year = {2020}, author = {Suggett, DJ and Smith, DJ}, title = {Coral bleaching patterns are the outcome of complex biological and environmental networking.}, journal = {Global change biology}, volume = {26}, number = {1}, pages = {68-79}, doi = {10.1111/gcb.14871}, pmid = {31618499}, issn = {1365-2486}, support = {DP160100271//Australian Research Council/International ; DP180100074//Australian Research Council/International ; }, mesh = {Animals ; *Anthozoa ; Climate Change ; Coral Reefs ; Ecology ; }, abstract = {Continued declines in coral reef health over the past three decades have been punctuated by severe mass coral bleaching-induced mortality events that have grown in intensity and frequency under climate change. Intensive global research efforts have therefore persistently focused on bleaching phenomena to understand where corals bleach, when and why-resulting in a large-yet still somewhat patchy-knowledge base. Particularly catastrophic bleaching-induced coral mortality events in the past 5 years have catalyzed calls for a more diverse set of reef management tools, extending far beyond climate mitigation and reef protection, to also include more aggressive interventions. However, the effectiveness of these various tools now rests on rapidly assimilating our knowledge base of coral bleaching into more integrated frameworks. Here, we consider how the past three decades of intensive coral bleaching research has established the basis for complex biological and environmental networks, which together regulate outcomes of bleaching severity. We discuss how we now have enough scaffold for conceptual biological and environmental frameworks underpinning bleaching susceptibility, but that new tools are urgently required to translate this to an operational system informing-and testing-bleaching outcomes. Specifically, adopting network models that can fully describe and predict metabolic functioning of coral holobionts, and how this functioning is regulated by complex doses and interactions among environmental factors. Identifying knowledge gaps limiting operation of such models is the logical step to immediately guide and prioritize future experiments and observations. We are at a time-critical point where we can implement new capacity to resolve how coral bleaching patterns emerge from complex biological-environmental networks, and so more effectively inform rapidly evolving ecological management and social adaptation frameworks aimed at securing the future of coral reefs.}, }
@article {pmid31614303, year = {2020}, author = {Fiori, J and Turroni, S and Candela, M and Gotti, R}, title = {Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {177}, number = {}, pages = {112867}, doi = {10.1016/j.jpba.2019.112867}, pmid = {31614303}, issn = {1873-264X}, mesh = {Bile Acids and Salts/analysis/metabolism ; Chromatography/methods ; Fatty Acids, Volatile/analysis/metabolism ; Feces/*chemistry ; Gastrointestinal Microbiome/*immunology ; Host Microbial Interactions/*immunology ; Humans ; Mass Spectrometry/methods ; Metabolomics/*methods ; Neurotransmitter Agents/analysis/metabolism ; Polyamines/analysis/metabolism ; Specimen Handling/*methods ; Vitamins/analysis/metabolism ; }, abstract = {Gut microbiota, the specific microbial community of the gastrointestinal tract, by means of the production of microbial metabolites provides the host with several functions affecting metabolic and immunological homeostasis. Insights into the intricate relationships between gut microbiota and the host require not only the understanding of its structure and function but also the measurement of effector molecules acting along the gut microbiota axis. This article reviews the literature on targeted chromatographic approaches in analysis of gut microbiota specific metabolites in feces as the most accessible biological matrix which can directly probe the connection between intestinal bacteria and the (patho)physiology of the holobiont. Together with a discussion on sample collection and preparation, the chromatographic methods targeted to determination of some classes of microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, low molecular masses amines and polyamines, vitamins, neurotransmitters and related compounds) are discussed and their main characteristics, summarized in Tables.}, }
@article {pmid31601819, year = {2019}, author = {Wada, N and Ishimochi, M and Matsui, T and Pollock, FJ and Tang, SL and Ainsworth, TD and Willis, BL and Mano, N and Bourne, DG}, title = {Characterization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {14662}, pmid = {31601819}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Australia ; Bacteria/genetics/*isolation &amp; purification ; Coral Reefs ; DNA, Bacterial/isolation &amp; purification ; In Situ Hybridization, Fluorescence ; Japan ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Bacterial diversity associated with corals has been studied extensively, however, localization of bacterial associations within the holobiont is still poorly resolved. Here we provide novel insight into the localization of coral-associated microbial aggregates (CAMAs) within tissues of the coral Acropora hyacinthus. In total, 318 and 308 CAMAs were characterized via histological and fluorescent in situ hybridization (FISH) approaches respectively, and shown to be distributed extensively throughout coral tissues collected from five sites in Japan and Australia. The densities of CAMAs within the tissues were negatively correlated with the distance from the coastline (i.e. lowest densities at offshore sites). CAMAs were randomly distributed across the six coral tissue regions investigated. Within each CAMA, bacterial cells had similar morphological characteristics, but bacterial morphologies varied among CAMAs, with at least five distinct types identified. Identifying the location of microorganisms associated with the coral host is a prerequisite for understanding their contributions to fitness. Localization of tissue-specific communities housed within CAMAs is particularly important, as these communities are potentially important contributors to vital metabolic functions of the holobiont.}, }
@article {pmid31600498, year = {2019}, author = {Leigh, BA}, title = {Cooperation among Conflict: Prophages Protect Bacteria from Phagocytosis.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {4}, pages = {450-452}, doi = {10.1016/j.chom.2019.09.003}, pmid = {31600498}, issn = {1934-6069}, support = {F32 AI140694/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria ; *Bacteriophages ; *Eukaryota ; Immune Evasion ; Phagocytosis ; Prophages ; }, abstract = {Bacteriophages, viruses that infect bacteria, are the most abundant biological entities within the holobiont. In this issue of Cell Host &amp; Microbe, Jahn et al. (2019) describe a group of phages that can suppress immune cell function in marine sponges using secreted ankyrin proteins. They call these phages Ankyphages.}, }
@article {pmid31596993, year = {2019}, author = {Walker, NS and Fernández, R and Sneed, JM and Paul, VJ and Giribet, G and Combosch, DJ}, title = {Differential gene expression during substrate probing in larvae of the Caribbean coral Porites astreoides.}, journal = {Molecular ecology}, volume = {28}, number = {22}, pages = {4899-4913}, pmid = {31596993}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*genetics ; Caribbean Region ; Coral Reefs ; Dinoflagellida/genetics ; Gene Expression/*genetics ; Larva/*genetics ; Symbiosis/genetics ; Transcriptome/genetics ; }, abstract = {The transition from larva to adult is a critical step in the life history strategy of most marine animals. However, the genetic basis of this life history change remains poorly understood in many taxa, including most coral species. Recent evidence suggests that coral planula larvae undergo significant changes at the physiological and molecular levels throughout the development. To investigate this, we characterized differential gene expression (DGE) during the transition from planula to adult polyp in the abundant Caribbean reef-building coral Porites astreoides, that is from nonprobing to actively substrate-probing larva, a stage required for colony initiation. This period is crucial for the coral, because it demonstrates preparedness to locate appropriate substrata for settlement based on vital environmental cues. Through RNA-Seq, we identified 860 differentially expressed holobiont genes between probing and nonprobing larvae (p ≤ .01), the majority of which were upregulated in probing larvae. Surprisingly, differentially expressed genes of endosymbiotic dinoflagellate origin greatly outnumbered coral genes, compared with a nearly 1:1 ratio of coral-to-dinoflagellate gene representation in the holobiont transcriptome. This unanticipated result suggests that dinoflagellate endosymbionts may play a significant role in the transition from nonprobing to probing behaviour in dinoflagellate-rich larvae. Putative holobiont genes were largely involved in protein and nucleotide binding, metabolism and transport. Genes were also linked to environmental sensing and response and integral signalling pathways. Our results thus provide detailed insight into molecular changes prior to larval settlement and highlight the complex physiological and biochemical changes that occur in early transition stages from pelagic to benthic stages in corals, and perhaps more importantly, in their endosymbionts.}, }
@article {pmid31595051, year = {2020}, author = {Yang, Y and Sun, J and Sun, Y and Kwan, YH and Wong, WC and Zhang, Y and Xu, T and Feng, D and Zhang, Y and Qiu, JW and Qian, PY}, title = {Genomic, transcriptomic, and proteomic insights into the symbiosis of deep-sea tubeworm holobionts.}, journal = {The ISME journal}, volume = {14}, number = {1}, pages = {135-150}, pmid = {31595051}, issn = {1751-7370}, mesh = {Animals ; Bacteria/*genetics/*metabolism/pathogenicity ; Carbon Cycle ; Gene Expression Profiling ; Genomics ; Hydrothermal Vents/microbiology ; Immunity, Innate/genetics ; Polychaeta/genetics/immunology/metabolism/*microbiology ; Proteomics ; *Symbiosis/genetics ; }, abstract = {Deep-sea hydrothermal vents and methane seeps are often densely populated by animals that host chemosynthetic symbiotic bacteria, but the molecular mechanisms of such host-symbiont relationship remain largely unclear. We characterized the symbiont genome of the seep-living siboglinid Paraescarpia echinospica and compared seven siboglinid-symbiont genomes. Our comparative analyses indicate that seep-living siboglinid endosymbionts have more virulence traits for establishing infections and modulating host-bacterium interaction than the vent-dwelling species, and have a high potential to resist environmental hazards. Metatranscriptome and metaproteome analyses of the Paraescarpia holobiont reveal that the symbiont is highly versatile in its energy use and efficient in carbon fixation. There is close cooperation within the holobiont in production and supply of nutrients, and the symbiont may be able to obtain nutrients from host cells using virulence factors. Moreover, the symbiont is speculated to have evolved strategies to mediate host protective immunity, resulting in weak expression of host innate immunity genes in the trophosome. Overall, our results reveal the interdependence of the tubeworm holobiont through mutual nutrient supply, a pathogen-type regulatory mechanism, and host-symbiont cooperation in energy utilization and nutrient production, which is a key adaptation allowing the tubeworm to thrive in deep-sea chemosynthetic environments.}, }
@article {pmid31568517, year = {2019}, author = {Freire, I and Gutner-Hoch, E and Muras, A and Benayahu, Y and Otero, A}, title = {The effect of bacteria on planula-larvae settlement and metamorphosis in the octocoral Rhytisma fulvum fulvum.}, journal = {PloS one}, volume = {14}, number = {9}, pages = {e0223214}, pmid = {31568517}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/microbiology/*physiology ; Bacteria/growth &amp; development ; Coral Reefs ; Dinoflagellida/*physiology ; Indian Ocean ; Israel ; Larva/*growth &amp; development/microbiology ; Metamorphosis, Biological/*physiology ; Microbiota/*physiology ; Seawater ; Symbiosis/*physiology ; }, abstract = {While increasing evidence supports a key role of bacteria in coral larvae settlement and development, the relative importance of environmentally-acquired versus vertically-transferred bacterial population is not clear. Here we have attempted to elucidate the role of post-brooding-acquired bacteria on the development of planula-larvae of the octocoral Rhytisma f. fulvum, in an in vitro cultivation system employing different types of filtered (FSW) and autoclaved (ASW) seawater and with the addition of native bacteria. A good development of larvae was obtained in polystyrene 6-well cell culture plates in the absence of natural reef substrata, achieving a 60-80% of larvae entering metamorphosis after 32 days, even in bacteria-free seawater, indicating that the bacteria acquired during the brooding period are sufficient to support planulae development. No significant difference in planulae attachment and development was observed when using 0.45 μm or 0.22 μm FSW, although autoclaving the 0.45 μm FSW negatively affected larval development, indicating the presence of beneficial bacteria. Autoclaving the different FSW homogenized the development of the larvae among the different treatments. The addition of bacterial strains isolated from the different FSW did not cause any significant effect on planulae development, although some specific strains of the genus Alteromonas seem to be beneficial for larvae development. Light was beneficial for planulae development after day 20, although no Symbiodinium cells could be observed, indicating either that light acts as a positive cue for larval development or the presence of beneficial phototrophic bacteria in the coral microbiome. The feasibility of obtaining advanced metamorphosed larvae in sterilized water provides an invaluable tool for studying the physiological role of the bacterial symbionts in the coral holobiont and the specificity of bacteria-coral interactions.}, }
@article {pmid31565856, year = {2019}, author = {Gilbert, SF}, title = {Evolutionary transitions revisited: Holobiont evo-devo.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {332}, number = {8}, pages = {307-314}, doi = {10.1002/jez.b.22903}, pmid = {31565856}, issn = {1552-5015}, mesh = {Animals ; *Biological Evolution ; *Developmental Biology ; Host Microbial Interactions ; Life Cycle Stages ; Microbiota ; *Symbiosis ; }, abstract = {John T. Bonner lists four essential transformations in the evolution of life: the emergence of the eukaryotic cell, meiosis, multicellularity, and the nervous system. This paper analyses the mechanisms for those transitions in light of three of Dr. Bonner's earlier hypotheses: (a) that the organism is its life cycle, (b) that evolution consists of alterations of the life cycle, and (c) that development extends beyond the body and into interactions with other organisms. Using the notion of the holobiont life cycle, this paper attempts to show that these evolutionary transitions can be accomplished through various means of symbiosis. Perceiving the organism both as an interspecies consortium and as a life cycle supports a twofold redefinition of the organism as a holobiont constructed by integrating together the life cycles of several species. These findings highlight the importance of symbiosis and the holobiont development in analyses of evolution.}, }
@article {pmid31565613, year = {2019}, author = {Bordoni, B and Simonelli, M and Morabito, B}, title = {The Fascial Breath.}, journal = {Cureus}, volume = {11}, number = {7}, pages = {e5208}, pmid = {31565613}, issn = {2168-8184}, abstract = {The word diaphragm comes from the Greek (διάϕραγμα), which meant something that divides, but also expressed a concept related to emotions and intellect. Breath is part of a concept of symmorphosis, that is the maximum ability to adapt to multiple functional questions in a defined biological context. The act of breathing determines and defines our holobiont: how we react and who we are. The article reviews the fascial structure that involves and forms the diaphragm muscle with the aim of changing the vision of this complex muscle: from an anatomical and mechanistic form to a fractal and asynchronous form. Another step forward for understanding the diaphragm muscle is that it is not only covered, penetrated and made up of connective tissue, but the contractile tissue itself is a fascial tissue with the same embryological derivation. All the diaphragm muscle is fascia.}, }
@article {pmid31563048, year = {2019}, author = {Villegas-Plazas, M and Sanabria, J and Junca, H}, title = {A composite taxonomical and functional framework of microbiomes under acid mine drainage bioremediation systems.}, journal = {Journal of environmental management}, volume = {251}, number = {}, pages = {109581}, doi = {10.1016/j.jenvman.2019.109581}, pmid = {31563048}, issn = {1095-8630}, mesh = {Acids ; Biodegradation, Environmental ; Bioreactors ; *Microbiota ; *Mining ; }, abstract = {Mining-industry is one of the most important activities in the economic development of many countries and produces highly significant alterations on the environment, mainly due to the release of a strong acidic metal-rich wastewater called acid mine drainage (AMD). Consequently, the establishment of multiple wastewater treatment strategies remains as a fundamental challenge in AMD research. Bioremediation, as a constantly-evolving multidisciplinary endeavor had been complemented during the last decades by novel tools of increasingly higher resolution such as those based on omics approaches, which are providing detailed insights into the ecology, evolution and mechanisms of microbial communities acting in bioremediation processes. This review specifically addresses, reanalyzes and reexamines in a composite comparative manner, the available sequence information and associated metadata available in public databases about AMD impacted microbial communities; summarizing our understanding of its composition and functions, and proposing potential genetic enhancements for improved bioremediation strategies. 16 S rRNA gene-targeted sequencing data from 9 studies previously published including AMD systems reported and studied around the world, were collected and reanalyzed to compare and identify the core and most abundant genera in four distinct AMD ecosystems: surface biofilm, water, impacted soils/sediments and bioreactor microbiomes. We determined that the microbial communities of bioreactors were the most diverse in bacterial types detected. The metabolic pathways predicted strongly suggest the key role of syntrophic communities with denitrification, methanogenesis, manganese, sulfate and iron reduction. The perspectives to explore the dynamics of engineering systems by high-throughput sequencing and biochemical techniques are discussed and foreseen application of synthetic biology and omics exploration on improved AMD biotransformation are proposed.}, }
@article {pmid31548681, year = {2019}, author = {Robbins, SJ and Singleton, CM and Chan, CX and Messer, LF and Geers, AU and Ying, H and Baker, A and Bell, SC and Morrow, KM and Ragan, MA and Miller, DJ and Forêt, S and ,  and Voolstra, CR and Tyson, GW and Bourne, DG}, title = {A genomic view of the reef-building coral Porites lutea and its microbial symbionts.}, journal = {Nature microbiology}, volume = {4}, number = {12}, pages = {2090-2100}, pmid = {31548681}, issn = {2058-5276}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Archaea/*genetics ; Bacteria/*genetics ; Coral Reefs ; Dinoflagellida/genetics ; *Genome ; Metagenomics ; Microbiota ; *Symbiosis ; }, abstract = {Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change[1]. However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health[2,3]. Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.}, }
@article {pmid31548380, year = {2019}, author = {van Vliet, S and Doebeli, M}, title = {The role of multilevel selection in host microbiome evolution.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {116}, number = {41}, pages = {20591-20597}, pmid = {31548380}, issn = {1091-6490}, mesh = {Animals ; *Biological Evolution ; *Microbiota ; Phenotype ; *Selection, Genetic ; Symbiosis ; }, abstract = {Animals are associated with a microbiome that can affect their reproductive success. It is, therefore, important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial, and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here, we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared with the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.}, }
@article {pmid31546574, year = {2019}, author = {Kormas, KA}, title = {Editorial for the Special Issue: Gut Microorganisms of Aquatic Animals.}, journal = {Microorganisms}, volume = {7}, number = {10}, pages = {}, pmid = {31546574}, issn = {2076-2607}, abstract = {Since the introduction of the term holobiont [...].}, }
@article {pmid31545807, year = {2019}, author = {Planes, S and Allemand, D and Agostini, S and Banaigs, B and Boissin, E and Boss, E and Bourdin, G and Bowler, C and Douville, E and Flores, JM and Forcioli, D and Furla, P and Galand, PE and Ghiglione, JF and Gilson, E and Lombard, F and Moulin, C and Pesant, S and Poulain, J and Reynaud, S and Romac, S and Sullivan, MB and Sunagawa, S and Thomas, OP and Troublé, R and de Vargas, C and Vega Thurber, R and Voolstra, CR and Wincker, P and Zoccola, D and , }, title = {The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.}, journal = {PLoS biology}, volume = {17}, number = {9}, pages = {e3000483}, pmid = {31545807}, issn = {1545-7885}, mesh = {Animals ; Anthozoa/*microbiology ; *Coral Reefs ; *Expeditions ; Metabolomics ; Metagenomics ; *Microbiota ; Pacific Ocean ; Symbiosis ; }, abstract = {Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.}, }
@article {pmid31544365, year = {2019}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Jomchai, N and Sonthirod, C and Naktang, C and Kongkachana, W and Tangphatsornruang, S}, title = {Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea.}, journal = {MicrobiologyOpen}, volume = {8}, number = {12}, pages = {e935}, pmid = {31544365}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; Ecosystem ; *Hot Temperature ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae ; *Stress, Physiological ; }, abstract = {The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral-associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full-length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio-related sequences in our heat-stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full-length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.}, }
@article {pmid31541308, year = {2020}, author = {Thomas-Vaslin, V}, title = {Individuation and the Organization in Complex Living Ecosystem: Recursive Integration and Self-assertion by Holon-Lymphocytes.}, journal = {Acta biotheoretica}, volume = {68}, number = {1}, pages = {171-199}, doi = {10.1007/s10441-019-09364-w}, pmid = {31541308}, issn = {1572-8358}, mesh = {Aging/genetics ; *Ecosystem ; Environment ; *Feedback ; *Gene Transfer, Horizontal ; Humans ; *Identification, Psychological ; Immune System/*immunology/metabolism ; *Individuation ; Lymphocytes/*immunology ; }, abstract = {Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living "holon" displaying dynamic self-assertion and integration is used here to explain the ecosystems dynamic processes. The update of the living holon state according to the continuous change of the dynamic system allows for its viability. This is interpreted as adaptation, selection and organization by the human that observes the system a posteriori from its level. Our model concerns the complex dynamics of the adaptive immune system, integrating holon-lymphocytes that collectively preserve the identity and integrity of the organism. Each lymphocyte individualizes as a dynamic holon-lymphocyte, with somatic gene individuation leading to an individual, singular antigen immunoreceptor type, promoting the self-assertion. In turn, the "Immunoception" allows for perception of the environmental antigenic context, thus integration of the holon in its environment. The self-assertion/integration of holon-lymphocyte starts from fetal stages and is influenced by mother Lamarckian acquired historicity transmissions, a requisite for the integrity of the holobiont-organism. We propose a dynamic model of the perception by holon-lymphocyte, and at the supra-clonal level of the immune system functions that sustain the identity and integrity of the holon-holobiont organism.}, }
@article {pmid31528630, year = {2019}, author = {García-López, R and Pérez-Brocal, V and Moya, A}, title = {Beyond cells - The virome in the human holobiont.}, journal = {Microbial cell (Graz, Austria)}, volume = {6}, number = {9}, pages = {373-396}, pmid = {31528630}, issn = {2311-2638}, abstract = {Viromics, or viral metagenomics, is a relatively new and burgeoning field of research that studies the complete collection of viruses forming part of the microbiota in any given niche. It has strong foundations rooted in over a century of discoveries in the field of virology and recent advances in molecular biology and sequencing technologies. Historically, most studies have deconstructed the concept of viruses into a simplified perception of viral agents as mere pathogens, which demerits the scope of large-scale viromic analyses. Viruses are, in fact, much more than regular parasites. They are by far the most dynamic and abundant entity and the greatest killers on the planet, as well as the most effective geo-transforming genetic engineers and resource recyclers, acting on all life strata in any habitat. Yet, most of this uncanny viral world remains vastly unexplored to date, greatly hindered by the bewildering complexity inherent to such studies and the methodological and conceptual limitations. Viromic studies are just starting to address some of these issues but they still lag behind microbial metagenomics. In recent years, however, higher-throughput analysis and resequencing have rekindled interest in a field that is just starting to show its true potential. In this review, we take a look at the scientific and technological developments that led to the advent of viral and bacterial metagenomics with a particular, but not exclusive, focus on human viromics from an ecological perspective. We also address some of the most relevant challenges that current viral studies face and ponder on the future directions of the field.}, }
@article {pmid31527783, year = {2020}, author = {Porro, B and Mallien, C and Hume, BCC and Pey, A and Aubin, E and Christen, R and Voolstra, CR and Furla, P and Forcioli, D}, title = {The many faced symbiotic snakelocks anemone (Anemonia viridis, Anthozoa): host and symbiont genetic differentiation among colour morphs.}, journal = {Heredity}, volume = {124}, number = {2}, pages = {351-366}, pmid = {31527783}, issn = {1365-2540}, mesh = {Animals ; Atlantic Ocean ; DNA, Ribosomal Spacer/genetics ; Dinoflagellida/*genetics ; England ; Genetic Variation ; Genetics, Population ; Mediterranean Sea ; Pigmentation/*genetics ; Sea Anemones/*genetics ; *Symbiosis ; }, abstract = {How can we explain morphological variations in a holobiont? The genetic determinism of phenotypes is not always obvious and could be circumstantial in complex organisms. In symbiotic cnidarians, it is known that morphology or colour can misrepresent a complex genetic and symbiotic diversity. Anemonia viridis is a symbiotic sea anemone from temperate seas. This species displays different colour morphs based on pigment content and lives in a wide geographical range. Here, we investigated whether colour morph differentiation correlated with host genetic diversity or associated symbiotic genetic diversity by using RAD sequencing and symbiotic dinoflagellate typing of 140 sea anemones from the English Channel and the Mediterranean Sea. We did not observe genetic differentiation among colour morphs of A. viridis at the animal host or symbiont level, rejecting the hypothesis that A. viridis colour morphs correspond to species level differences. Interestingly, we however identified at least four independent animal host genetic lineages in A. viridis that differed in their associated symbiont populations. In conclusion, although the functional role of the different morphotypes of A. viridis remains to be determined, our approach provides new insights on the existence of cryptic species within A. viridis.}, }
@article {pmid31521200, year = {2019}, author = {Rausch, P and Rühlemann, M and Hermes, BM and Doms, S and Dagan, T and Dierking, K and Domin, H and Fraune, S and von Frieling, J and Hentschel, U and Heinsen, FA and Höppner, M and Jahn, MT and Jaspers, C and Kissoyan, KAB and Langfeldt, D and Rehman, A and Reusch, TBH and Roeder, T and Schmitz, RA and Schulenburg, H and Soluch, R and Sommer, F and Stukenbrock, E and Weiland-Bräuer, N and Rosenstiel, P and Franke, A and Bosch, T and Baines, JF}, title = {Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {133}, pmid = {31521200}, issn = {2049-2618}, mesh = {Animals ; Bacteria/classification/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/genetics/*physiology ; Microbiota/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution, and development of both players. These interdependencies inspired a new view of multicellular organisms as "metaorganisms." The goal of the Collaborative Research Center "Origin and Function of Metaorganisms" is to understand why and how microbial communities form long-term associations with hosts from diverse taxonomic groups, ranging from sponges to humans in addition to plants.<br><br>METHODS: In order to optimize the choice of analysis procedures, which may differ according to the host organism and question at hand, we systematically compared the two main technical approaches for profiling microbial communities, 16S rRNA gene amplicon and metagenomic shotgun sequencing across our panel of ten host taxa. This includes two commonly used 16S rRNA gene regions and two amplification procedures, thus totaling five different microbial profiles per host sample.<br><br>CONCLUSION: While 16S rRNA gene-based analyses are subject to much skepticism, we demonstrate that many aspects of bacterial community characterization are consistent across methods. The resulting insight facilitates the selection of appropriate methods across a wide range of host taxa. Overall, we recommend single- over multi-step amplification procedures, and although exceptions and trade-offs exist, the V3&#x2009;V4 over the V1&#x2009;V2 region of the 16S rRNA gene. Finally, by contrasting taxonomic and functional profiles and performing phylogenetic analysis, we provide important and novel insight into broad evolutionary patterns among metaorganisms, whereby the transition of animals from an aquatic to a terrestrial habitat marks a major event in the evolution of host-associated microbial composition.}, }
@article {pmid31513766, year = {2019}, author = {Lee, JH and Lee, WJ}, title = {Stealing from the Future: Injured Larvae Spend Stem Cell Deposits.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {3}, pages = {301-303}, doi = {10.1016/j.chom.2019.08.013}, pmid = {31513766}, issn = {1934-6069}, mesh = {Animals ; *Drosophila ; Intestines ; Larva ; Stem Cells ; *Theft ; }, abstract = {Because Drosophila larvae do not possess intestinal stem cells, it is unknown how damaged gut cells are replenished. In this issue of Cell Host &amp; Microbe, Houtz et al. (2019) show that larvae have a unique gut repair mechanism that involves borrowing stem cells originally reserved for adult gut formation.}, }
@article {pmid31494678, year = {2019}, author = {Yang, Q and Franco, CMM and Lin, HW and Zhang, W}, title = {Untapped sponge microbiomes: structure specificity at host order and family levels.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {9}, pages = {}, doi = {10.1093/femsec/fiz136}, pmid = {31494678}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; DNA, Bacterial/genetics ; Host Specificity ; *Microbiota ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Sponges are complex holobionts in which the structure of the microbiome has seldom been characterized above the host species level. The hypothesis tested in this study is that the structure of the sponge microbiomes is specific to the host at the order and family levels. This was done by using 33 sponge species belonging to 19 families representing five orders. A combination of three primer sets covering the V1-V8 regions of the 16S rRNA gene provided a more comprehensive coverage of the microbiomes. Both the diversity and structure of sponge microbiomes were demonstrated to be highly specific to the host phylogeny at the order and family levels. There are always dominant operational taxonomic units (OTUs) (relative abundance >1%) shared between microbial communities of sponges within the same family or order, but these shared OTUs showed high levels of dissimilarity between different sponge families and orders. The unique OTUs for a particular sponge family or order could be regarded as their 'signature identity'. 70%-87% of these unique OTUs (class level) are unaffiliated and represent a vast resource of untapped microbiota. This study contributes to a deeper understanding on the concept of host-specificity of sponge microbiomes and highlights a hidden reservoir of sponge-associated microbial resources.}, }
@article {pmid31487470, year = {2019}, author = {Bana, B and Cabreiro, F}, title = {The Microbiome and Aging.}, journal = {Annual review of genetics}, volume = {53}, number = {}, pages = {239-261}, doi = {10.1146/annurev-genet-112618-043650}, pmid = {31487470}, issn = {1545-2948}, support = {MC_UP_1605/6/MRC_/Medical Research Council/United Kingdom ; 102532/Z/12/Z//Wellcome Trust/International ; MC-A654-5QC80/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Aging/*physiology ; Animals ; Epigenesis, Genetic ; Female ; Gastrointestinal Microbiome/physiology ; Humans ; Immune System/microbiology ; Inflammation/microbiology ; Intestinal Absorption ; Male ; Microbiota/*physiology ; Proteostasis ; Telomere/physiology ; }, abstract = {Aging is a natural process of organismal decay that underpins the development of myriad diseases and disorders. Extensive efforts have been made to understand the biology of aging and its regulation, but most studies focus solely on the host organism. Considering the pivotal role of the microbiota in host health and metabolism, we propose viewing the host and its microbiota as a single biological entity whose aging phenotype is influenced by the complex interplay between host and bacterial genetics. In this review we present how the microbiota changes as the host ages, but also how the intricate relationship between host and indigenous bacteria impacts organismal aging and life span. In addition, we highlight other microbiota-dependent mechanisms that potentially regulate aging, and present experimental animal models for addressing these questions. Importantly, we propose microbiome dysbiosis as an additional hallmark and biomarker of aging.}, }
@article {pmid31479939, year = {2019}, author = {Li, J and Wang, T and Yu, S and Bai, J and Qin, S}, title = {Community characteristics and ecological roles of bacterial biofilms associated with various algal settlements on coastal reefs.}, journal = {Journal of environmental management}, volume = {250}, number = {}, pages = {109459}, doi = {10.1016/j.jenvman.2019.109459}, pmid = {31479939}, issn = {1095-8630}, mesh = {Animals ; *Anthozoa ; Biofilms ; Coral Reefs ; Ecology ; *Microbiota ; }, abstract = {Bacterial biofilms, which are a group of bacteria attaching to and ultimately forming communities on reefs, perform essential ecological functions in coastal ecosystems. Particularly, they may attract or repulse the settling down of opportunistic algae. However, this phenomenon and the interaction mechanism are not fully understood. This study investigated reefs from the Changdao coastal zone to determine the structures and functions of bacterial biofilms symbiosing with various algae using high-throughput sequencing analysis. The Shannon diversity index of microbiota with algal symbiosis reached 5.34, which was higher than that of microbiota wherein algae were absent (4.80). The beta diversity results for 11 samples revealed that there existed a separation between bacterial communities on reefs with and without attached algae, while communities with similar algae clustered together. The taxa mostly associated with algae-symbiotic microbiota are the Actinobacteria phylum, and the Flavobacteriia and Gammaproteobacteria classes. The Cyanobacteria phylum was not associated with algae-symbiotic microbiota. As revealed by functional analysis, the bacteria mostly involved in the metabolism of sulfur were represented by brown and red algae in the biofilm symbiosis. Bacteria related to the metabolism of certain trace elements were observed only in specific groups. Moreover, phototrophy-related bacteria were less abundant in samples coexisting with algae. This study established the link between bacterial biofilms and algal settlements on costal reefs, and revealed the possible holobiont relationship between them. This may provide new technical directions toward realizing algal cultivation and management during the construction of artificial reef ecosystems.}, }
@article {pmid31474958, year = {2019}, author = {Pupier, CA and Bednarz, VN and Grover, R and Fine, M and Maguer, JF and Ferrier-Pagès, C}, title = {Divergent Capacity of Scleractinian and Soft Corals to Assimilate and Transfer Diazotrophically Derived Nitrogen to the Reef Environment.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1860}, pmid = {31474958}, issn = {1664-302X}, abstract = {Corals are associated with dinitrogen (N2)-fixing bacteria that potentially represent an additional nitrogen (N) source for the coral holobiont in oligotrophic reef environments. Nevertheless, the few studies investigating the assimilation of diazotrophically derived nitrogen (DDN) by tropical corals are limited to a single scleractinian species (i.e., Stylophora pistillata). The present study quantified DDN assimilation rates in four scleractinian and three soft coral species from the shallow waters of the oligotrophic Northern Red Sea using the [15]N2 tracer technique. All scleractinian species significantly stimulated N2 fixation in the coral-surrounding seawater (and mucus) and assimilated DDN into their tissue. Interestingly, N2 fixation was not detected in the tissue and surrounding seawater of soft corals, despite the fact that soft corals were able to take up DDN from a culture of free-living diazotrophs. Soft coral mucus likely represents an unfavorable habitat for the colonization and activity of diazotrophs as it contains a low amount of particulate organic matter, with a relatively high N content, compared to the mucus of scleractinian corals. In addition, it is known to present antimicrobial properties. Overall, this study suggests that DDN assimilation into coral tissues depends on the presence of active diazotrophs in the coral's mucus layer and/or surrounding seawater. Since N is often a limiting nutrient for primary productivity in oligotrophic reef waters, the divergent capacity of scleractinian and soft corals to promote N2 fixation may have implications for N availability and reef biogeochemistry in scleractinian versus soft coral-dominated reefs.}, }
@article {pmid31466521, year = {2019}, author = {Gantt, SE and McMurray, SE and Stubler, AD and Finelli, CM and Pawlik, JR and Erwin, PM}, title = {Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {124}, pmid = {31466521}, issn = {2049-2618}, mesh = {Animals ; Archaea/classification/isolation &amp; purification ; Bacteria/classification/isolation &amp; purification ; Belize ; Carbon/*metabolism ; Caribbean Region ; *Coral Reefs ; Florida ; *Microbiota ; Nutrients/*metabolism ; Porifera/*microbiology ; }, abstract = {BACKGROUND: Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO4, NOx, NH4) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart).<br><br>RESULTS: Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO4, and NOx flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH4 flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH4 flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum.<br><br>CONCLUSIONS: Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.}, }
@article {pmid31430401, year = {2019}, author = {Mathé-Hubert, H and Kaech, H and Hertaeg, C and Jaenike, J and Vorburger, C}, title = {Nonrandom associations of maternally transmitted symbionts in insects: The roles of drift versus biased cotransmission and selection.}, journal = {Molecular ecology}, volume = {28}, number = {24}, pages = {5330-5346}, doi = {10.1111/mec.15206}, pmid = {31430401}, issn = {1365-294X}, mesh = {Animals ; Aphids/*genetics/microbiology ; Bayes Theorem ; Drosophila/genetics/microbiology ; Gene Transfer, Horizontal/genetics ; Maternal Inheritance/genetics ; Microbiota/genetics ; Phylogeny ; Spiroplasma/*genetics ; Symbiosis/*genetics ; Wolbachia/*genetics ; }, abstract = {Virtually all higher organisms form holobionts with associated microbiota. To understand the biology of holobionts we need to know how species assemble and interact. Controlled experiments are suited to study interactions between particular symbionts, but they only accommodate a tiny portion of the diversity within each species. Alternatively, interactions can be inferred by testing if associations among symbionts in the field are more or less frequent than expected under random assortment. However, random assortment may not be a valid null hypothesis for maternally transmitted symbionts since drift alone can result in associations. Here, we analyse a European field survey of endosymbionts in pea aphids (Acyrthosiphon pisum), confirming that symbiont associations are pervasive. To interpret them, we develop a model simulating the effect of drift on symbiont associations. We show that drift induces apparently nonrandom assortment, even though horizontal transmissions and maternal transmission failures tend to randomise symbiont associations. We also use this model in the approximate Bayesian computation framework to revisit the association between Spiroplasma and Wolbachia in Drosophila neotestacea. New field data reported here reveal that this association has disappeared in the investigated location, yet a significant interaction between Spiroplasma and Wolbachia can still be inferred. Our study confirms that negative and positive associations are pervasive and often induced by symbiont-symbiont interactions. Nevertheless, some associations are also likely to be driven by drift. This possibility needs to be considered when performing such analyses, and our model is helpful for this purpose.}, }
@article {pmid31422890, year = {2019}, author = {Liu, H and Macdonald, CA and Cook, J and Anderson, IC and Singh, BK}, title = {An Ecological Loop: Host Microbiomes across Multitrophic Interactions.}, journal = {Trends in ecology &amp; evolution}, volume = {34}, number = {12}, pages = {1118-1130}, doi = {10.1016/j.tree.2019.07.011}, pmid = {31422890}, issn = {1872-8383}, mesh = {Animals ; Ecology ; Insecta ; *Microbiota ; Plants ; Rhizosphere ; }, abstract = {Our knowledge of host-associated microorganisms and their role in host functions is rapidly evolving. Stress-affected plants assemble beneficial microbes in their rhizosphere to maximize survival and growth. Similarly, insects have gut microbiomes that extend their functional repertoire in fighting stress. A strong microbial linkage between soil, plants, and pollinators is emerging and this can influence pollination services and overall ecosystem health. Yet, the nature of microbial interactions between different ecosystem components remains poorly understood. Here we highlight the acquisition pathways of beneficial microbes and their functions in protecting hosts against stress. By adopting a new 'eco-holobiont' approach, which explicitly incorporates biotic feedbacks, we can significantly expand our ecological understanding and better develop sustainable environmental management.}, }
@article {pmid31417510, year = {2019}, author = {Tourneroche, A and Lami, R and Hubas, C and Blanchet, E and Vallet, M and Escoubeyrou, K and Paris, A and Prado, S}, title = {Bacterial-Fungal Interactions in the Kelp Endomicrobiota Drive Autoinducer-2 Quorum Sensing.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1693}, pmid = {31417510}, issn = {1664-302X}, abstract = {Brown macroalgae are an essential component of temperate coastal ecosystems and a growing economic sector. They harbor diverse microbial communities that regulate algal development and health. This algal holobiont is dynamic and achieves equilibrium via a complex network of microbial and host interactions. We now report that bacterial and fungal endophytes associated with four brown algae (Ascophyllum nodosum, Pelvetia canaliculata, Laminaria digitata, and Saccharina latissima) produce metabolites that interfere with bacterial autoinducer-2 quorum sensing, a signaling system implicated in virulence and host colonization. Additionally, we performed co-culture experiments combined to a metabolomic approach and demonstrated that microbial interactions influence production of metabolites, including metabolites involved in quorum sensing. Collectively, the data highlight autoinducer-2 quorum sensing as a key metabolite in the complex network of interactions within the algal holobiont.}, }
@article {pmid31416417, year = {2019}, author = {Yang, QS and Dong, JD and Ahmad, M and Ling, J and Zhou, WG and Tan, YH and Zhang, YZ and Shen, DD and Zhang, YY}, title = {Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs.}, journal = {BMC microbiology}, volume = {19}, number = {1}, pages = {188}, pmid = {31416417}, issn = {1471-2180}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics ; China ; DNA, Bacterial/*genetics ; Nitrogen Fixation ; Nitrogenase/*genetics ; Phylogeny ; Plankton/*microbiology ; Seawater/microbiology ; }, abstract = {BACKGROUND: Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the community composition and nifH expression profile of PADs with > 100 μm size fraction in the euphotic zone of the northern South China Sea.<br><br>RESULTS: The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. We characterized the 20 most abundant OTUs by ranking the sum of sequence reads across 9 sampling stations for individual OTUs in both nifH DNA and RNA libraries, and then assessed their phylogenetic relatedness. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high.<br><br>CONCLUSIONS: The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.}, }
@article {pmid31415772, year = {2020}, author = {Miller, WB and Torday, JS and Baluška, F}, title = {The N-space Episenome unifies cellular information space-time within cognition-based evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {150}, number = {}, pages = {112-139}, doi = {10.1016/j.pbiomolbio.2019.08.006}, pmid = {31415772}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Cell Communication ; Cell Physiological Phenomena ; Cells ; Cognition/*physiology ; Genome ; *Homeostasis ; Humans ; Morphogenesis/*genetics ; Time Factors ; }, abstract = {Self-referential cellular homeostasis is maintained by the measured assessment of both internal status and external conditions based within an integrated cellular information field. This cellular field attachment to biologic information space-time coordinates environmental inputs by connecting the cellular senome, as the sum of the sensory experiences of the cell, with its genome and epigenome. In multicellular organisms, individual cellular information fields aggregate into a collective information architectural matrix, termed a N-space Episenome, that enables mutualized organism-wide information management. It is hypothesized that biological organization represents a dual heritable system constituted by both its biological materiality and a conjoining N-space Episenome. It is further proposed that morphogenesis derives from reciprocations between these inter-related facets to yield coordinated multicellular growth and development. The N-space Episenome is conceived as a whole cell informational projection that is heritable, transferable via cell division and essential for the synchronous integration of the diverse self-referential cells that constitute holobionts.}, }
@article {pmid31409660, year = {2019}, author = {Zhang, S and Song, W and Wemheuer, B and Reveillaud, J and Webster, N and Thomas, T}, title = {Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31409660}, issn = {2379-5077}, abstract = {Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "Candidatus [U]Nitrosopumilus hexadellus," "Candidatus [U]Nitrosopumilus detritiferus," and "Candidatus [U]Cenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "Ca [U]Cenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca [U]Nitrosopumilus detritiferus" and "Ca [U]Nitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.}, }
@article {pmid31409048, year = {2019}, author = {Drago, L and Panelli, S and Bandi, C and Zuccotti, G and Perini, M and D'Auria, E}, title = {What Pediatricians Should Know Before Studying Gut Microbiota.}, journal = {Journal of clinical medicine}, volume = {8}, number = {8}, pages = {}, pmid = {31409048}, issn = {2077-0383}, abstract = {Billions of microorganisms, or "microbiota", inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term "microbiome" is commonly used to refer to the genetic make-up and gene-gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical interpretation of results are addressed. This basic knowledge aims to provide the pediatricians with a key tool to avoid data dispersion and pitfalls during child microbiota study.}, }
@article {pmid31409030, year = {2019}, author = {Meron, D and Maor-Landaw, K and Weizman, E and Waldman Ben-Asher, H and Eyal, G and Banin, E and Loya, Y and Levy, O}, title = {The Algal Symbiont Modifies the Transcriptome of the Scleractinian Coral Euphyllia paradivisa During Heat Stress.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, pmid = {31409030}, issn = {2076-2607}, abstract = {The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship-coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphylliaparadivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of "symbiosis differentially expressed genes" and "coral heat-stress genes" in order to compare between the treatments. The symbiotic and apo-symbiotic samples were segregated into two separate groups with several different enriched gene ontologies. Our findings suggest that the presence of endosymbionts has a greater negative impact on the host than the environmental temperature conditions experienced by the holobiont. The peak of the stress reaction was identified as 28 °C, with the highest number of differentially expressed genes. We suggest that the algal symbionts increase coral holobiont susceptibility to elevated temperatures. Currently, we can only speculate whether coral species, such as E.paradivisa, with the plasticity to also flourish as apo-symbionts, may have a greater chance to withstand the upcoming global climate change challenge.}, }
@article {pmid31404250, year = {2019}, author = {Abdelfattah, A and Sanzani, SM and Wisniewski, M and Berg, G and Cacciola, SO and Schena, L}, title = {Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {922}, pmid = {31404250}, issn = {1664-462X}, abstract = {Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs (flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes (5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community (92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i.e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.}, }
@article {pmid31396197, year = {2019}, author = {Damjanovic, K and van Oppen, MJH and Menéndez, P and Blackall, LL}, title = {Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1702}, pmid = {31396197}, issn = {1664-302X}, abstract = {Coral-associated microorganisms are essential for maintaining the health of the coral holobiont by participating in nutrient cycling and protecting the coral host from pathogens. Under stressful conditions, disruption of the coral prokaryotic microbiome is linked to increased susceptibility to diseases and mortality. Inoculation of corals with beneficial microbes could confer enhanced stress tolerance to the host and may be a powerful tool to help corals thrive under challenging environmental conditions. Here, we explored the feasibility of coral early life stage microbiome manipulation by repeatedly inoculating coral recruits with a bacterial cocktail generated in the laboratory. Co-culturing the two species Acropora tenuis and Platygyra daedalea allowed us to simultaneously investigate the effect of host factors on the coral microbiome. Inoculation cocktails were regularly prepared from freshly grown pure bacterial cultures, which were hence assumed viable, and characterized via the optical density measurement of each individual strain put in suspension. Coral early recruits were inoculated seven times over 3 weeks and sampled once 36 h following the last inoculation event. At this time point, the cumulative inoculations with the bacterial cocktails had a strong effect on the bacterial community composition in recruits of both coral species. While the location of bacterial cells within the coral hosts was not assessed, metabarcoding using the 16S rRNA gene revealed that two and six of the seven bacterial strains administered through the cocktails were significantly enriched in inoculated recruits of A. tenuis and P. daedalea, respectively, compared to control recruits. Despite being reared in the same environment, A. tenuis and P. daedalea established significantly different bacterial communities, both in terms of taxonomic composition and diversity measurements. These findings indicate that coral host factors as well as the environmental bacterial pool play a role in shaping coral-associated bacterial community composition. Host factors may include microbe transmission mode (horizontal versus maternal) and host specificity. While the long-term stability of taxa included in the bacterial inocula as members of the host-associated microbiome remains to be evaluated, our results provide support for the feasibility of coral microbiome manipulation, at least in a laboratory setting.}, }
@article {pmid31378758, year = {2019}, author = {Rouzé, R and Moné, A and Delbac, F and Belzunces, L and Blot, N}, title = {The Honeybee Gut Microbiota Is Altered after Chronic Exposure to Different Families of Insecticides and Infection by Nosema ceranae.}, journal = {Microbes and environments}, volume = {34}, number = {3}, pages = {226-233}, pmid = {31378758}, issn = {1347-4405}, mesh = {Animals ; Bacteria/classification/drug effects/genetics/isolation &amp; purification ; Bees/*drug effects/*microbiology/physiology ; Environmental Exposure ; Gastrointestinal Microbiome/*drug effects/physiology ; Homeostasis ; Insecticides/*toxicity ; Nosema/*physiology ; }, abstract = {The gut of the European honeybee Apis mellifera is the site of exposure to multiple stressors, such as pathogens and ingested chemicals. Therefore, the gut microbiota, which contributes to host homeostasis, may be altered by these stressors. The abundance of major bacterial taxa in the gut was evaluated in response to infection with the intestinal parasite Nosema ceranae or chronic exposure to low doses of the neurotoxic insecticides coumaphos, fipronil, thiamethoxam, and imidacloprid. Experiments were performed under laboratory conditions on adult workers collected from hives in February (winter bees) and July (summer bees) and revealed season-dependent changes in the bacterial community composition. N. ceranae and a lethal fipronil treatment increased the relative abundance of both Gilliamella apicola and Snodgrassella alvi in surviving winter honeybees. The parasite and a sublethal exposure to all insecticides decreased the abundance of Bifidobacterium spp. and Lactobacillus spp. regardless of the season. The similar effects induced by insecticides belonging to distinct molecular families suggested a shared and indirect mode of action on the gut microbiota, possibly through aspecific alterations in gut homeostasis. These results demonstrate that infection and chronic exposure to low concentrations of insecticides may affect the honeybee holobiont.}, }
@article {pmid31373053, year = {2019}, author = {Geva-Zatorsky, N and Elinav, E and Pettersson, S}, title = {When Cultures Meet: The Landscape of "Social" Interactions between the Host and Its Indigenous Microbes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {10}, pages = {e1900002}, doi = {10.1002/bies.201900002}, pmid = {31373053}, issn = {1521-1878}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Host Microbial Interactions ; Humans ; Microbiota/*physiology ; }, abstract = {Animals exist as biodiverse composite organisms that include microbial residents, eukaryotic cells, and organs that collectively form a human being. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body or the holobiont secures growth, health, and reproduction. As such, the survival of a holobiont is dependent on the maintenance of biological order including metabolic homeostasis by tight regulation of the communication between its eukaryotic and prokaryotic residents. In this review an overview and perspective are provided on the bidirectional communication between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships between the components of the holobiont. An emphasis is placed on exemplifying microbiome-mediated effects on host functions-aiming to integrate microbiome functionality to host physiology, be it health or disease. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex transkingdom interactions are provided.}, }
@article {pmid31361932, year = {2020}, author = {Carrasco, J and Preston, GM}, title = {Growing edible mushrooms: a conversation between bacteria and fungi.}, journal = {Environmental microbiology}, volume = {22}, number = {3}, pages = {858-872}, doi = {10.1111/1462-2920.14765}, pmid = {31361932}, issn = {1462-2920}, support = {742966//European Union's Horizon 2020/International ; }, mesh = {Agaricales/*physiology ; *Bacterial Physiological Phenomena ; Mycorrhizae/physiology ; Plants/microbiology ; *Soil Microbiology ; }, abstract = {Mushroom cropping consists of the development and fructification of different fungal species in soil or selective substrates that provide nutrients and support for the crop. The microorganisms present in these environments strongly influence, and in some cases are required for the growth and fructification of cultivated mushrooms. Some fungi such as truffles and morels form ectomycorrhizal associations with host plants. For these fungi, helper bacteria play an important role in the establishment of plant-fungal symbioses. Selective processes acting on the microbiota present in substrates and soils determine the composition of the microbiota inhabiting the fruit bodies or interacting with fungal hyphae, and both configure the mushroom holobiont, understood as the fungus plus associated microorganisms. Here, we review current knowledge regarding the cross-talk between bacteria and fungi during mushroom cultivation. We highlight the potential use of bioinoculants as agronomical amendments to increase mushroom productivity through growth promotion or as biocontrol agents to control pests and diseases.}, }
@article {pmid31341668, year = {2019}, author = {Taffner, J and Cernava, T and Erlacher, A and Berg, G}, title = {Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.).}, journal = {Journal of advanced research}, volume = {19}, number = {}, pages = {39-48}, pmid = {31341668}, issn = {2090-1232}, abstract = {A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.}, }
@article {pmid31341665, year = {2019}, author = {Hartmann, A and Fischer, D and Kinzel, L and Chowdhury, SP and Hofmann, A and Baldani, JI and Rothballer, M}, title = {Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges - A review.}, journal = {Journal of advanced research}, volume = {19}, number = {}, pages = {3-13}, pmid = {31341665}, issn = {2090-1232}, abstract = {Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ identification by immunological and molecular genetic techniques combined with high resolving microscopic tools and 3D-image analysis contributed substantially to a better understanding of the functional interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level. Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allocated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present high resolving approaches for analysis of the composition and key functions of plant microbiota, focusing on interactions of diazotrophic plant growth promoting bacteria, like Azospirillum brasilense, with non-legume host plants. Combining high resolving microscopic analyses with specific immunological detection methods and molecular genetic tools, including especially transcriptome analyses of both the bacterial and plant partners, enables new insights into key traits of beneficial bacteria-plant interactions in holobiontic systems.}, }
@article {pmid31332951, year = {2020}, author = {Gilbert, SF}, title = {Developmental symbiosis facilitates the multiple origins of herbivory.}, journal = {Evolution &amp; development}, volume = {22}, number = {1-2}, pages = {154-164}, doi = {10.1111/ede.12291}, pmid = {31332951}, issn = {1525-142X}, support = {IOS-145177//National Science Foundation/International ; }, mesh = {Animals ; *Biological Evolution ; *Herbivory ; Invertebrates/*growth &amp; development ; Life History Traits ; Phenotype ; *Symbiosis ; Vertebrates/*growth &amp; development ; }, abstract = {Developmental bias toward particular evolutionary trajectories can be facilitated through symbiosis. Organisms are holobionts, consisting of zygote-derived cells and a consortia of microbes, and the development, physiology, and immunity of animals are properties of complex interactions between the zygote-derived cells and microbial symbionts. Such symbionts can be agents of developmental plasticity, allowing an organism to develop in particular directions. This plasticity can lead to genetic assimilation either through the incorporation of microbial genes into host genomes or through the direct maternal transmission of the microbes. Such plasticity can lead to niche construction, enabling the microbes to remodel host anatomy and/or physiology. In this article, I will focus on the ability of symbionts to bias development toward the evolution of herbivory. I will posit that the behavioral and morphological manifestations of herbivorous phenotypes must be preceded by the successful establishment of a community of symbiotic microbes that can digest cell walls and detoxify plant poisons. The ability of holobionts to digest plant materials can range from being a plastic trait, dependent on the transient incorporation of environmental microbes, to becoming a heritable trait of the holobiont organism, transmitted through the maternal propagation of symbionts or their genes.}, }
@article {pmid31331734, year = {2019}, author = {Díaz-Sánchez, S and Estrada-Peña, A and Cabezas-Cruz, A and de la Fuente, J}, title = {Evolutionary Insights into the Tick Hologenome.}, journal = {Trends in parasitology}, volume = {35}, number = {9}, pages = {725-737}, doi = {10.1016/j.pt.2019.06.014}, pmid = {31331734}, issn = {1471-5007}, mesh = {Animals ; *Biological Evolution ; Genome/*genetics ; Host Microbial Interactions/physiology ; Microbiota/physiology ; Symbiosis ; Ticks/classification/*genetics/*microbiology ; }, abstract = {Recently, our knowledge of the composition and complexity of tick microbial communities has increased and supports microbial impact on tick biology. Results support a phylogenetic association between ticks and their microbiota across evolution; this is known as phylosymbiosis. Herein, using published datasets, we confirm the existence of phylosymbiosis between Ixodes ticks and their microbial communities. The strong phylosymbiotic signal and the phylogenetic structure of microbial communities associated with Ixodid ticks revealed that phylosymbiosis may be a widespread phenomenon in tick-microbiota evolution. This finding supports the existence of a species-specific tick hologenome with a largely unexplored influence on tick biology and pathogen transmission. These results may provide potential targets for the construction of paratransgenic ticks to control tick infestations and tick-borne diseases.}, }
@article {pmid31329312, year = {2019}, author = {Chan, WY and Peplow, LM and Menéndez, P and Hoffmann, AA and van Oppen, MJH}, title = {The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals.}, journal = {Molecular ecology}, volume = {28}, number = {16}, pages = {3830-3843}, doi = {10.1111/mec.15187}, pmid = {31329312}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Australia ; Bacteria/*classification ; DNA Barcoding, Taxonomic ; Dinoflagellida/*classification ; Hybridization, Genetic ; Life Cycle Stages ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; *Symbiosis ; }, abstract = {The bacterial and microalgal endosymbiont (Symbiodiniaceae spp.) communities associated with corals have important roles in their health and resilience, yet little is known about the factors driving their succession during early coral life stages. Using 16S rRNA gene and ITS2 metabarcoding, we compared these communities in four Acropora coral species and their hybrids obtained from two laboratory crosses (Acropora tenuis × Acropora loripes and Acropora sarmentosa × Acropora florida) across the parental, recruit (7 months old) and juvenile (2 years old) life stages. We tested whether microbiomes differed between (a) life stages, (b) hybrids and purebreds, and (c) treatment conditions (ambient/elevated temperature and pCO2). Microbial communities of early life stage corals were highly diverse, lacked host specificity and were primarily determined by treatment conditions. Over time, a winnowing process occurred, and distinct microbial communities developed between the two species pair crosses by 2 years of age, irrespective of hybrid or purebred status. These findings suggest that the microbial communities of corals have a period of flexibility prior to adulthood, which can be valuable to future research aimed at the manipulation of coral microbial communities.}, }
@article {pmid31325911, year = {2019}, author = {Perez-Lamarque, B and Morlon, H}, title = {Characterizing symbiont inheritance during host-microbiota evolution: Application to the great apes gut microbiota.}, journal = {Molecular ecology resources}, volume = {19}, number = {6}, pages = {1659-1671}, doi = {10.1111/1755-0998.13063}, pmid = {31325911}, issn = {1755-0998}, support = {Programme Bettencourt//Ecole Doctorale FIRE/ ; //Ecole normale sup&#xe9;rieure/ ; //Centre National de la Recherche Scientifique/ ; PANDA/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; //&#xc9;cole Normale Sup&#xe9;rieure/ ; }, mesh = {Animals ; Bacteria/genetics ; DNA Barcoding, Taxonomic/methods ; Disease Transmission, Infectious ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Hominidae/*microbiology ; Infectious Disease Transmission, Vertical ; Microbiota/*genetics ; Phylogeny ; Symbiosis/*genetics ; }, abstract = {Microbiota play a central role in the functioning of multicellular life, yet understanding their inheritance during host evolutionary history remains an important challenge. Symbiotic microorganisms are either acquired from the environment during the life of the host (i.e. environmental acquisition), transmitted across generations with a faithful association with their hosts (i.e. strict vertical transmission), or transmitted with occasional host switches (i.e. vertical transmission with horizontal switches). These different modes of inheritance affect microbes' diversification, which at the two extremes can be independent from that of their associated host or follow host diversification. The few existing quantitative tools for investigating the inheritance of symbiotic organisms rely on cophylogenetic approaches, which require knowledge of both host and symbiont phylogenies, and are therefore often not well adapted to DNA metabarcoding microbial data. Here, we develop a model-based framework for identifying vertically transmitted microbial taxa. We consider a model for the evolution of microbial sequences on a fixed host phylogeny that includes vertical transmission and horizontal host switches. This model allows estimating the number of host switches and testing for strict vertical transmission and independent evolution. We test our approach using simulations. Finally, we illustrate our framework on gut microbiota high-throughput sequencing data of the family Hominidae and identify several microbial taxonomic units, including fibrolytic bacteria involved in carbohydrate digestion, that tend to be vertically transmitted.}, }
@article {pmid31325209, year = {2020}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution: do mothers matter most?.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {129-137}, doi = {10.1111/1471-0528.15882}, pmid = {31325209}, issn = {1471-0528}, mesh = {Adaptation, Biological/genetics/*physiology ; Adaptation, Physiological/genetics/*physiology ; Adult ; Animals ; Biological Evolution ; Evolution, Molecular ; Female ; Gene Transfer, Horizontal/*genetics ; Genetic Speciation ; Genetic Variation ; Heredity ; Host Microbial Interactions/*physiology ; Humans ; Male ; Microbiota/genetics/*physiology ; *Mothers ; Plants ; Pregnancy ; }, abstract = {The hologenome concept of evolution is discussed, with special emphasis placed upon the microbiome of women. The microbiome is dynamic, changing under different conditions, and differs between women and men. Genetic variation occurs not only in the host, but also in the microbiome by the acquisition of novel microbes, the amplification of specific microbes, and horizontal gene transfer. The majority of unique genes in human holobionts are found in microbiomes, and mothers are responsible for transferring most of these to their offspring during birth, breastfeeding, and physical contact. Thus, mothers are likely to be the primary providers of the majority of genetic information to offspring via mitochondria and the microbiome. TWEETABLE ABSTRACT: Microbiomes differ between women and men. Most genes in humans are in the microbiome. Mothers transfer most of these genes to offspring.}, }
@article {pmid31312870, year = {2020}, author = {Shih, JL and Selph, KE and Wall, CB and Wallsgrove, NJ and Lesser, MP and Popp, BN}, title = {Trophic Ecology of the Tropical Pacific Sponge Mycale grandis Inferred from Amino Acid Compound-Specific Isotopic Analyses.}, journal = {Microbial ecology}, volume = {79}, number = {2}, pages = {495-510}, pmid = {31312870}, issn = {1432-184X}, support = {NA14OAR4170071//Hawai'i Sea Grant, University of Hawai'i/ ; }, mesh = {Amino Acids/chemistry/*metabolism ; Animals ; Bacteria/*metabolism ; Isotopes/analysis ; Microbiota/*physiology ; Nutrients/metabolism ; Porifera/*metabolism/*microbiology ; }, abstract = {Many sponges host abundant and active microbial communities that may play a role in the uptake of dissolved organic matter (DOM) by the sponge holobiont, although the mechanism of DOM uptake and metabolism is uncertain. Bulk and compound-specific isotopic analysis of whole sponge, isolated sponge cells, and isolated symbiotic microbial cells of the shallow water tropical Pacific sponge Mycale grandis were used to elucidate the trophic relationships between the host sponge and its associated microbial community. δ[15]N and δ[13]C values of amino acids in M. grandis isolated sponge cells are not different from those of its bacterial symbionts. Consequently, there is no difference in trophic position of the sponge and its symbiotic microbes indicating that M. grandis sponge cell isolates do not display amino acid isotopic characteristics typical of metazoan feeding. Furthermore, both the isolated microbial and sponge cell fractions were characterized by a similarly high ΣV value-a measure of bacterial-re-synthesis of organic matter calculated from the sum of variance among individual δ[15]N values of trophic amino acids. These high ΣV values observed in the sponge suggest that M. grandis is not reliant on translocated photosynthate from photosymbionts or feeding on water column picoplankton, but obtains nutrition through the uptake of amino acids of bacterial origin. Our results suggest that direct assimilation of bacterially synthesized amino acids from its symbionts, either in a manner similar to translocation observed in the coral holobiont or through phagotrophic feeding, is an important if not primary pathway of amino acid acquisition for M. grandis.}, }
@article {pmid31312497, year = {2019}, author = {Pollock, FJ and Lamb, JB and van de Water, JAJM and Smith, HA and Schaffelke, B and Willis, BL and Bourne, DG}, title = {Reduced diversity and stability of coral-associated bacterial communities and suppressed immune function precedes disease onset in corals.}, journal = {Royal Society open science}, volume = {6}, number = {6}, pages = {190355}, pmid = {31312497}, issn = {2054-5703}, abstract = {Disease is an emerging threat to coral reef ecosystems worldwide, highlighting the need to understand how environmental conditions interact with coral immune function and associated microbial communities to affect holobiont health. Increased coral disease incidence on reefs adjacent to permanently moored platforms on Australia's Great Barrier Reef provided a unique case study to investigate environment-host-microbe interactions in situ. Here, we evaluate coral-associated bacterial community (16S rRNA amplicon sequencing), immune function (protein-based prophenoloxidase-activating system), and water quality parameters before, during and after a disease event. Over the course of the study, 31% of tagged colonies adjacent to platforms developed signs of white syndrome (WS), while all control colonies on a platform-free reef remained visually healthy. Corals adjacent to platforms experienced significant reductions in coral immune function. Additionally, the corals at platform sites that remained visually healthy throughout the study had reduced bacterial diversity compared to healthy colonies at the platform-free site. Interestingly, prior to the observation of macroscopic disease, corals that would develop WS had reduced bacterial diversity and significantly greater community heterogeneity between colonies compared to healthy corals at the same location. These results suggest that activities associated with offshore marine infrastructure impacts coral immunocompetence and associated bacterial community, which affects the susceptibility of corals to disease.}, }
@article {pmid31311878, year = {2019}, author = {van Opstal, EJ and Bordenstein, SR}, title = {Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps.}, journal = {mBio}, volume = {10}, number = {4}, pages = {}, pmid = {31311878}, issn = {2150-7511}, mesh = {Animals ; Biological Evolution ; Fertility ; Host Microbial Interactions ; Larva ; Longevity ; *Microbiota ; *Phylogeny ; *Quantitative Trait, Heritable ; *Symbiosis ; Wasps/*classification/*microbiology ; }, abstract = {Phylosymbiosis is defined as microbial community relationships that recapitulate the phylogeny of hosts. As evidence for phylosymbiosis rapidly accumulates in different vertebrate and invertebrate holobionts, a central question is what evolutionary forces cause this pattern. We use intra- and interspecific gut microbiota transplants to test for evidence of selective pressures that contribute to phylosymbiosis. We leverage three closely related species of the parasitoid wasp model Nasonia that recently diverged between 0.4 and 1 million years ago: N. vitripennis, N. giraulti, and N. longicornis Upon exposure of germfree larvae to heat-inactivated microbiota from intra- or interspecific larvae, we measure larval growth, pupation rate, and adult reproductive capacity. We report three key findings: (i) larval growth significantly slows when hosts receive an interspecific versus intraspecific gut microbiota, (ii) marked decreases in pupation and resulting adult survival occur from interspecific gut microbiota exposure, and (iii) adult reproductive capacities including male fertility and longevity are unaffected by early life exposure to an interspecific microbiota. Overall, these findings reveal developmental and survival costs to Nasonia upon larval exposures to interspecific microbiota and provide evidence that selective pressures on phenotypes produced by host-microbiota interactions may underpin phylosymbiosis.IMPORTANCE Phylosymbiosis is an ecoevolutionary hypothesis and emerging pattern in animal-microbiota studies whereby the host phylogenetic relationships parallel the community relationships of the host-associated microbiota. A central prediction of phylosymbiosis is that closely related hosts exhibit a lower microbiota beta diversity than distantly related hosts. While phylosymbiosis has emerged as a widespread trend in a field often challenged to find trends across systems, two critical and understudied questions are whether or not phylosymbiosis is consequential to host biology and if adaptive evolutionary forces underpin the pattern. Here, using germfree rearing in the phylosymbiosis model Nasonia, we demonstrate that early life exposure to heat-inactivated microbiota from more distantly related species poses more severe developmental and survival costs than microbiota from closely related or the same species. This study advances a functional understanding of the consequences and potential selective pressures underpinning phylosymbiosis.}, }
@article {pmid31311470, year = {2019}, author = {McIlroy, SE and Thompson, PD and Yuan, FL and Bonebrake, TC and Baker, DM}, title = {Subtropical thermal variation supports persistence of corals but limits productivity of coral reefs.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1907}, pages = {20190882}, pmid = {31311470}, issn = {1471-2954}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/physiology ; *Climate Change ; *Coral Reefs ; Hong Kong ; Hot Temperature ; Models, Biological ; Species Specificity ; }, abstract = {Concomitant to the decline of tropical corals caused by increasing global sea temperatures is the potential removal of barriers to species range expansions into subtropical and temperate habitats. In these habitats, species must tolerate lower annual mean temperature, wider annual temperature ranges and lower minimum temperatures. To understand ecophysiological traits that will impact geographical range boundaries, we monitored populations of five coral species within a marginal habitat and used a year of in situ measures to model thermal performance of vital host, symbiont and holobiont physiology. Metabolic responses to temperature revealed two acclimatization strategies: peak productivity occurring at annual midpoint temperatures (4-6°C lower than tropical counterparts), or at annual maxima. Modelled relationships between temperature and P:R were compared to a year of daily subtropical sea temperatures and revealed that the relatively short time spent at any one temperature, limited optimal performance of all strategies to approximately half the days of the year. Thus, while subtropical corals can adjust their physiology to persist through seasonal lows, seasonal variation seems to be the key factor limiting coral productivity. This constraint on rapid reef accretion within subtropical environments provides insight into the global distribution of future coral reefs and their ecosystem services.}, }
@article {pmid31301206, year = {2019}, author = {Wright, RM and Mera, H and Kenkel, CD and Nayfa, M and Bay, LK and Matz, MV}, title = {Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors.}, journal = {Global change biology}, volume = {25}, number = {10}, pages = {3294-3304}, doi = {10.1111/gcb.14764}, pmid = {31301206}, issn = {1365-2486}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; Hydrogen-Ion Concentration ; Seawater ; }, abstract = {Climate change threatens organisms in a variety of interactive ways that requires simultaneous adaptation of multiple traits. Predicting evolutionary responses requires an understanding of the potential for interactions among stressors and the genetic variance and covariance among fitness-related traits that may reinforce or constrain an adaptive response. Here we investigate the capacity of Acropora millepora, a reef-building coral, to adapt to multiple environmental stressors: rising sea surface temperature, ocean acidification, and increased prevalence of infectious diseases. We measured growth rates (weight gain), coral color (a proxy for Symbiodiniaceae density), and survival, in addition to nine physiological indicators of coral and algal health in 40 coral genets exposed to each of these three stressors singly and combined. Individual stressors resulted in predicted responses (e.g., corals developed lesions after bacterial challenge and bleached under thermal stress). However, corals did not suffer substantially more when all three stressors were combined. Nor were trade-offs observed between tolerances to different stressors; instead, individuals performing well under one stressor also tended to perform well under every other stressor. An analysis of genetic correlations between traits revealed positive covariances, suggesting that selection to multiple stressors will reinforce rather than constrain the simultaneous evolution of traits related to holobiont health (e.g., weight gain and algal density). These findings support the potential for rapid coral adaptation under climate change and emphasize the importance of accounting for corals' adaptive capacity when predicting the future of coral reefs.}, }
@article {pmid31300639, year = {2019}, author = {Ziegler, M and Grupstra, CGB and Barreto, MM and Eaton, M and BaOmar, J and Zubier, K and Al-Sofyani, A and Turki, AJ and Ormond, R and Voolstra, CR}, title = {Coral bacterial community structure responds to environmental change in a host-specific manner.}, journal = {Nature communications}, volume = {10}, number = {1}, pages = {3092}, pmid = {31300639}, issn = {2041-1723}, support = {Baseline Funds//King Abdullah University of Science and Technology (KAUST)/International ; }, mesh = {Acclimatization/*physiology ; Animals ; Anthozoa/*microbiology/*physiology ; Bacterial Translocation/*physiology ; Coral Reefs ; Host Microbial Interactions/*physiology ; Microbiota/*physiology ; Symbiosis ; }, abstract = {The global decline of coral reefs heightens the need to understand how corals respond to changing environmental conditions. Corals are metaorganisms, so-called holobionts, and restructuring of the associated bacterial community has been suggested as a means of holobiont adaptation. However, the potential for restructuring of bacterial communities across coral species in different environments has not been systematically investigated. Here we show that bacterial community structure responds in a coral host-specific manner upon cross-transplantation between reef sites with differing levels of anthropogenic impact. The coral Acropora hemprichii harbors a highly flexible microbiome that differs between each level of anthropogenic impact to which the corals had been transplanted. In contrast, the microbiome of the coral Pocillopora verrucosa remains remarkably stable. Interestingly, upon cross-transplantation to unaffected sites, we find that microbiomes become indistinguishable from back-transplanted controls, suggesting the ability of microbiomes to recover. It remains unclear whether differences to associate with bacteria flexibly reflects different holobiont adaptation mechanisms to respond to environmental change.}, }
@article {pmid31297102, year = {2019}, author = {Zhang, Z and Yang, J and Feng, Q and Chen, B and Li, M and Liang, C and Li, M and Li, Z and Xu, Q and Zhang, L and Chen, W}, title = {Compositional and Functional Analysis of the Microbiome in Tissue and Saliva of Oral Squamous Cell Carcinoma.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1439}, pmid = {31297102}, issn = {1664-302X}, abstract = {Oral squamous cell carcinoma (OSCC) is affected by the interaction between oral pathogen and holobionts, or the combination of the host and its microbial communities. Studies have indicated the structure and feature of the microbiome in OSCC tissue and saliva, the relationships between microbiota and OSCC sites, stages remain unclear. In the present study, OSCC tissue (T), saliva (S) and mouthwash (W) samples were collected from the same subjects and carried out the microbiome study by 16S sequencing. The results showed the T group was significantly different from the S and W groups with the character of lower richness and diversity. Proteobacteria were most enriched in the T group at the phylum level, while Firmicutes were predominant in groups S and W. At the genus level, the predominant taxa of group T were Acinetobacter and Fusobacterium, and for group S and W, the predominant taxa were Streptococcus and Prevotella. The genera related to late stage tumors were Acinetobacter and Fusobacterium, suggesting microbiota may be implicated in OSCC developing. Both compositional and functional analyses indicated that microbes in tumor tissue were potential indicator for the initiation and development of OSCC.}, }
@article {pmid31288964, year = {2019}, author = {Uroz, S and Courty, PE and Oger, P}, title = {Plant Symbionts Are Engineers of the Plant-Associated Microbiome.}, journal = {Trends in plant science}, volume = {24}, number = {10}, pages = {905-916}, doi = {10.1016/j.tplants.2019.06.008}, pmid = {31288964}, issn = {1878-4372}, mesh = {Biological Evolution ; *Microbiota ; Plant Development ; Plants ; Symbiosis ; }, abstract = {Plants interact throughout their lives with environmental microorganisms. These interactions determine plant development, nutrition, and fitness in a dynamic and stressful environment, forming the basis for the holobiont concept in which plants and plant-associated microbes are not considered as independent entities but as a single evolutionary unit. A primary open question concerns whether holobiont structure is shaped by its microbial members or solely by the plant. Current knowledge of plant-microbe interactions argues that the establishment of symbiosis directly and indirectly conditions the plant-associated microbiome. We propose to define the impact of the symbiont on the plant microbiome as the 'symbiosis cascade effect', in which the symbionts and their plant host jointly shape the plant microbiome.}, }
@article {pmid31285574, year = {2019}, author = {Björk, JR and Díez-Vives, C and Astudillo-García, C and Archie, EA and Montoya, JM}, title = {Vertical transmission of sponge microbiota is inconsistent and unfaithful.}, journal = {Nature ecology &amp; evolution}, volume = {3}, number = {8}, pages = {1172-1183}, pmid = {31285574}, issn = {2397-334X}, support = {726176/ERC_/European Research Council/International ; }, mesh = {Animals ; Bacteria ; Biodiversity ; *Microbiota ; Phylogeny ; *Porifera ; }, abstract = {Co-evolutionary theory predicts that if beneficial microbial symbionts improve host fitness, they should be faithfully transmitted to offspring. More recently, the hologenome theory of evolution predicts resemblance between parent and offspring microbiomes and high partner fidelity between host species and their vertically transmitted microbes. Here, we test these ideas in multiple coexisting host species with highly diverse microbiota, leveraging known parent-offspring pairs sampled from eight species of wild marine sponges (Porifera). We found that the processes governing vertical transmission were both neutral and selective. A neutral model was a better fit to larval (R[2] = 0.66) than to the adult microbiota (R[2] = 0.27), suggesting that the importance of non-neutral processes increases as the sponge host matures. Microbes that are enriched above neutral expectations in adults were disproportionately transferred to offspring. Patterns of vertical transmission were, however, incomplete: larval sponges shared, on average, 44.8% of microbes with their parents, which was not higher than the fraction they shared with nearby non-parental adults. Vertical transmission was also inconsistent across siblings, as larval sponges from the same parent shared only 17% of microbes. Finally, we found no evidence that vertically transmitted microbes are faithful to a single sponge host species. Surprisingly, larvae were as likely to share vertically transmitted microbes with larvae from other sponge species as they were with their own species. Our study demonstrates that common predictions of vertical transmission that stem from species-poor systems are not necessarily true when scaling up to diverse and complex microbiomes.}, }
@article {pmid31283425, year = {2020}, author = {Apprill, A}, title = {The Role of Symbioses in the Adaptation and Stress Responses of Marine Organisms.}, journal = {Annual review of marine science}, volume = {12}, number = {}, pages = {291-314}, doi = {10.1146/annurev-marine-010419-010641}, pmid = {31283425}, issn = {1941-0611}, mesh = {Adaptation, Physiological/*physiology ; Animals ; Anthozoa/microbiology/parasitology ; Aquatic Organisms/*physiology ; Bacteria ; Climate Change ; Fishes/physiology ; Oceans and Seas ; Stress, Physiological/*physiology ; *Symbiosis ; }, abstract = {Ocean ecosystems are experiencing unprecedented rates of climate and anthropogenic change, which can often initiate stress in marine organisms. Symbioses, or associations between different organisms, are plentiful in the ocean and could play a significant role in facilitating organismal adaptations to stressful ocean conditions. This article reviews current knowledge about the role of symbiosis in marine organismal acclimation and adaptation. It discusses stress and adaptations in symbioses from coral reef ecosystems, which are among the most affected environments in the ocean, including the relationships between corals and microalgae, corals and bacteria, anemones and clownfish, and cleaner fish and client fish. Despite the importance of this subject, knowledge of how marine organisms adapt to stress is still limited, and there are vast opportunities for research and technological development in this area. Attention to this subject will enhance our understanding of the capacity of symbioses to alleviate organismal stress in the oceans.}, }
@article {pmid31203761, year = {2019}, author = {Jurriaans, S and Hoogenboom, MO}, title = {Thermal performance of scleractinian corals along a latitudinal gradient on the Great Barrier Reef.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {374}, number = {1778}, pages = {20180546}, pmid = {31203761}, issn = {1471-2970}, mesh = {Acclimatization ; Animals ; Anthozoa/growth &amp; development/*physiology ; Climate Change ; Coral Reefs ; Electron Transport ; Photosynthesis ; Respiration ; Seasons ; Seawater/chemistry ; Symbiosis ; Temperature ; }, abstract = {Species have evolved different mechanisms to cope with spatial and temporal temperature variability. Species with broad geographical distributions may be thermal generalists that perform well across a broad range of temperatures, or they might contain subpopulations of locally adapted thermal specialists. We quantified the variation in thermal performance of two coral species, Porites cylindrica and Acropora spp., along a latitudinal gradient over which temperature varies by approximately 6°C. Photosynthesis rates, respiration rates, maximum quantum yield and maximum electron transport rates were measured on coral fragments exposed to an acute temperature increase and decrease up to 5°C above and below the local average temperature. Results showed geographical variation in the performance curves of both species at holobiont and symbiont level, but this did not lead to an alignment of the optimal temperature for performance with the average temperature of the local environment, suggesting suboptimal coral performance of these coral populations in summer. Furthermore, symbiont thermal performance generally had an optimum closer to the average environmental temperature than holobiont performance, suggesting that symbionts have a higher capacity for acclimatization than the coral host, and can aid the coral host when temperatures are unfavourable. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.}, }
@article {pmid31190278, year = {2019}, author = {Lee, SJ and Morse, D and Hijri, M}, title = {Holobiont chronobiology: mycorrhiza may be a key to linking aboveground and underground rhythms.}, journal = {Mycorrhiza}, volume = {29}, number = {5}, pages = {403-412}, pmid = {31190278}, issn = {1432-1890}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Microbiota/*physiology ; Mycorrhizae/*physiology ; *Plant Physiological Phenomena ; Symbiosis/*physiology ; }, abstract = {Circadian clocks are nearly ubiquitous timing mechanisms that can orchestrate rhythmic behavior and gene expression in a wide range of organisms. Clock mechanisms are becoming well understood in fungal, animal, and plant model systems, yet many of these organisms are surrounded by a complex and diverse microbiota which should be taken into account when examining their biology. Of particular interest are the symbiotic relationships between organisms that have coevolved over time, forming a unit called a holobiont. Several studies have now shown linkages between the circadian rhythms of symbiotic partners. Interrelated regulation of holobiont circadian rhythms seems thus important to coordinate shifts in activity over the day for all the partners. Therefore, we suggest that the classical view of "chronobiological individuals" should include "a holobiont" rather than an organism. Unfortunately, mechanisms that may regulate interspecies temporal acclimation and the evolution of the circadian clock in holobionts are far from being understood. For the plant holobiont, our understanding is particularly limited. In this case, the holobiont encompasses two different ecosystems, one above and the other below the ground, with the two potentially receiving timing information from different synchronizing signals (Zeitgebers). The arbuscular mycorrhizal (AM) symbiosis, formed by plant roots and fungi, is one of the oldest and most widespread associations between organisms. By mediating the nutritional flux between the plant and the many microbes in the soil, AM symbiosis constitutes the backbone of the plant holobiont. Even though the importance of the AM symbiosis has been well recognized in agricultural and environmental sciences, its circadian chronobiology remains almost completely unknown. We have begun to study the circadian clock of arbuscular mycorrhizal fungi, and we compile and here discuss the available information on the subject. We propose that analyzing the interrelated temporal organization of the AM symbiosis and determining its underlying mechanisms will advance our understanding of the role and coordination of circadian clocks in holobionts in general.}, }
@article {pmid31187114, year = {2019}, author = {Feng, G and Zhang, F and Banakar, S and Karlep, L and Li, Z}, title = {Analysis of functional gene transcripts suggests active CO2 assimilation and CO oxidation by diverse bacteria in marine sponges.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {7}, pages = {}, doi = {10.1093/femsec/fiz087}, pmid = {31187114}, issn = {1574-6941}, mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; Bacterial Proteins/*genetics ; Carbon/metabolism ; Carbon Dioxide/*metabolism ; Carbon Monoxide/*metabolism ; Host Specificity ; Oxidation-Reduction ; Phylogeny ; Porifera/classification/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Transcription, Genetic ; }, abstract = {Bacteria are the dominant symbionts in sponges and are regarded as important contributors to ocean nutrient cycling; however, their roles in carbon utilization in sponge holobionts are seldom identified. Here, the in situ active bacteria and their CO2 assimilation and CO oxidation functions in sponges Theonella swinhoei, Plakortis simplex and Phakellia fusca were evaluated using the analysis of functional gene transcripts. Phylogenetically diverse bacteria belonging to 16 phyla were detected by 16S rRNA analysis. Particularly, some of the active bacteria appeared to be sponge-specific or even sponge species-specific. Transcribed autotrophic CO2 assimilation genes rbcL and rbcM, anaplerotic CO2 assimilation gene accC and aerobic CO oxidation gene coxL were uncovered and assigned to a wide variety of bacterial lineages. Some of these carbon metabolism genes showed specificity to sponge species or different transcriptional activity among the sponge species. This study uncovered the phylogenetic diversity of transcriptionally active bacteria especially with CO2 assimilation or CO oxidation functions, providing insights into the ecological functions of the sponge-symbiotic bacteria regarding carbon metabolism.}, }
@article {pmid31182168, year = {2019}, author = {Kellogg, CA}, title = {Microbiomes of stony and soft deep-sea corals share rare core bacteria.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {90}, pmid = {31182168}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/classification/*microbiology ; Bacteria/*classification ; Biodiversity ; Conserved Sequence ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {BACKGROUND: Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved "core microbiomes" of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis.<br><br>RESULTS: Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians.<br><br>CONCLUSIONS: Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts' phylogeny.}, }
@article {pmid31168761, year = {2019}, author = {Thapa, S and Li, H and OHair, J and Bhatti, S and Chen, FC and Nasr, KA and Johnson, T and Zhou, S}, title = {Biochemical Characteristics of Microbial Enzymes and Their Significance from Industrial Perspectives.}, journal = {Molecular biotechnology}, volume = {61}, number = {8}, pages = {579-601}, pmid = {31168761}, issn = {1559-0305}, mesh = {*Bacterial Proteins ; DNA, Recombinant/genetics/metabolism ; *Enzymes ; *Fungal Proteins ; *Industrial Microbiology ; *Metabolic Engineering ; }, abstract = {Microbes are ubiquitously distributed in nature and are a critical part of the holobiont fitness. They are perceived as the most potential biochemical reservoir of inordinately diverse and multi-functional enzymes. The robust nature of the microbial enzymes with thermostability, pH stability and multi-functionality make them potential candidates for the efficient biotechnological processes under diverse physio-chemical conditions. The need for sustainable solutions to various environmental challenges has further surged the demand for industrial enzymes. Fueled by the recent advent of recombinant DNA technology, genetic engineering, and high-throughput sequencing and omics techniques, numerous microbial enzymes have been developed and further exploited for various industrial and therapeutic applications. Most of the hydrolytic enzymes (protease being the dominant hydrolytic enzyme) have broad range of industrial uses such as food and feed processing, polymer synthesis, production of pharmaceuticals, manufactures of detergents, paper and textiles, and bio-fuel refinery. In this review article, after a short overview of microbial enzymes, an approach has been made to highlight and discuss their potential relevance in biotechnological applications and industrial bio-processes, significant biochemical characteristics of the microbial enzymes, and various tools that are revitalizing the novel enzymes discovery.}, }
@article {pmid31157928, year = {2019}, author = {Finlay, BB and Pettersson, S and Melby, MK and Bosch, TCG}, title = {The Microbiome Mediates Environmental Effects on Aging.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {10}, pages = {e1800257}, doi = {10.1002/bies.201800257}, pmid = {31157928}, issn = {1521-1878}, support = {//CIHR/Canada ; }, mesh = {*Aging ; Animals ; Diet ; Humans ; *Microbiota ; }, abstract = {Humans' indigenous microbes strongly influence organ functions in an age- and diet-dependent manner, adding an important dimension to aging biology that remains poorly understood. Although age-related differences in the gut microbiota composition correlate with age-related loss of organ function and diseases, including inflammation and frailty, variation exists among the elderly, especially centenarians and people living in areas of extreme longevity. Studies using short-lived as well as nonsenescent model organisms provide surprising functional insights into factors affecting aging and implicate attenuating effects of microbes as well as a crucial role for certain transcription factors like forkhead box O. The unexpected beneficial effects of microbes on aged animals imply an even more complex interplay between the gut microbiome and the host. The microbiome constitutes the major interface between humans and the environment, is influenced by biosocial stressors and behaviors, and mediates effects on health and aging processes, while being moderated by sex and developmental stages.}, }
@article {pmid31139158, year = {2019}, author = {Ahmed, HI and Herrera, M and Liew, YJ and Aranda, M}, title = {Long-Term Temperature Stress in the Coral Model Aiptasia Supports the "Anna Karenina Principle" for Bacterial Microbiomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {975}, pmid = {31139158}, issn = {1664-302X}, abstract = {The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.}, }
@article {pmid31132110, year = {2019}, author = {Hammer, TJ and Sanders, JG and Fierer, N}, title = {Not all animals need a microbiome.}, journal = {FEMS microbiology letters}, volume = {366}, number = {10}, pages = {}, doi = {10.1093/femsle/fnz117}, pmid = {31132110}, issn = {1574-6968}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {It is often taken for granted that all animals host and depend upon a microbiome, yet this has only been shown for a small proportion of species. We propose that animals span a continuum of reliance on microbial symbionts. At one end are the famously symbiont-dependent species such as aphids, humans, corals and cows, in which microbes are abundant and important to host fitness. In the middle are species that may tolerate some microbial colonization but are only minimally or facultatively dependent. At the other end are species that lack beneficial symbionts altogether. While their existence may seem improbable, animals are capable of limiting microbial growth in and on their bodies, and a microbially independent lifestyle may be favored by selection under some circumstances. There is already evidence for several 'microbiome-free' lineages that represent distantly related branches in the animal phylogeny. We discuss why these animals have received such little attention, highlighting the potential for contaminants, transients, and parasites to masquerade as beneficial symbionts. We also suggest ways to explore microbiomes that address the limitations of DNA sequencing. We call for further research on microbiome-free taxa to provide a more complete understanding of the ecology and evolution of macrobe-microbe interactions.}, }
@article {pmid31128651, year = {2019}, author = {Horváthová, T and Babik, W and Kozłowski, J and Bauchinger, U}, title = {Vanishing benefits - The loss of actinobacterial symbionts at elevated temperatures.}, journal = {Journal of thermal biology}, volume = {82}, number = {}, pages = {222-228}, doi = {10.1016/j.jtherbio.2019.04.015}, pmid = {31128651}, issn = {0306-4565}, mesh = {Actinobacteria/genetics/*physiology ; Animals ; Hot Temperature ; Isopoda/*microbiology/physiology ; Oxygen/metabolism ; RNA, Ribosomal, 16S/genetics ; *Symbiosis ; Temperature ; }, abstract = {Only a few insect species are known to engage in symbiotic associations with antibiotic-producing Actinobacteria and profit from this kind of protection against pathogens. However, it still remains elusive how widespread the symbiotic interactions with Actinobacteria in other organisms are and how these partnerships benefit the hosts in terms of the growth and survival. We characterized a drastic temperature-induced change in the occurrence of Actinobacteria in the gut of the terrestrial isopod Porcellio scaber reared under two different temperature (15 °C and 22 °C) and oxygen conditions (10% and 22% O2) using 16S rRNA gene sequencing. We show that the relative abundance of actinobacterial gut symbionts correlates with increased host growth at lower temperature. Actinobacterial symbionts were almost completely absent at 22 °C under both high and low oxygen conditions. In addition, we identified members of nearly half of the known actinobacterial families in the isopod microbiome, and most of these include members that are known to produce antibiotics. Our study suggests that hosting diverse actinobacterial symbionts may provide conditions favorable for host growth. These findings show how a temperature-driven decline in microbiome diversity may cause a loss of beneficial functions with negative effects on ectotherms.}, }
@article {pmid31121908, year = {2019}, author = {Sartor, F and Eelderink-Chen, Z and Aronson, B and Bosman, J and Hibbert, LE and Dodd, AN and Kovács, &#xc1;T and Merrow, M}, title = {Are There Circadian Clocks in Non-Photosynthetic Bacteria?.}, journal = {Biology}, volume = {8}, number = {2}, pages = {}, pmid = {31121908}, issn = {2079-7737}, abstract = {Circadian clocks in plants, animals, fungi, and in photosynthetic bacteria have been well-described. Observations of circadian rhythms in non-photosynthetic Eubacteria have been sporadic, and the molecular basis for these potential rhythms remains unclear. Here, we present the published experimental and bioinformatical evidence for circadian rhythms in these non-photosynthetic Eubacteria. From this, we suggest that the timekeeping functions of these organisms will be best observed and studied in their appropriate complex environments. Given the rich temporal changes that exist in these environments, it is proposed that microorganisms both adapt to and contribute to these daily dynamics through the process of temporal mutualism. Understanding the timekeeping and temporal interactions within these systems will enable a deeper understanding of circadian clocks and temporal programs and provide valuable insights for medicine and agriculture.}, }
@article {pmid31099411, year = {2019}, author = {Bosch, TCG and Guillemin, K and McFall-Ngai, M}, title = {Evolutionary "Experiments" in Symbiosis: The Study of Model Animals Provides Insights into the Mechanisms Underlying the Diversity of Host-Microbe Interactions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {10}, pages = {e1800256}, pmid = {31099411}, issn = {1521-1878}, support = {P01 GM125576/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Biological Evolution ; Disease Models, Animal ; *Host Microbial Interactions ; *Microbiota ; *Symbiosis ; }, abstract = {Current work in experimental biology revolves around a handful of animal species. Studying only a few organisms limits science to the answers that those organisms can provide. Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host-microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host-microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease.}, }
@article {pmid31088923, year = {2019}, author = {Lachnit, T and Bosch, TCG and Deines, P}, title = {Exposure of the Host-Associated Microbiome to Nutrient-Rich Conditions May Lead to Dysbiosis and Disease Development-an Evolutionary Perspective.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31088923}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; Diet, Western/adverse effects ; Dysbiosis/*etiology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Inflammation/etiology ; Inflammatory Bowel Diseases/etiology ; Mice ; Nutrients/adverse effects/*pharmacology ; }, abstract = {Inflammatory diseases, such as inflammatory bowel diseases, are dramatically increasing worldwide, but an understanding of the underlying factors is lacking. We here present an ecoevolutionary perspective on the emergence of inflammatory diseases. We propose that adaptation has led to fine-tuned host-microbe interactions, which are maintained by secreted host metabolites nourishing the associated microbes. A constant elevation of nutrients in the gut environment leads to an increased activity and changed functionality of the microbiota, thus severely disturbing host-microbe interactions and leading to dysbiosis and disease development. In the past, starvation and pathogen infections, causing diarrhea, were common incidences that reset the gut bacterial community to its "human-specific-baseline." However, these natural clearing mechanisms have been virtually eradicated in developed countries, allowing a constant uncontrolled growth of bacteria. This leads to an increase of bacterial products that stimulate the immune system and ultimately might initiate inflammatory reactions.}, }
@article {pmid31056303, year = {2019}, author = {van der Loos, LM and Eriksson, BK and Falcão Salles, J}, title = {The Macroalgal Holobiont in a Changing Sea.}, journal = {Trends in microbiology}, volume = {27}, number = {7}, pages = {635-650}, doi = {10.1016/j.tim.2019.03.002}, pmid = {31056303}, issn = {1878-4380}, mesh = {Biodiversity ; Climate Change ; Ecosystem ; Environment ; Host-Pathogen Interactions ; *Microbiota ; Oceans and Seas ; *Seaweed ; *Water Microbiology ; }, abstract = {When studying the effects of climate change on eukaryotic organisms we often oversee a major ecological process: the interaction with microbes. Eukaryotic hosts and microbes form functional units, termed holobionts, where microbes play crucial roles in host functioning. Environmental stress may disturb these complex mutualistic relations. Macroalgae form the foundation of coastal ecosystems worldwide and provide important ecosystem services - services they could likely not provide without their microbial associates. Still, today we do not know how environmental stress will affect the macroalgal holobiont in an increasingly changing ocean. In this review, we provide a conceptual framework that contributes to understanding the different levels at which the holobiont and environment interact, and we suggest a manipulative experimental approach as a guideline for future research.}, }
@article {pmid31050668, year = {2019}, author = {Melo-Bolívar, JF and Ruiz Pardo, RY and Hume, ME and Nisbet, DJ and Rodríguez-Villamizar, F and Alzate, JF and Junca, H and Villamil Díaz, LM}, title = {Establishment and characterization of a competitive exclusion bacterial culture derived from Nile tilapia (Oreochromis niloticus) gut microbiomes showing antibacterial activity against pathogenic Streptococcus agalactiae.}, journal = {PloS one}, volume = {14}, number = {5}, pages = {e0215375}, pmid = {31050668}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*classification/isolation &amp; purification ; Bacterial Load ; Bacteriological Techniques ; Cichlids/*microbiology ; Colombia ; Fusobacteria/isolation &amp; purification/physiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/*veterinary ; Lactococcus/isolation &amp; purification/physiology ; Microbial Viability ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus agalactiae/*growth &amp; development ; }, abstract = {This study reports the characterization of the microbial community composition, and the establishment and dynamics of a continuous-flow competitive exclusion culture (CFCEC) derived from gut microbiomes of Nile tilapia (Oreochromis niloticus) specimens reared on aquaculture farms in Colombia. 16S rRNA gene amplicon Illumina sequencing was used to identify taxonomical changes in the CFCEC microbial community over time. The CFCEC was developed from adult tilapia from two farms in Colombia, and CFCEC samples were collected over two months. The pH varied from 6.25 to 6.35 throughout culturing, while anaerobic and aerobic cell counts stabilized at day 9, at 109 CFU mL-1 and were maintained to day 68. A variation in the CFCEC bacterial composition was observed over time. Cetobacterium was the most abundant in the first two days and coincided with a higher CFCEC supernatant antimicrobial effect against the fish pathogen Streptococcus agalactiae. Antimicrobial activity against S. agalactiae disappeared by day 3. Changes in bacterial composition continued to day 33 with Lactococcus spp. becoming the most abundant member of the community. In conclusion, the study of the CFCEC from intestinal tract of Nile tilapia (Oreochromis niloticus) by 16S rRNA gene sequencing allowed identification of predominant bacterial genera in the continuous-flow competitive exclusion culture exhibiting antibacterial activity against the fish pathogen Streptococcus agalactiae.}, }
@article {pmid31024496, year = {2019}, author = {Morrissey, KL and Çavaş, L and Willems, A and De Clerck, O}, title = {Disentangling the Influence of Environment, Host Specificity and Thallus Differentiation on Bacterial Communities in Siphonous Green Seaweeds.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {717}, pmid = {31024496}, issn = {1664-302X}, abstract = {Siphonous green seaweeds, such as Caulerpa, are among the most morphologically complex algae with differentiated algal structures (morphological niches). Caulerpa is also host to a rich diversity of bacterial endo- and epibionts. The degree to which these bacterial communities are species-, or even niche-specific remains largely unknown. To address this, we investigated the diversity of bacteria associated to different morphological niches of both native and invasive species of Caulerpa from different geographic locations along the Turkish coastline of the Aegean sea. Associated bacteria were identified using the 16S rDNA marker gene for three morphological niches, such as the endobiome, epibiome, and rhizobiome. Bacterial community structure was explored and deterministic factors behind bacterial variation were investigated. Of the total variation, only 21.5% could be explained. Pronounced differences in bacterial community composition were observed and variation was partly explained by a combination of host species, biogeography and nutrient levels. The majority of the explained bacterial variation within the algal holobiont was attributed to the micro-environments established by distinct morphological niches. This study further supports the hypothesis that the bacterial assembly is largely stochastic in nature and bacterial community structure is most likely linked to functional genes rather than taxonomy.}, }
@article {pmid31015561, year = {2019}, author = {Ye, S and Badhiwala, KN and Robinson, JT and Cho, WH and Siemann, E}, title = {Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {2058-2067}, pmid = {31015561}, issn = {1751-7370}, mesh = {*Acclimatization ; Animals ; Chlorophyta/*physiology ; Cnidaria/*physiology ; Coral Reefs ; Ecosystem ; Food ; Fresh Water ; Hot Temperature ; Hydra/*physiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {Understanding factors affecting the susceptibility of organisms to thermal stress is of enormous interest in light of our rapidly changing climate. When adaptation is limited, thermal acclimation and deacclimation abilities of organisms are critical for population persistence through a period of thermal stress. Holobionts (hosts plus associated symbionts) are key components of various ecosystems, such as coral reefs, yet the contributions of their two partners to holobiont thermal plasticity are poorly understood. Here, we tested thermal plasticity of the freshwater cnidarian Hydra viridissima (green hydra) using individual behavior and population responses. We found that algal presence initially reduced hydra thermal tolerance. Hydra with algae (symbiotic hydra) had comparable acclimation rates, deacclimation rates, and thermal tolerance after acclimation to those without algae (aposymbiotic hydra) but they had higher acclimation capacity. Acclimation of the host (hydra) and/or symbiont (algae) to elevated temperatures increased holobiont thermal tolerance and these effects persisted for multiple asexual generations. In addition, acclimated algae presence enhanced hydra fitness under prolonged sublethal thermal stress, especially when food was limited. Our study indicates while less intense but sublethal stress may favor symbiotic organisms by allowing them to acclimate, sudden large, potentially lethal fluctuations in climate stress likely favor aposymbiotic organisms. It also suggests that thermally stressed colonies of holobionts could disperse acclimated hosts and/or symbionts to other colonies, thereby reducing their vulnerability to climate change.}, }
@article {pmid30994455, year = {2019}, author = {Inkpen, SA}, title = {Health, ecology and the microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30994455}, issn = {2050-084X}, mesh = {*Ecosystem ; *Health ; *Host Microbial Interactions ; Humans ; *Microbiota ; }, abstract = {Advances in microbiomics have changed the way in which many researchers think about health and disease. These changes have also raised a number of philosophical questions around these topics, such as the types of living systems to which these concepts can be applied. Here, I discuss the human microbiome from two perspectives: the first treats the microbiome as part of a larger system that includes the human; the second treats the microbiome as an independent ecosystem that provides services to humans. Drawing on the philosophy of medicine and ecology, I explore two questions: i) how can we make sense of disease and dysfunction in these two perspectives? ii) are these two perspectives complimentary or do they compete with each other?}, }
@article {pmid30979392, year = {2019}, author = {Jaspers, C and Fraune, S and Arnold, AE and Miller, DJ and Bosch, TCG and Voolstra, CR and , }, title = {Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches.}, journal = {Zoology (Jena, Germany)}, volume = {133}, number = {}, pages = {81-87}, doi = {10.1016/j.zool.2019.02.007}, pmid = {30979392}, issn = {1873-2720}, mesh = {Animals ; *Microbiota ; Symbiosis ; }, abstract = {Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.}, }
@article {pmid30978547, year = {2019}, author = {Munzi, S and Cruz, C and Corrêa, A}, title = {When the exception becomes the rule: An integrative approach to symbiosis.}, journal = {The Science of the total environment}, volume = {672}, number = {}, pages = {855-861}, doi = {10.1016/j.scitotenv.2019.04.038}, pmid = {30978547}, issn = {1879-1026}, mesh = {Animals ; Anthozoa/microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {Symbiosis, mainly due to the advances in -omics technology and to the microbiome revolution, is being increasingly acknowledged as fundamental to explain any aspect of life existence. Previously considered an exception, a peculiar characteristic of few systems like lichens, corals and mycorrhizas, symbiosis is nowadays recognized as the rule, with the microbiome being part of all living entities and systems. However, our knowledge of the ecological meaning and functioning of many symbiotic systems is still limited. Here, we discuss a new, integrative approach based on current findings that looks at commonalities among symbiotic systems to produce theoretical models and conceptual knowledge that would allow a more efficient exploitation of symbiosis-based biotechnologies. The microbiome recruitment and assemblage processes are indicated as one of the potential targets where a holistic approach could bring advantages. Finally, we reflect on the potential socio-economic and environmental consequences of a symbiotic view of the world, where co-dependence is the matrix of life.}, }
@article {pmid30972043, year = {2019}, author = {Mills, JG and Brookes, JD and Gellie, NJC and Liddicoat, C and Lowe, AJ and Sydnor, HR and Thomas, T and Weinstein, P and Weyrich, LS and Breed, MF}, title = {Relating Urban Biodiversity to Human Health With the 'Holobiont' Concept.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {550}, pmid = {30972043}, issn = {1664-302X}, abstract = {A relatively unaccounted ecosystem service from biodiversity is the benefit to human health via symbiotic microbiota from our environment. This benefit occurs because humans evolved alongside microbes and have been constantly exposed to diverse microbiota. Plants and animals, including humans, are organised as a host with symbiotic microbiota, whose collective genome and life history form a single holobiont. As such, there are interdependencies between biodiversity, holobionts, and public health which lead us to argue that human health outcomes could be improved by increasing contact with biodiversity in an urban context. We propose that humans, like all holobionts, likely require a diverse microbial habitat to appropriate resources for living healthy, long lives. We discuss how industrial urbanisation likely disrupts the symbiosis between microbiota and their hosts, leading to negative health outcomes. The industrialised urban habitat is low in macro and microbial biodiversity and discourages contact with beneficial environmental microbiota. These habitat factors, alongside diet, antibiotics, and others, are associated with the epidemic of non-communicable diseases in these societies. We suggest that restoration of urban microbial biodiversity and micro-ecological processes through microbiome rewilding can benefit holobiont health and aid in treating the urban non-communicable disease epidemic. Further, we identify research gaps and some solutions to economic and strategic hurdles in applying microbiome rewilding into daily urban life.}, }
@article {pmid30968206, year = {2019}, author = {de Oliveira, BFR and Cavalcanti, MD and de Oliveira Nunes, S and Lobo, LA and Domingues, RMCP and Muricy, G and Laport, MS}, title = {Paraclostridium is the Main Genus of Anaerobic Bacteria Isolated from New Species of the Marine Sponge Plakina in the Brazilian Southeast Coast.}, journal = {Current microbiology}, volume = {76}, number = {6}, pages = {713-722}, pmid = {30968206}, issn = {1432-0991}, support = {E-26/203.320/2017//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 23038.002486/2018-26//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior Programa de Excel&#xea;ncia Acad&#xea;mica/ ; 304477/2015-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 140840/2018-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 001//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; }, mesh = {Aerobiosis ; Anaerobiosis ; Animals ; Anti-Infective Agents/metabolism ; Aquatic Organisms/microbiology ; Atlantic Ocean ; Bacteria, Anaerobic/chemistry/*classification/genetics/*isolation &amp; purification ; Bacteriological Techniques ; Brazil ; Clostridiales/chemistry/*classification/genetics/*isolation &amp; purification ; Clostridium bifermentans ; Clostridium butyricum ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Mass Spectrometry ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Despite the broad assessment of sponge bacterial diversity through cultivation-independent and dependent strategies, the knowledge focusing on cultivable anaerobes from this holobiont is still incipient. Plakina is a genus with the highest number of described species from the smallest of poriferan classes, Homoscleromorpha. The Brazilian Atlantic coast has been presenting itself as a hotspot for the discovery of new plakinidae species, with initial surveys just now concerning to characterize their microbiome. The current study aimed to isolate and identify strict anaerobes from recently described species of Plakina collected at the coast of Cabo Frio, RJ. Samples of four sympatric morphotypes of Plakina cyanorosea and Plakina cabofriense were collected on the coast of Cabo Frio, RJ. Using five different culture media, a total of 93 bacterial isolates were recovered, among which 60 were strict anaerobes and, ultimately, 34 remaining viable. A total of 76.5% from these strains were mostly identified as Clostridium bifermentans by mass spectrometry and 82.4% identified by 16S rRNA sequencing, almost all of them affiliated to the genus Paraclostridium, and with one isolate identified as Clostridium butyricum by both techniques. None of the anaerobic bacteria exhibited antimicrobial activity by the adopted screening test. The present work highlights not only the need for cultivation and characterization of the anaerobic microbiota from marine sponges but also adds the existing scarce knowledge of culturable bacterial communities from Homoscleromorph sponges from Brazilian coast.}, }
@article {pmid30963929, year = {2019}, author = {Qiu, Z and Coleman, MA and Provost, E and Campbell, AH and Kelaher, BP and Dalton, SJ and Thomas, T and Steinberg, PD and Marzinelli, EM}, title = {Future climate change is predicted to affect the microbiome and condition of habitat-forming kelp.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1896}, pages = {20181887}, pmid = {30963929}, issn = {1471-2954}, mesh = {*Climate Change ; Ecosystem ; Global Warming ; Hydrogen-Ion Concentration ; Kelp/microbiology/*physiology ; *Microbiota ; Seawater/*chemistry ; }, abstract = {Climate change is driving global declines of marine habitat-forming species through physiological effects and through changes to ecological interactions, with projected trajectories for ocean warming and acidification likely to exacerbate such impacts in coming decades. Interactions between habitat-formers and their microbiomes are fundamental for host functioning and resilience, but how such relationships will change in future conditions is largely unknown. We investigated independent and interactive effects of warming and acidification on a large brown seaweed, the kelp Ecklonia radiata, and its associated microbiome in experimental mesocosms. Microbial communities were affected by warming and, during the first week, by acidification. During the second week, kelp developed disease-like symptoms previously observed in the field. The tissue of some kelp blistered, bleached and eventually degraded, particularly under the acidification treatments, affecting photosynthetic efficiency. Microbial communities differed between blistered and healthy kelp for all treatments, except for those under future conditions of warming and acidification, which after two weeks resembled assemblages associated with healthy hosts. This indicates that changes in the microbiome were not easily predictable as the severity of future climate scenarios increased. Future ocean conditions can change kelp microbiomes and may lead to host disease, with potentially cascading impacts on associated ecosystems.}, }
@article {pmid30945796, year = {2019}, author = {Paix, B and Othmani, A and Debroas, D and Culioli, G and Briand, JF}, title = {Temporal covariation of epibacterial community and surface metabolome in the Mediterranean seaweed holobiont Taonia atomaria.}, journal = {Environmental microbiology}, volume = {21}, number = {9}, pages = {3346-3363}, doi = {10.1111/1462-2920.14617}, pmid = {30945796}, issn = {1462-2920}, support = {//Ministry of Higher Education and Scientific Research/ ; }, abstract = {An integrative multi-omics approach allowed monthly variations for a year of the surface metabolome and the epibacterial community of the Mediterranean Phaeophyceae Taonia atomaria to be investigated. The LC-MS-based metabolomics and 16S rDNA metabarcoding data sets were integrated in a multivariate meta-omics analysis (multi-block PLS-DA from the MixOmic DIABLO analysis) showing a strong seasonal covariation (Mantel test: p < 0.01). A network based on positive and negative correlations between the two data sets revealed two clusters of variables, one relative to the 'spring period' and a second to the 'summer period'. The 'spring period' cluster was mainly characterized by dipeptides positively correlated with a single bacterial taxon of the Alteromonadaceae family (BD1-7 clade). Moreover, 'summer' dominant epibacterial taxa from the second cluster (including Erythrobacteraceae, Rhodospirillaceae, Oceanospirillaceae and Flammeovirgaceae) showed positive correlations with few metabolites known as macroalgal antifouling defences [e.g. dimethylsulphoniopropionate (DMSP) and proline] which exhibited a key role within the correlation network. Despite a core community that represents a significant part of the total epibacteria, changes in the microbiota structure associated with surface metabolome variations suggested that both environment and algal host shape the bacterial surface microbiota.}, }
@article {pmid30944875, year = {2019}, author = {Vannier, N and Mony, C and Bittebiere, AK and Theis, KR and Rosenberg, E and Vandenkoornhuyse, P}, title = {Clonal Plants as Meta-Holobionts.}, journal = {mSystems}, volume = {4}, number = {2}, pages = {}, pmid = {30944875}, issn = {2379-5077}, abstract = {The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all plants). Because of this heritability, and potentially reciprocal exchange of microbes between generations of ramets, we propose to extend the existing holobiont framework to the concept of meta-holobiont. A meta-holobiont is a network of holobionts that can exchange biomolecules and microbiota across generations, thus impacting the fitness of both biological scales: holobionts and meta-holobionts. Specifically, meta-holobiont dynamics can result in sharing, specialization, and division of labor across plant clonal generations. This paper, which coins the meta-holobiont concept, is expected to stimulate discussion and to be applied beyond the context of networked clonal plants (e.g., to social insects).}, }
@article {pmid30891218, year = {2019}, author = {Bayliss, SLJ and Scott, ZR and Coffroth, MA and terHorst, CP}, title = {Genetic variation in Breviolum antillogorgium, a coral reef symbiont, in response to temperature and nutrients.}, journal = {Ecology and evolution}, volume = {9}, number = {5}, pages = {2803-2813}, pmid = {30891218}, issn = {2045-7758}, abstract = {Symbionts within the family Symbiodiniaceae are important on coral reefs because they provide significant amounts of carbon to many different reef species. The breakdown of this mutualism that occurs as a result of increasingly warmer ocean temperatures is a major threat to coral reef ecosystems globally. Recombination during sexual reproduction and high rates of somatic mutation can lead to increased genetic variation within symbiont species, which may provide the fuel for natural selection and adaptation. However, few studies have asked whether such variation in functional traits exists within these symbionts. We used several genotypes of two closely related species, Breviolum antillogorgium and B. minutum, to examine variation of traits related to symbiosis in response to increases in temperature or nitrogen availability in laboratory cultures. We found significant genetic variation within and among symbiont species in chlorophyll content, photosynthetic efficiency, and growth rate. Two genotypes showed decreases in traits in response to increased temperatures predicted by climate change, but one genotype responded positively. Similarly, some genotypes within a species responded positively to high-nitrogen environments, such as those expected within hosts or eutrophication associated with global change, while other genotypes in the same species responded negatively, suggesting context-dependency in the strength of mutualism. Such variation in traits implies that there is potential for natural selection on symbionts in response to temperature and nutrients, which could confer an adaptive advantage to the holobiont.}, }
@article {pmid30883643, year = {2019}, author = {Tarquinio, F and Hyndes, GA and Laverock, B and Koenders, A and Säwström, C}, title = {The seagrass holobiont: understanding seagrass-bacteria interactions and their role in seagrass ecosystem functioning.}, journal = {FEMS microbiology letters}, volume = {366}, number = {6}, pages = {}, doi = {10.1093/femsle/fnz057}, pmid = {30883643}, issn = {1574-6968}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Ecosystem ; *Microbiota ; Plant Development ; Plant Growth Regulators/metabolism ; Plants/metabolism/*microbiology ; }, abstract = {This review shows that the presence of seagrass microbial community is critical for the development of seagrasses; from seed germination, through to phytohormone production and enhanced nutrient availability, and defence against pathogens and saprophytes. The tight seagrass-bacterial relationship highlighted in this review supports the existence of a seagrass holobiont and adds to the growing evidence for the importance of marine eukaryotic microorganisms in sustaining vital ecosystems. Incorporating a micro-scale view on seagrass ecosystems substantially expands our understanding of ecosystem functioning and may have significant implications for future seagrass management and mitigation against human disturbance.}, }
@article {pmid30868729, year = {2019}, author = {Thomashow, LS and Kwak, YS and Weller, DM}, title = {Root-associated microbes in sustainable agriculture: models, metabolites and mechanisms.}, journal = {Pest management science}, volume = {75}, number = {9}, pages = {2360-2367}, doi = {10.1002/ps.5406}, pmid = {30868729}, issn = {1526-4998}, support = {//OECD Co-operative Research Programme: Biological Resource Management for Sustainable Agricultural Systems/ ; }, mesh = {Crop Production/*methods ; Crops, Agricultural/growth &amp; development/*microbiology ; Plant Roots/*microbiology ; Rhizosphere ; *Soil Microbiology ; }, abstract = {Since the discovery of penicillin in 1928 and throughout the 'age of antibiotics' from the 1940s until the 1980s, the detection of novel antibiotics was restricted by lack of knowledge about the distribution and ecology of antibiotic producers in nature. The discovery that a phenazine compound produced by Pseudomonas bacteria could suppress soilborne plant pathogens, and its recovery from rhizosphere soil in 1990, provided the first incontrovertible evidence that natural metabolites could control plant pathogens in the environment and opened a new era in biological control by root-associated rhizobacteria. More recently, the advent of genomics, the availability of highly sensitive bioanalytical instrumentation, and the discovery of protective endophytes have accelerated progress toward overcoming many of the impediments that until now have limited the exploitation of beneficial plant-associated microbes to enhance agricultural sustainability. Here, we present key developments that have established the importance of these microbes in the control of pathogens, discuss concepts resulting from the exploration of classical model systems, and highlight advances emerging from ongoing investigations. © 2019 Society of Chemical Industry.}, }
@article {pmid30863387, year = {2019}, author = {Weigel, BL and Pfister, CA}, title = {Successional Dynamics and Seascape-Level Patterns of Microbial Communities on the Canopy-Forming Kelps Nereocystis luetkeana and Macrocystis pyrifera.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {346}, pmid = {30863387}, issn = {1664-302X}, abstract = {Canopy-forming kelps create underwater forests that are among the most productive marine ecosystems. On the Pacific coast of North America, two canopy-forming kelps with contrasting life histories co-occur; Macrocystis pyrifera, a perennial species, and Nereocystis luetkeana, an annual species. Kelp blade-associated microbes were sampled from 12 locations across a spatial gradient in Washington, United States, from the outer Pacific Coast to Puget Sound. Microbial communities were characterized using next-generation Illumina sequencing of 16S rRNA genes. At higher taxonomic levels (bacterial phylum and class), canopy-forming kelps hosted remarkably similar microbial communities, but at the amplicon sequence variant level, microbial communities on M. pyrifera and N. luetkeana were host-specific and distinct from free-living bacteria in the surrounding seawater. Microbial communities associated with blades of each kelp species displayed significant geographic variation. The microbiome of N. luetkeana changed along the spatial gradient and was significantly correlated to salinity, with outer Pacific coast sites enriched in Bacteroidetes (family Saprospiraceae) and Gammaproteobacteria (Granulosicoccus sp.), and southern Puget Sound sites enriched in Alphaproteobacteria (family Hyphomonadaceae). We also examined microbial community development and succession on meristematic and apical N. luetkeana blade tissues throughout the summer growing season on Tatoosh Island, WA. Across all dates, microbial communities were less diverse on younger, meristematic blade tissue compared to the older, apical tissues. In addition, phylogenetic relatedness among microbial taxa increased from meristematic to apical blade tissues, suggesting that the addition of microbial taxa to the community was a non-random process that selected for certain phylogenetic groups of microbes. Microbial communities on older, apical tissues displayed significant temporal variation throughout the summer and microbial taxa that were differentially abundant over time displayed clear patterns of community succession. Overall, we report that host species identity, geographic location, and blade tissue age shape the microbial communities on canopy-forming kelps.}, }
@article {pmid30830434, year = {2018}, author = {Reverter, M and Tribalat, MA and Pérez, T and Thomas, OP}, title = {Metabolome variability for two Mediterranean sponge species of the genus Haliclona: specificity, time, and space.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {14}, number = {9}, pages = {114}, pmid = {30830434}, issn = {1573-3890}, support = {PBA/MB/16/01//Marine Institute/International ; }, mesh = {Animals ; Chromatography, High Pressure Liquid ; Haliclona/*metabolism ; Mass Spectrometry ; *Metabolomics ; Species Specificity ; Time Factors ; }, abstract = {INTRODUCTION: The study of natural variation of metabolites brings valuable information on the physiological state of the organisms as well as their phenotypic traits. In marine organisms, metabolome variability has mostly been addressed through targeted studies on metabolites of ecological or pharmaceutical interest. However, comparative metabolomics has demonstrated its potential to address the overall and complex metabolic variability of organisms.<br><br>OBJECTIVES: In this study, the intraspecific (temporal and spatial) variability of two Mediterranean Haliclona sponges (H. fulva and H. mucosa) was investigated through an untargeted and then targeted metabolomics approach and further compared to their interspecific variability.<br><br>METHODS: Samples of both species were collected monthly during 1&#xa0;year in the coralligenous habitat of the Northwestern Mediterranean sae at Marseille and Nice. Their metabolomic profiles were obtained by UHPLC-QqToF analyses.<br><br>RESULTS: Marked variations were noticed in April and May for both species including a decrease in Shannon's diversity and concentration in specialized metabolites together with an increase in fatty acids and lyso-PAF like molecules. Spatial variations across different sampling sites could also be observed for both species, however in a lesser extent.<br><br>CONCLUSIONS: Synchronous metabolic changes possibly triggered by physiological factors like reproduction and/or environmental factors like an increase in the water temperature were highlighted for both Mediterranean Haliclona species inhabiting close habitats but displaying different biosynthetic pathways. Despite significative intraspecific variations, metabolomic variability remains minor when compared to interspecific variations for these congenerous species, therefore suggesting the predominance of genetic information of the holobiont in the observed metabolome.}, }
@article {pmid30830220, year = {2019}, author = {Helber, SB and Steinert, G and Wu, YC and Rohde, S and Hentschel, U and Muhando, CA and Schupp, PJ}, title = {Sponges from Zanzibar host diverse prokaryotic communities with potential for natural product synthesis.}, journal = {FEMS microbiology ecology}, volume = {95}, number = {4}, pages = {}, doi = {10.1093/femsec/fiz026}, pmid = {30830220}, issn = {1574-6941}, mesh = {Animals ; Biological Products/metabolism ; Coral Reefs ; Indian Ocean ; *Microbiota/genetics ; Porifera/chemistry/classification/*microbiology ; Prokaryotic Cells/*classification/metabolism ; Seawater/chemistry/microbiology ; Species Specificity ; Tanzania ; }, abstract = {Sponges are one of the most dominant organisms in marine ecosystems. One reason for their success is their association with microorganisms that are besides the host itself responsible for the chemical defence. Sponge abundances have been increasing on coral reefs in the Western Indian Ocean (WIO) and are predicted to increase further with rising anthropogenic impacts on coral reefs. However, there is a paucity of information on chemical ecology of sponges from the WIO and their prokaryotic community composition. We used a combination of Illumina sequencing and a predictive metagenomic analysis to (i) assess the prokaryotic community composition of sponges from Zanzibar, (ii) predict the presence of KEGG metabolic pathways responsible for bioactive compound production and (iii) relate their presence to the degree of observed chemical defence in their respective sponge host. We found that sponges from Zanzibar host diverse prokaryotic communities that are host species-specific. Sponge-species and respective specimens that showed strong chemical defences in previous studies were also predicted to be highly enriched in various pathways responsible for secondary metabolite production. Hence, the combined sequencing and predictive metagenomic approach proved to be a useful indicator for the metabolic potential of sponge holobionts.}, }
@article {pmid30813951, year = {2019}, author = {Zhao, ZB and He, JZ and Geisen, S and Han, LL and Wang, JT and Shen, JP and Wei, WX and Fang, YT and Li, PP and Zhang, LM}, title = {Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {33}, pmid = {30813951}, issn = {2049-2618}, mesh = {Bacteria/drug effects/growth &amp; development/isolation &amp; purification ; Crops, Agricultural/growth &amp; development ; Eukaryota/drug effects/*growth &amp; development/isolation &amp; purification ; Fertilizers/*analysis ; Fungi/drug effects/growth &amp; development/isolation &amp; purification ; Nitrogen/*adverse effects ; Phylogeny ; Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Agricultural food production is at the base of food and fodder, with fertilization having fundamentally and continuously increased crop yield over the last decades. The performance of crops is intimately tied to their microbiome as they together form holobionts. The importance of the microbiome for plant performance is, however, notoriously ignored in agricultural systems as fertilization disconnects the dependency of plants for often plant-beneficial microbial processes. Moreover, we lack a holistic understanding of how fertilization regimes affect the soil microbiome. Here, we examined the effect of a 2-year fertilization regime (no nitrogen fertilization control, nitrogen fertilization, and nitrogen fertilization plus straw amendment) on entire soil microbiomes (bacteria, fungi, and protist) in three common agricultural soil types cropped with maize in two seasons.<br><br>RESULTS: We found that the application of nitrogen fertilizers more strongly affected protist than bacterial and fungal communities. Nitrogen fertilization indirectly reduced protist diversity through changing abiotic properties and bacterial and fungal communities which differed between soil types and sampling seasons. Nitrogen fertilizer plus straw amendment had greater effects on soil physicochemical properties and microbiome diversity than nitrogen addition alone. Moreover, nitrogen fertilization, even more together with straw, increased soil microbiome network complexity, suggesting that the application of nitrogen fertilizers tightened soil microbiomes interactions.<br><br>CONCLUSIONS: Together, our results suggest that protists are the most susceptible microbiome component to the application of nitrogen fertilizers. As protist communities also exhibit the strongest seasonal dynamics, they serve as the most sensitive bioindicators of soil changes. Changes in protist communities might have long-term effects if some of the key protist hubs that govern microbiome complexities as top microbiome predators are altered. This study serves as the stepping stone to promote protists as promising agents in targeted microbiome engineering to help in reducing the dependency on exogenous unsustainably high fertilization and pesticide applications.}, }
@article {pmid30811993, year = {2019}, author = {Kong, HG and Kim, HH and Chung, JH and Jun, J and Lee, S and Kim, HM and Jeon, S and Park, SG and Bhak, J and Ryu, CM}, title = {The Galleria mellonella Hologenome Supports Microbiota-Independent Metabolism of Long-Chain Hydrocarbon Beeswax.}, journal = {Cell reports}, volume = {26}, number = {9}, pages = {2451-2464.e5}, doi = {10.1016/j.celrep.2019.02.018}, pmid = {30811993}, issn = {2211-1247}, mesh = {Animals ; Evolution, Molecular ; Fatty Acids/metabolism ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Genome, Insect ; Larva/metabolism/microbiology ; Moths/growth &amp; development/*metabolism/microbiology ; Multigene Family ; Transcriptome ; Waxes/*metabolism ; }, abstract = {The greater wax moth, Galleria mellonella, degrades wax and plastic molecules. Despite much interest, the genetic basis of these hallmark traits remains poorly understood. Herein, we assembled high-quality genome and transcriptome data from G. mellonella to investigate long-chain hydrocarbon wax metabolism strategies. Specific carboxylesterase and lipase and fatty-acid-metabolism-related enzymes in the G. mellonella genome are transcriptionally regulated during feeding on beeswax. Strikingly, G. mellonella lacking intestinal microbiota successfully decomposes long-chain fatty acids following wax metabolism, although the intestinal microbiome performs a supplementary role in short-chain fatty acid degradation. Notably, final wax derivatives were detected by gas chromatography even in the absence of gut microbiota. Our findings provide insight into wax moth adaptation and may assist in the development of unique wax-degradation strategies with a similar metabolic approach for a plastic molecule polyethylene biodegradation using organisms without intestinal microbiota.}, }
@article {pmid30811665, year = {2019}, author = {Fuentes, A}, title = {Holobionts, Multispecies Ecologies, and the Biopolitics of Care: Emerging Landscapes of Praxis in a Medical Anthropology of the Anthropocene.}, journal = {Medical anthropology quarterly}, volume = {33}, number = {1}, pages = {156-162}, doi = {10.1111/maq.12492}, pmid = {30811665}, issn = {0745-5194}, mesh = {Animals ; *Anthropology, Medical ; *Biological Evolution ; *Ecology ; Humans ; }, abstract = {Medical anthropology, given its diversity of practical and historical entanglements with (and outside of) numerous threads of anthropology, is a key site for productive theoretical and methodological confluences in the Anthropocene. Multispecies approaches, ethnographically, theoretically and methodologically, are developing as central locations for the hybridization and mingling of diverse and innovative research questions, particularly those engaging the processes, patterns, and constructs of health.}, }
@article {pmid30809207, year = {2019}, author = {Chakravarti, LJ and Negri, AP and van Oppen, MJH}, title = {Thermal and Herbicide Tolerances of Chromerid Algae and Their Ability to Form a Symbiosis With Corals.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {173}, pmid = {30809207}, issn = {1664-302X}, abstract = {Reef-building corals form an obligate symbiosis with photosynthetic microalgae in the family Symbiodiniaceae that meet most of their energy requirements. This symbiosis is under threat from the unprecedented rate of ocean warming as well as the simultaneous pressure of local stressors such as poor water quality. Only 1°C above mean summer sea surface temperatures (SSTs) on the Great Barrier Reef (GBR) can trigger the loss of Symbiodiniaceae from the host, and very low concentrations of the most common herbicide, diuron, can disrupt the photosynthetic activity of microalgae. In an era of rapid environmental change, investigation into the assisted evolution of the coral holobiont is underway in an effort to enhance the resilience of corals. Apicomplexan-like microalgae were discovered in 2008 and the Phylum Chromerida (chromerids) was created. Chromerids have been isolated from corals and contain a functional photosynthetic plastid. Their discovery therefore opens a new avenue of research into the use of alternative/additional photosymbionts of corals. However, only two studies to-date have investigated the symbiotic nature of Chromera velia with corals and thus little is known about the coral-chromerid relationship. Furthermore, the response of chromerids to environmental stressors has not been examined. Here we tested the performance of four chromerid strains and the common dinoflagellate symbiont Cladocopium goreaui (formerly Symbiodinium goreaui, ITS2 type C1) in response to elevated temperature, diuron and their combined exposure. Three of the four chromerid strains exhibited high thermal tolerances and two strains showed exceptional herbicide tolerances, greater than observed for any photosynthetic microalgae, including C. goreaui. We also investigated the onset of symbiosis between the chromerids and larvae of two common GBR coral species under ambient and stress conditions. Levels of colonization of coral larvae with the chromerid strains were low compared to colonization with C. goreaui. We did not observe any overall negative or positive larval fitness effects of the inoculation with chromerid algae vs. C. goreaui. However, we cannot exclude the possibility that chromerid algae may have more important roles in later coral life stages and recommend this be the focus of future studies.}, }
@article {pmid30806338, year = {2019}, author = {Durand, AA and Constant, P and Déziel, E and Guertin, C}, title = {The symbiotic complex of Dendroctonus simplex: implications in the beetle attack and its life cycle.}, journal = {Bulletin of entomological research}, volume = {109}, number = {6}, pages = {723-732}, doi = {10.1017/S0007485319000051}, pmid = {30806338}, issn = {1475-2670}, mesh = {Animals ; Bacteria/genetics ; Fungi/genetics ; Larix/microbiology/parasitology ; Life Cycle Stages ; *Microbiota ; Quebec ; Sequence Analysis, DNA ; *Symbiosis ; Weevils/*microbiology/physiology ; }, abstract = {The eastern larch beetle (Dendroctonus simplex Le Conte) is recognized as a serious destructive forest pest in the upper part of North America. Under epidemic conditions, this beetle can attack healthy trees, causing severe damages to larch stands. Dendroctonus species are considered as holobionts, as they engage in multipartite interactions with microorganisms, such as bacteria, filamentous fungi, and yeasts, which are implicated in physiological processes of the insect, such as nutrition. They also play a key role in the beetle's attack, as they are responsible for the detoxification of the subcortical environment and weaken the tree's defense mechanisms. The eastern larch beetle is associated with bacteria and fungi, but their implication in the success of the beetle remains unknown. Here, we investigated the bacterial and fungal microbiota of this beetle pest throughout its ontogeny (pioneer adults, larvae and pupae) by high-throughput sequencing. A successional microbial assemblage was identified throughout the beetle developmental stages, reflecting the beetle's requirements. These results indicate that a symbiotic association between the eastern larch beetle and some of these microorganisms takes place and that this D. simplex symbiotic complex is helping the insect to colonize its host tree and survive the conditions encountered.}, }
@article {pmid30802335, year = {2019}, author = {Sáenz, JS and Roldan, F and Junca, H and Arbeli, Z}, title = {Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities.}, journal = {Journal of applied microbiology}, volume = {126}, number = {5}, pages = {1454-1467}, doi = {10.1111/jam.14231}, pmid = {30802335}, issn = {1365-2672}, support = {//Pontificia Universidad Javeriana/ ; }, mesh = {Archaea/*genetics ; Bacteria/*genetics ; *DNA, Archaeal/genetics/isolation &amp; purification ; *DNA, Bacterial/genetics/isolation &amp; purification ; Polymerase Chain Reaction ; *Soil Microbiology ; }, abstract = {AIMS: This study evaluated the effects of DNA extraction method, DNA purification and pooling of PCR amplification products on the description of bacterial and archaeal diversity.<br><br>METHODS AND RESULTS: Soil DNA was extracted by the Power Soil DNA extraction kit and a customized Griffiths' protocol. Both methods are based on cell disruption by bead beating. In total, we used three soils and six independent extractions from each soil obtained by each of the two methods. Then, three of the six extracts of each treatment were further purified by spin columns filled with Sepharose 2B and polyvinylpolypyrrolidone (PVPP). The V4 hypervariable region of the 16S rRNA gene was amplified from each extract using the 515F/806R primer pair in four independent reactions. Three amplification products were combined and sequenced as a pooled sample, while the additional amplification product was sequenced individually. The resulting 72 amplification products were sequenced by Illumina MiSeq platform. DNA extraction method had a statistically significant effect on the estimation of the composition of microbial communities that might overwhelm differences in microbial communities from distinct soils. On the other hand, a further DNA purification step or pooling of PCR amplification products had a minor effect on the description of bacterial and archaeal communities.<br><br>CONCLUSIONS: DNA extraction had the strongest effect on the description of bacterial and archaeal communities; low concentration of impurities, which allow PCR amplification, can still generate a minor additional bias, while PCR stochastic variability had the lowest effect.<br><br>Although it is well known that methodological factors affect the description of microbial communities, the relative importance of each step is still unknown. The present study determined that of the factors tested, the DNA extraction method had the strongest effects on the description of bacterial and archaeal communities.}, }
@article {pmid30773714, year = {2019}, author = {Estellé, J}, title = {Benefits from the joint analysis of host genomes and metagenomes: Select the holobiont.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {136}, number = {2}, pages = {75-76}, doi = {10.1111/jbg.12383}, pmid = {30773714}, issn = {1439-0388}, mesh = {Animals ; Genetic Variation ; *Genome ; Genotyping Techniques ; *Metagenome ; Symbiosis/*genetics ; }, }
@article {pmid30740275, year = {2019}, author = {Glasl, B and Smith, CE and Bourne, DG and Webster, NS}, title = {Disentangling the effect of host-genotype and environment on the microbiome of the coral Acropora tenuis.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6377}, pmid = {30740275}, issn = {2167-8359}, abstract = {Genotype-specific contributions to the environmental tolerance and disease susceptibility of corals are widely accepted. Yet our understanding of how host genotype influences the composition and stability of the coral microbiome subjected to environmental fluctuations is limited. To gain insight into the community dynamics and environmental stability of microbiomes associated with distinct coral genotypes, we assessed the microbial community associated with Acropora tenuis under single and cumulative pressure experiments. Experimental treatments comprised either a single pulse of reduced salinity (minimum of 28 psu) or exposure to the cumulative pressures of reduced salinity (minimum of 28 psu), elevated seawater temperature (+2 °C), elevated pCO2 (900 ppm), and the presence of macroalgae. Analysis of 16S rRNA gene amplicon sequence data revealed that A. tenuis microbiomes were highly host-genotype specific and maintained high compositional stability irrespective of experimental treatment. On average, 48% of the A. tenuis microbiome was dominated by Endozoicomonas. Amplicon sequence variants (ASVs) belonging to this genus were significantly different between host individuals. Although no signs of stress were evident in the coral holobiont and the vast majority of ASVs remained stable across treatments, a microbial indicator approach identified 26 ASVs belonging to Vibrionaceae, Rhodobacteraceae, Hahellaceae, Planctomycetes, Phylobacteriaceae, Flavobacteriaceae, and Cryomorphaceae that were significantly enriched in corals exposed to single and cumulative stressors. While several recent studies have highlighted the efficacy of microbial indicators as sensitive markers for environmental disturbance, the high host-genotype specificity of coral microbiomes may limit their utility and we therefore recommend meticulous control of host-genotype effects in coral microbiome research.}, }
@article {pmid30738790, year = {2019}, author = {Liu, H and Brettell, LE}, title = {Plant Defense by VOC-Induced Microbial Priming.}, journal = {Trends in plant science}, volume = {24}, number = {3}, pages = {187-189}, doi = {10.1016/j.tplants.2019.01.008}, pmid = {30738790}, issn = {1878-4372}, mesh = {Plants ; Rhizosphere ; *Volatile Organic Compounds ; }, abstract = {The plant holobiont extends the plant's capacity for nutrient acquisition and stress protection. Recent studies show that under biotic stress plants can promote the acquisition of certain beneficial bacteria to their rhizosphere. Active emission of volatile organic compounds (VOCs) is a newly identified mechanism utilized by plants for this process.}, }
@article {pmid30727955, year = {2019}, author = {Détrée, C and Haddad, I and Demey-Thomas, E and Vinh, J and Lallier, FH and Tanguy, A and Mary, J}, title = {Global host molecular perturbations upon in situ loss of bacterial endosymbionts in the deep-sea mussel Bathymodiolus azoricus assessed using proteomics and transcriptomics.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {109}, pmid = {30727955}, issn = {1471-2164}, mesh = {Animals ; Bacteria/*metabolism ; *Chemoautotrophic Growth ; Gene Expression Profiling ; *Gene Expression Regulation ; Gills/microbiology ; Hydrothermal Vents ; Microbiota ; Mytilidae/genetics/*microbiology ; Proteomics ; *Symbiosis ; }, abstract = {BACKGROUND: Colonization of deep-sea hydrothermal vents by most invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers in these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts loss on the deep-sea mussel Bathymodiolus azoricus' molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels.<br><br>RESULTS: Global proteomic and transcriptomic results evidenced a global disruption of host machinery in aposymbiotic organisms. We observed that the total number of proteins identified decreased from 1118 in symbiotic mussels to 790 in partially depleted mussels and 761 in aposymbiotic mussels. Using microarrays we identified 4300 transcripts differentially expressed between symbiont-depleted and symbiotic mussels. Among these transcripts, 799 were found differentially expressed in aposymbiotic mussels and almost twice as many in symbiont-depleted mussels as compared to symbiotic mussels. Regarding apoptotic and immune system processes - known to be largely involved in symbiotic interactions - an overall up-regulation of associated proteins and transcripts was observed in symbiont-depleted mussels.<br><br>CONCLUSION: Overall, our study showed a global impairment of host machinery and an activation of both the immune and apoptotic system following symbiont-depletion. One of the main assumptions is the involvement of symbiotic bacteria in the inhibition and regulation of immune and apoptotic systems. As such, symbiotic bacteria may increase their lifespan in gill cells while managing the defense of the holobiont against putative pathogens.}, }
@article {pmid30723123, year = {2019}, author = {O'Brien, PA and Webster, NS and Miller, DJ and Bourne, DG}, title = {Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts.}, journal = {mBio}, volume = {10}, number = {1}, pages = {}, pmid = {30723123}, issn = {2150-7511}, mesh = {Animals ; Aquatic Organisms/*microbiology ; *Biological Evolution ; Invertebrates/*microbiology ; *Microbiota ; }, abstract = {Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.}, }
@article {pmid30720424, year = {2019}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The Hologenome Concept of Evolution: Medical Implications.}, journal = {Rambam Maimonides medical journal}, volume = {10}, number = {1}, pages = {}, pmid = {30720424}, issn = {2076-9172}, abstract = {All natural animals and plants are holobionts, consisting of the host and microbiome, which is composed of abundant and diverse microorganisms. Health and disease of holobionts depend as much on interactions between host and microbiome and within the microbiome, as on interactions between organs and body parts of the host. Recent evidence indicates that a significant fraction of the microbiome is transferred by a variety of mechanisms from parent to offspring for many generations. Genetic variation in holobionts can occur in the microbiome as well as in the host genome, and it occurs more rapidly and by more mechanisms in genomes of microbiomes than in host genomes (e.g. via acquisition of novel microbes and horizontal gene transfer of microbial genes into host chromosomes). Evidence discussed in this review supports the concept that holobionts with their hologenomes can be considered levels of selection in evolution. Though changes in the microbiome can lead to evolution of the holobiont, it can also lead to dysbiosis and diseases (e.g. obesity, diarrhea, inflammatory bowel disease, and autism). In practice, the possibility of manipulating microbiomes offers the potential to prevent and cure diseases.}, }
@article {pmid30718608, year = {2019}, author = {Longford, SR and Campbell, AH and Nielsen, S and Case, RJ and Kjelleberg, S and Steinberg, PD}, title = {Interactions within the microbiome alter microbial interactions with host chemical defences and affect disease in a marine holobiont.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {1363}, pmid = {30718608}, issn = {2045-2322}, mesh = {Aquatic Organisms/classification/*microbiology ; Colony Count, Microbial ; *Microbial Interactions ; *Microbiota ; Phylogeny ; Principal Component Analysis ; Seaweed/*chemistry/classification/*microbiology ; }, abstract = {Our understanding of diseases has been transformed by the realisation that people are holobionts, comprised of a host and its associated microbiome(s). Disease can also have devastating effects on populations of marine organisms, including dominant habitat formers such as seaweed holobionts. However, we know very little about how interactions between microorganisms within microbiomes - of humans or marine organisms - affect host health and there is no underpinning theoretical framework for exploring this. We applied ecological models of succession to bacterial communities to understand how interactions within a seaweed microbiome affect the host. We observed succession of surface microbiomes on the red seaweed Delisea pulchra in situ, following a disturbance, with communities 'recovering' to resemble undisturbed states after only 12 days. Further, if this recovery was perturbed, a bleaching disease previously described for this seaweed developed. Early successional strains of bacteria protected the host from colonisation by a pathogenic, later successional strain. Host chemical defences also prevented disease, such that within-microbiome interactions were most important when the host's chemical defences were inhibited. This is the first experimental evidence that interactions within microbiomes have important implications for host health and disease in a dominant marine habitat-forming organism.}, }
@article {pmid30691243, year = {2019}, author = {Wemheuer, B and Thomas, T and Wemheuer, F}, title = {Fungal Endophyte Communities of Three Agricultural Important Grass Species Differ in Their Response Towards Management Regimes.}, journal = {Microorganisms}, volume = {7}, number = {2}, pages = {}, pmid = {30691243}, issn = {2076-2607}, support = {Functional Biodiversity Research//Nieders&#xe4;chsisches Ministerium f&#xfc;r Wissenschaft und Kultur/ ; Starting Grant//Georg-August-Universit&#xe4;t G&#xf6;ttingen/ ; }, abstract = {Despite the importance of endophytic fungi for plant health, it remains unclear how these fungi are influenced by grassland management practices. Here, we investigated the effect of fertilizer application and mowing frequency on fungal endophyte communities and their life strategies in aerial tissues of three agriculturally important grass species (Dactylis glomerata L., Festuca rubra L. and Lolium perenne L.) over two consecutive years. Our results showed that the management practices influenced fungal communities in the plant holobiont, but observed effects differed between grass species and sampling year. Phylogenetic diversity of fungal endophytes in D. glomerata was significantly affected by mowing frequency in 2010, whereas fertilizer application and the interaction of fertilization with mowing frequency had a significant impact on community composition of L. perenne in 2010 and 2011, respectively. Taken together, our research provides a basis for future studies on responses of fungal endophytes towards management practices. To the best of our knowledge, this is the first study simultaneously assessing fungal endophyte communities in aerial parts of three agriculturally important grass species over two consecutive years.}, }
@article {pmid30680121, year = {2019}, author = {Helmkampf, M and Bellinger, MR and Frazier, M and Takabayashi, M}, title = {Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata.}, journal = {Ecology and evolution}, volume = {9}, number = {1}, pages = {378-392}, pmid = {30680121}, issn = {2045-7758}, abstract = {Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.}, }
@article {pmid30662570, year = {2019}, author = {Töpel, M and Pinder, MIM and Johansson, ON and Kourtchenko, O and Clarke, AK and Godhe, A}, title = {Complete Genome Sequence of Novel Sulfitobacter pseudonitzschiae Strain SMR1, Isolated from a Culture of the Marine Diatom Skeletonema marinoi.}, journal = {Journal of genomics}, volume = {7}, number = {}, pages = {7-10}, pmid = {30662570}, issn = {1839-9940}, abstract = {When studying diatoms, an important consideration is the role of associated bacteria in the diatom-microbiome holobiont. To that end, bacteria isolated from a culture of Skeletonema marinoi strain R05AC were sequenced, one of which being bacterial strain SMR1, presented here. The genome consists of a circular chromosome and seven circular plasmids, totalling 5,121,602 bp. After phylotaxonomic analysis and 16S rRNA sequence comparison, we place this strain in the taxon Sulfitobacter pseudonitzschiae on account of similarity to the type strain. The annotated genome suggests similar interactions between strain SMR1 and its host diatom as have been shown previously in diatom-associated Sulfitobacter, for example bacterial production of growth hormone for its host, and breakdown of diatom-derived DMSP by Sulfitobacter for use as a sulfur source.}, }
@article {pmid30635058, year = {2019}, author = {Simon, JC and Marchesi, JR and Mougel, C and Selosse, MA}, title = {Host-microbiota interactions: from holobiont theory to analysis.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {5}, pmid = {30635058}, issn = {2049-2618}, mesh = {Animals ; Food Microbiology ; *Host Microbial Interactions ; Humans ; *Microbiota ; Plants/microbiology ; Symbiosis ; }, abstract = {In the recent years, the holobiont concept has emerged as a theoretical and experimental framework to study the interactions between hosts and their associated microbial communities in all types of ecosystems. The spread of this concept in many branches of biology results from the fairly recent realization of the ubiquitous nature of host-associated microbes and their central role in host biology, ecology, and evolution. Through this special series "Host-microbiota interactions: from holobiont theory to analysis," we wanted to promote this field of research which has considerable implications for human health, food production, and ecosystem protection. In this preface, we highlight a collection of articles selected for this special issue that show, use, or debate the concept of holobiont to approach taxonomically and ecologically diverse organisms, from humans and plants to sponges and insects. We also identify some theoretical and methodological challenges and propose directions for future research on holobionts.}, }
@article {pmid30621755, year = {2018}, author = {Osmanovic, D and Kessler, DA and Rabin, Y and Soen, Y}, title = {Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.}, journal = {Biology direct}, volume = {13}, number = {1}, pages = {24}, pmid = {30621755}, issn = {1745-6150}, mesh = {*Adaptation, Biological ; Bacteria/*genetics ; Bacterial Physiological Phenomena/genetics ; *Host-Pathogen Interactions ; *Microbiota ; Models, Genetic ; *Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {BACKGROUND: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.<br><br>RESULTS: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent ("detox"). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host's offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).<br><br>CONCLUSIONS: These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.<br><br>REVIEWERS: This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.}, }
@article {pmid30618841, year = {2018}, author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M}, title = {Modeling the Role of the Microbiome in Evolution.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {1836}, pmid = {30618841}, issn = {1664-042X}, abstract = {There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.}, }
@article {pmid30613848, year = {2019}, author = {Ye, S and Bhattacharjee, M and Siemann, E}, title = {Thermal Tolerance in Green Hydra: Identifying the Roles of Algal Endosymbionts and Hosts in a Freshwater Holobiont Under Stress.}, journal = {Microbial ecology}, volume = {77}, number = {2}, pages = {537-545}, pmid = {30613848}, issn = {1432-184X}, mesh = {Animals ; Chlorophyta/*physiology ; Fresh Water/chemistry/parasitology ; Hot Temperature ; Hydra/*parasitology/physiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {It has been proposed that holobionts (host-symbiont units) could swap endosymbionts, rapidly alter the hologenome (host plus symbiont genome), and increase their stress tolerance. However, experimental tests of individual and combined contributions of hosts and endosymbionts to holobiont stress tolerance are needed to test this hypothesis. Here, we used six green hydra (Hydra viridissima) strains to tease apart host (hydra) and symbiont (algae) contributions to thermal tolerance. Heat shock experiments with (1) hydra with their original symbionts, (2) aposymbiotic hydra (algae removed), (3) novel associations (a single hydra strain hosting different algae individually), and (4) control hydra (aposymbiotic hydra re-associated with their original algae) showed high variation in thermal tolerance in each group. Relative tolerances of strains were the same within original, aposymbiotic, and control treatments, but reversed in the novel associations group. Aposymbiotic hydra had similar or higher thermal tolerance than hydra with algal symbionts. Selection on the holobiont appears to be stronger than on either partner alone, suggesting endosymbiosis could become an evolutionary trap under climate change. Our results suggest that green hydra thermal tolerance is strongly determined by the host, with a smaller, non-positive role for the algal symbiont. Once temperatures exceed host tolerance limits, swapping symbionts is unlikely to allow these holobionts to persist. Rather, increases in host tolerance through in situ adaptation or migration of pre-adapted host strains appear more likely to increase local thermal tolerance. Overall, our results indicate green hydra is a valuable system for studying aquatic endosymbiosis under changing environmental conditions, and demonstrate how the host and the endosymbiont contribute to holobiont stress tolerance.}, }
@article {pmid30611207, year = {2019}, author = {Kamm, K and Schierwater, B and DeSalle, R}, title = {Innate immunity in the simplest animals - placozoans.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {5}, pmid = {30611207}, issn = {1471-2164}, support = {Schi-277/26//Deutsche Forschungsgemeinschaft/ ; Schi-277/27//Deutsche Forschungsgemeinschaft/ ; Schi-277/29//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; Genome/*immunology ; Immunity, Innate/*genetics ; Invertebrates/genetics/immunology ; *Phylogeny ; Placozoa/genetics/*immunology ; Symbiosis/genetics/immunology ; }, abstract = {BACKGROUND: Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our knowledge about innate immunity stems from a few animal model systems, but substantial variation between metazoan phyla has been revealed by comparative genomic studies. The exploration of more taxa is still needed to better understand the evolution of immunity related mechanisms. Placozoans are morphologically the simplest organized metazoans and the association between these enigmatic animals and their rickettsial endosymbionts has recently been elucidated. Our analyses of the novel placozoan nuclear genome of Trichoplax sp. H2 and its associated rickettsial endosymbiont genome clearly pointed to a mutualistic and co-evolutionary relationship. This discovery raises the question of how the placozoan holobiont manages symbiosis and, conversely, how it defends against harmful microorganisms. In this study, we examined the annotated genome of Trichoplax sp. H2 for the presence of genes involved in innate immune recognition and downstream signaling.<br><br>RESULTS: A rich repertoire of genes belonging to the Toll-like and NOD-like receptor pathways, to scavenger receptors and to secreted fibrinogen-related domain genes was identified in the genome of Trichoplax sp. H2. Nevertheless, the innate immunity related pathways in placozoans deviate in several instances from well investigated vertebrates and invertebrates. While true Toll- and NOD-like receptors are absent, the presence of many genes of the downstream signaling cascade suggests at least primordial Toll-like receptor signaling in Placozoa. An abundance of scavenger receptors, fibrinogen-related domain genes and Apaf-1 genes clearly constitutes an expansion of the immunity related gene repertoire specific to Placozoa.<br><br>CONCLUSIONS: The found wealth of immunity related genes present in Placozoa is surprising and quite striking in light of the extremely simple placozoan body plan and their sparse cell type makeup. Research is warranted to reveal how Placozoa utilize this immune repertoire to manage and maintain their associated microbiota as well as to fend-off pathogens.}, }
@article {pmid30598811, year = {2018}, author = {Rodriguez-Casariego, JA and Ladd, MC and Shantz, AA and Lopes, C and Cheema, MS and Kim, B and Roberts, SB and Fourqurean, JW and Ausio, J and Burkepile, DE and Eirin-Lopez, JM}, title = {Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis.}, journal = {Ecology and evolution}, volume = {8}, number = {23}, pages = {12193-12207}, pmid = {30598811}, issn = {2045-7758}, abstract = {Nutrient pollution and thermal stress constitute two of the main drivers of global change in the coastal oceans. While different studies have addressed the physiological effects and ecological consequences of these stressors in corals, the role of acquired modifications in the coral epigenome during acclimatory and adaptive responses remains unknown. The present work aims to address that gap by monitoring two types of epigenetic mechanisms, namely histone modifications and DNA methylation, during a 7-week-long experiment in which staghorn coral fragments (Acropora cervicornis) were exposed to nutrient stress (nitrogen, nitrogen + phosphorus) in the presence of thermal stress. The major conclusion of this experiment can be summarized by two main results: First, coral holobiont responses to the combined effects of nutrient enrichment and thermal stress involve the post-translational phosphorylation of the histone variant H2A.X (involved in responses to DNA damage), as well as nonsignificant modifications in DNA methylation trends. Second, the reduction in H2A.X phosphorylation (and the subsequent potential impairment of DNA repair mechanisms) observed after prolonged coral exposure to nitrogen enrichment and thermal stress is consistent with the symbiont-driven phosphorus limitation previously observed in corals subject to nitrogen enrichment. The alteration of this epigenetic mechanism could help to explain the synergistic effects of nutrient imbalance and thermal stress on coral fitness (i.e., increased bleaching and mortality) while supporting the positive effect of phosphorus addition to improving coral resilience to thermal stress. Overall, this work provides new insights into the role of epigenetic mechanisms during coral responses to global change, discussing future research directions and the potential benefits for improving restoration, management and conservation of coral reef ecosystems worldwide.}, }
@article {pmid30568641, year = {2018}, author = {Mahnert, A and Haratani, M and Schmuck, M and Berg, G}, title = {Enriching Beneficial Microbial Diversity of Indoor Plants and Their Surrounding Built Environment With Biostimulants.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2985}, pmid = {30568641}, issn = {1664-302X}, support = {P 29285/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Microbial diversity is suggested as the key for plant and human health. However, how microbial diversity can be enriched is largely unknown but of great interest for health issues. Biostimulants offer the way to directly augment our main living areas by the healthy microbiome of indoor plants. Here, we investigated shifts of the microbiome on leaves of spider plants (Chlorophytum comosum) and its surrounding abiotic surfaces in the built environment after irrigation with a vermicompost-based biostimulant for 12 weeks. The biostimulant could not only promote plant growth, but changed the composition of the microbiome and abundance of intact microbial cells on plant leaves and even stronger on abiotic surfaces in close vicinity under constant conditions of the microclimate. Biostimulant treatments stabilized microbial diversity and resulted in an increase of Bacteroidetes and a surprising transient emerge of new phyla, e.g., Verrucomicrobia, Acidobacteria, and Thaumarchaeota. The proportion of potentially beneficial microorganisms like Brevibacillus, Actinoallomurus, Paenibacillus, Sphaerisporangium increased relatively; microbial diversity was stabilized, and the built environment became more plant-like. Detected metabolites like indole-3-acetic acid in the biostimulant were potentially contributed by species of Pseudomonas. Overall, effects of the biostimulant on the composition of the microbiome could be predicted with an accuracy of 87%. This study shows the potential of biostimulants not only for the plant itself, but also for other living holobionts like humans in the surrounding environment.}, }
@article {pmid30566939, year = {2019}, author = {Esser, D and Lange, J and Marinos, G and Sieber, M and Best, L and Prasse, D and Bathia, J and Rühlemann, MC and Boersch, K and Jaspers, C and Sommer, F}, title = {Functions of the Microbiota for the Physiology of Animal Metaorganisms.}, journal = {Journal of innate immunity}, volume = {11}, number = {5}, pages = {393-404}, pmid = {30566939}, issn = {1662-8128}, mesh = {Aging ; Animals ; Computational Biology ; Health Status ; Host Microbial Interactions/*physiology ; Humans ; Microbiota/*physiology ; Models, Biological ; Mucus/microbiology/virology ; Symbiosis/physiology ; }, abstract = {Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms.}, }
@article {pmid30564562, year = {2018}, author = {Proal, A and Marshall, T}, title = {Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity.}, journal = {Frontiers in pediatrics}, volume = {6}, number = {}, pages = {373}, pmid = {30564562}, issn = {2296-2360}, abstract = {The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.}, }
@article {pmid30555453, year = {2018}, author = {Cernava, T and Vasfiu, Q and Erlacher, A and Aschenbrenner, IA and Francesconi, K and Grube, M and Berg, G}, title = {Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2959}, pmid = {30555453}, issn = {1664-302X}, support = {I 882/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl[-1] in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances.}, }
@article {pmid30551821, year = {2018}, author = {Lee, KA and Lee, WJ}, title = {Immune-metabolic interactions during systemic and enteric infection in Drosophila.}, journal = {Current opinion in insect science}, volume = {29}, number = {}, pages = {21-26}, doi = {10.1016/j.cois.2018.05.014}, pmid = {30551821}, issn = {2214-5753}, mesh = {Animals ; Drosophila/*immunology/*metabolism/microbiology ; Drosophila Proteins/*genetics/metabolism ; *Host-Pathogen Interactions ; Phenotype ; Signal Transduction/physiology ; }, abstract = {Immune-metabolic interactions are evolutionarily conserved phenomena observed in all metazoans, from invertebrates to vertebrates. Although it is believed that immune activation drives chronic metabolic diseases, clear conclusions about the reasons and mechanisms of cross-talk between immune and metabolic signaling cannot be drawn. The Drosophila insect model equipped with genetically well-defined immune and metabolic signaling pathways is suitable in understanding the molecular codes underlying immune-metabolic interactions. In this report, we present and discuss the following: how immune signaling induces metabolic phenotypes and how metabolic signaling sequentially induces immune phenotypes in Drosophila. Further genetic studies on immune-metabolic interactions in Drosophila are warranted to increase the understanding of the etiology of different dysregulated immune-metabolic interaction-caused diseases.}, }
@article {pmid30542077, year = {2019}, author = {Gibbin, E and Gavish, A and Krueger, T and Kramarsky-Winter, E and Shapiro, O and Guiet, R and Jensen, L and Vardi, A and Meibom, A}, title = {Vibrio coralliilyticus infection triggers a behavioural response and perturbs nutritional exchange and tissue integrity in a symbiotic coral.}, journal = {The ISME journal}, volume = {13}, number = {4}, pages = {989-1003}, pmid = {30542077}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/anatomy &amp; histology/metabolism/*microbiology/physiology ; Behavior, Animal ; Dinoflagellida/metabolism ; Host-Pathogen Interactions ; Nutrients ; *Symbiosis ; Temperature ; Vibrio/*physiology ; }, abstract = {Under homoeostatic conditions, the relationship between the coral Pocillopora damicornis and Vibrio coralliilyticus is commensal. An increase in temperature, or in the abundance of V. coralliilyticus, can turn this association pathogenic, causing tissue lysis, expulsion of the corals' symbiotic algae (genus Symbiodinium), and eventually coral death. Using a combination of microfluidics, fluorescence microscopy, stable isotopes, electron microscopy and NanoSIMS isotopic imaging, we provide insights into the onset and progression of V. coralliilyticus infection in the daytime and at night, at the tissue and (sub-)cellular level. The objective of our study was to connect the macro-scale behavioural response of the coral to the micro-scale nutritional interactions that occur between the host and its symbiont. In the daytime, polyps enhanced their mucus production, and actively spewed pathogens. Vibrio infection primarily resulted in the formation of tissue lesions in the coenosarc. NanoSIMS analysis revealed infection reduced [13]C-assimilation in Symbiodinium, but increased [13]C-assimilation in the host. In the night incubations, no mucus spewing was observed, and a mucus film was formed on the coral surface. Vibrio inoculation and infection at night showed reduced [13]C-turnover in Symbiodinium, but did not impact host [13]C-turnover. Our results show that both the nutritional interactions that occur between the two symbiotic partners and the behavioural response of the host organism play key roles in determining the progression and severity of host-pathogen interactions. More generally, our approach provides a new means of studying interactions (ranging from behavioural to metabolic scales) between partners involved in complex holobiont systems, under both homoeostatic and pathogenic conditions.}, }
@article {pmid30524390, year = {2018}, author = {Gobet, A and Barbeyron, T and Matard-Mann, M and Magdelenat, G and Vallenet, D and Duchaud, E and Michel, G}, title = {Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9[T] to Adapt to Macroalgal Niches.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2740}, pmid = {30524390}, issn = {1664-302X}, abstract = {About half of seaweed biomass is composed of polysaccharides. Most of these complex polymers have a marked polyanionic character. For instance, the red algal cell wall is mainly composed of sulfated galactans, agars and carrageenans, while brown algae contain alginate and fucose-containing sulfated polysaccharides (FCSP) as cell wall polysaccharides. Some marine heterotrophic bacteria have developed abilities to grow on such macroalgal polysaccharides. This is the case of Pseudoalteromonas carrageenovora 9[T] (ATCC 43555[T]), a marine gammaproteobacterium isolated in 1955 and which was an early model organism for studying carrageenan catabolism. We present here the genomic analysis of P. carrageenovora. Its genome is composed of two chromosomes and of a large plasmid encompassing 109 protein-coding genes. P. carrageenovora possesses a diverse repertoire of carbohydrate-active enzymes (CAZymes), notably specific for the degradation of macroalgal polysaccharides (laminarin, alginate, FCSP, carrageenans). We confirm these predicted capacities by screening the growth of P. carrageenovora with a large collection of carbohydrates. Most of these CAZyme genes constitute clusters located either in the large chromosome or in the small one. Unexpectedly, all the carrageenan catabolism-related genes are found in the plasmid, suggesting that P. carrageenovora acquired its hallmark capacity for carrageenan degradation by horizontal gene transfer (HGT). Whereas P. carrageenovora is able to use lambda-carrageenan as a sole carbon source, genomic and physiological analyses demonstrate that its catabolic pathway for kappa- and iota-carrageenan is incomplete. This is due to the absence of the recently discovered 3,6-anhydro-D-galactosidase genes (GH127 and GH129 families). A genomic comparison with 52 Pseudoalteromonas strains confirms that carrageenan catabolism has been recently acquired only in a few species. Even though the loci for cellulose biosynthesis and alginate utilization are located on the chromosomes, they were also horizontally acquired. However, these HGTs occurred earlier in the evolution of the Pseudoalteromonas genus, the cellulose- and alginate-related loci being essentially present in one large, late-diverging clade (LDC). Altogether, the capacities to degrade cell wall polysaccharides from macroalgae are not ancestral in the Pseudoalteromonas genus. Such catabolism in P. carrageenovora resulted from a succession of HGTs, likely allowing an adaptation to the life on the macroalgal surface.}, }
@article {pmid30533318, year = {2018}, author = {Kenkel, CD and Bay, LK}, title = {Exploring mechanisms that affect coral cooperation: symbiont transmission mode, cell density and community composition.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e6047}, pmid = {30533318}, issn = {2167-8359}, abstract = {The coral symbiosis is the linchpin of the reef ecosystem, yet the mechanisms that promote and maintain cooperation between hosts and symbionts have not been fully resolved. We used a phylogenetically controlled design to investigate the role of vertical symbiont transmission, an evolutionary mechanism in which symbionts are inherited directly from parents, predicted to enhance cooperation and holobiont fitness. Six species of coral, three vertical transmitters and their closest horizontally transmitting relatives, which exhibit environmental acquisition of symbionts, were fragmented and subjected to a 2-week thermal stress experiment. Symbiont cell density, photosynthetic function and translocation of photosynthetically fixed carbon between symbionts and hosts were quantified to assess changes in physiological performance and cooperation. All species exhibited similar decreases in symbiont cell density and net photosynthesis in response to elevated temperature, consistent with the onset of bleaching. Yet baseline cooperation, or translocation of photosynthate, in ambient conditions and the reduction in cooperation in response to elevated temperature differed among species. Although Porites lobata and Galaxea acrhelia did exhibit the highest levels of baseline cooperation, we did not observe universally higher levels of cooperation in vertically transmitting species. Post hoc sequencing of the Symbiodinium ITS-2 locus was used to investigate the potential role of differences in symbiont community composition. Interestingly, reductions in cooperation at the onset of bleaching tended to be associated with increased symbiont community diversity among coral species. The theoretical benefits of evolving vertical transmission are based on the underlying assumption that the host-symbiont relationship becomes genetically uniform, thereby reducing competition among symbionts. Taken together, our results suggest that it may not be vertical transmission per se that influences host-symbiont cooperation, but genetic uniformity of the symbiont community, although additional work is needed to test this hypothesis.}, }
@article {pmid30514367, year = {2018}, author = {Marasco, R and Mosqueira, MJ and Fusi, M and Ramond, JB and Merlino, G and Booth, JM and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {215}, pmid = {30514367}, issn = {2049-2618}, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Alphaproteobacteria/classification/genetics/isolation &amp; purification ; Ascomycota/classification/genetics/isolation &amp; purification ; Bacteria/classification/*isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Fungal/genetics ; Desert Climate ; Fungi/classification/*isolation &amp; purification ; Metagenomics/*methods ; Phylogeny ; Plant Roots/microbiology ; Poaceae/*microbiology ; Rhizosphere ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {BACKGROUND: The rhizosheath-root system is an adaptive trait of sandy-desert speargrasses in response to unfavourable moisture and nutritional conditions. Under the deserts' polyextreme conditions, plants interact with edaphic microorganisms that positively affect their fitness and resistance. However, the trophic simplicity and environmental harshness of desert ecosystems have previously been shown to strongly influence soil microbial community assembly. We hypothesize that sand-driven ecological filtering constrains the microbial recruitment processes in the speargrass rhizosheath-root niche, prevailing over the plant-induced selection.<br><br>METHODS: Bacterial and fungal communities from the rhizosheath-root compartments (endosphere root tissues, rhizosheath and rhizosphere) of three Namib Desert speargrass species (Stipagrostis sabulicola, S. seelyae and Cladoraphis spinosa) along with bulk sand have been studied to test our hypothesis. To minimize the variability determined by edaphic and climatic factors, plants living in a single dune were studied. We assessed the role of plant species vs the sandy substrate on the recruitment and selection, phylogenetic diversity and co-occurrence microbial networks of the rhizosheath-root system microbial communities.<br><br>RESULTS: Microorganisms associated with the speargrass rhizosheath-root system were recruited from the surrounding bulk sand population and were significantly enriched in the rhizosheath compartments (10[5] and 10[4] of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 10[8] and 10[7] copies per gram, respectively). Furthermore, each rhizosheath-root system compartment hosted a specific microbial community demonstrating strong niche-partitioning. The rhizosheath-root systems of the three speargrass species studied were dominated by desert-adapted Actinobacteria and Alphaproteobacteria (e.g. Lechevalieria, Streptomyces and Microvirga) as well as saprophytic Ascomycota fungi (e.g. Curvularia, Aspergillus and Thielavia). Our results clearly showed a random phylogenetic turnover of rhizosheath-root system associated microbial communities, independent of the plant species, where stochastic factors drive neutral assembly. Co-occurrence network analyses also indicated that the bacterial and fungal community members of the rhizosheath-root systems established a higher number of interactions than those in the barren bulk sand, suggesting that the former are more stable and functional than the latter.<br><br>CONCLUSION: Our study demonstrates that the rhizosheath-root system microbial communities of desert dune speargrasses are stochastically assembled and host-independent. This finding supports the concept that the selection determined by the desert sand prevails over that imposed by the genotype of the different plant species.}, }
@article {pmid30509793, year = {2018}, author = {Baquiran, JIP and Conaco, C}, title = {Sponge-microbe partnerships are stable under eutrophication pressure from mariculture.}, journal = {Marine pollution bulletin}, volume = {136}, number = {}, pages = {125-134}, doi = {10.1016/j.marpolbul.2018.09.011}, pmid = {30509793}, issn = {1879-3363}, mesh = {Animals ; Coral Reefs ; *Ecosystem ; Environmental Monitoring/*methods ; *Eutrophication ; Fisheries ; *Microbiota/genetics ; Philippines ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Sponges harbor a great diversity of symbiotic microorganisms. However, environmental stresses can affect this partnership and influence the health and abundance of the host sponges. In Bolinao, Pangasinan, Philippines, chronic input of organic materials from mariculture activities contributes to a eutrophic coastal environment. To understand how these conditions might affect sponge-microbial partnerships, transplantation experiments were conducted with the marine sponge Gelliodes obtusa. High-throughput sequencing of 16S rRNA revealed that the associated microbial community of the sponges did not exhibit significant shifts after six weeks of transplantation at a eutrophic fish farm site compared to sponges grown at a coral reef or a seagrass area. However, sponges at the fish farm revealed higher abundance of the amoA gene, suggesting that microbiome members are responsive to increased ammonium levels at the site. The stable association between G. obtusa and its microbiome indicates that the sponge holobiont can withstand eutrophication pressure from mariculture.}, }
@article {pmid30487315, year = {2018}, author = {Matthews, JL and Oakley, CA and Lutz, A and Hillyer, KE and Roessner, U and Grossman, AR and Weis, VM and Davy, SK}, title = {Partner switching and metabolic flux in a model cnidarian-dinoflagellate symbiosis.}, journal = {Proceedings. Biological sciences}, volume = {285}, number = {1892}, pages = {}, pmid = {30487315}, issn = {1471-2954}, mesh = {Animals ; Dinoflagellida/*physiology ; *Energy Metabolism ; Sea Anemones/*physiology ; *Symbiosis ; }, abstract = {Metabolite exchange is fundamental to the viability of the cnidarian-Symbiodiniaceae symbiosis and survival of coral reefs. Coral holobiont tolerance to environmental change might be achieved through changes in Symbiodiniaceae species composition, but differences in the metabolites supplied by different Symbiodiniaceae species could influence holobiont fitness. Using [13]C stable-isotope labelling coupled to gas chromatography-mass spectrometry, we characterized newly fixed carbon fate in the model cnidarian Exaiptasia pallida (Aiptasia) when experimentally colonized with either native Breviolum minutum or non-native Durusdinium trenchii Relative to anemones containing B. minutum, D. trenchii-colonized hosts exhibited a 4.5-fold reduction in [13]C-labelled glucose and reduced abundance and diversity of [13]C-labelled carbohydrates and lipogenesis precursors, indicating symbiont species-specific modifications to carbohydrate availability and lipid storage. Mapping carbon fate also revealed significant alterations to host molecular signalling pathways. In particular, D. trenchii-colonized hosts exhibited a 40-fold reduction in [13]C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. [13]C-labelling also highlighted differential antioxidant- and ammonium-producing pathway activities, suggesting physiological responses to different symbiont species. Such differences in symbiont metabolite contribution and host utilization may limit the proliferation of stress-driven symbioses; this contributes valuable information towards future scenarios that select in favour of less-competent symbionts in response to environmental change.}, }
@article {pmid30472481, year = {2019}, author = {Marangoni, LFB and Pinto, MMAN and Marques, JA and Bianchini, A}, title = {Copper exposure and seawater acidification interaction: Antagonistic effects on biomarkers in the zooxanthellate scleractinian coral Mussismilia harttii.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {206}, number = {}, pages = {123-133}, doi = {10.1016/j.aquatox.2018.11.005}, pmid = {30472481}, issn = {1879-1514}, mesh = {Animals ; Anthozoa/*drug effects ; Biomarkers/*metabolism ; Chlorophyll A/analysis ; Copper/*toxicity ; Hydrogen-Ion Concentration ; Photosynthesis/drug effects ; Seawater/*chemistry ; Water Pollutants, Chemical/toxicity ; }, abstract = {Coral reefs are threatened by global and local impacts, such as ocean acidification (OA) and metal contamination. Toxicity of metals, such as copper (Cu), is expected to be enhanced with OA. However, the interaction between these environmental stressors is still poorly evaluated. In the present study, the interactive effects of seawater acidification and increasing Cu concentrations were evaluated in a zooxanthellate scleractinian coral (Mussismilia harttii), using biochemical biomarkers involved in the coral calcification process and the photosynthetic metabolism of endosymbionts. Corals were kept under control conditions (no seawater acidification and no Cu addition in seawater) or exposed to combined treatments of reduced seawater pH (8.1, 7.8, 7.5 and 7.2) and environmentally relevant concentrations of dissolved Cu (measured: 1.0, 1.6, 2.3 and 3.2 μg/L) in a mesocosm system. After 15- and 35-days exposure, corals were analyzed for photochemical efficiency (Fv/Fm), chlorophyll a content, Ca-ATPase and carbonic anhydrase (CA) activity. Results showed that 76% of the interactions between reduced seawater pH and increasing Cu concentrations were antagonistic. Only 24% of these interactions were additive or synergistic. In general, the combination of stressors had no significant deleterious effects in the photosynthetic metabolism of endosymbionts or Ca-ATPase activity. In fact, the lowest dissolved Cu concentration tested had a consistent positive effect on Ca-ATPase activity in corals facing any of the reduced seawater pH conditions tested. In turn, potentially deleterious effects on acid-base balance in M. harttii, associated with changes in CA activity, were intensified by the combination of stressors. Findings reported here indicate that Cu toxicity in future OA scenarios can be less severe than previously suggested in this coral holobiont.}, }
@article {pmid30454554, year = {2018}, author = {Kokou, F and Sasson, G and Nitzan, T and Doron-Faigenboim, A and Harpaz, S and Cnaani, A and Mizrahi, I}, title = {Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature.}, journal = {eLife}, volume = {7}, number = {}, pages = {}, pmid = {30454554}, issn = {2050-084X}, support = {Grant 640384//European Research Council/International ; }, mesh = {Adaptation, Physiological/*genetics ; Animals ; Biodiversity ; Buffers ; *Cold Temperature ; Gastrointestinal Microbiome/genetics ; Gene Dosage ; Linear Models ; Liver/metabolism ; Microbiota/*genetics ; Phenotype ; Phylogeny ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Selection, Genetic ; Tilapia/*genetics/*physiology ; Transcriptome/genetics ; }, abstract = {The hologenome concept proposes that microbes and their host organism are an independent unit of selection. Motivated by this concept, we hypothesized that thermal acclimation in poikilothermic organisms, owing to their inability to maintain their body temperature, is connected to their microbiome composition. To test this hypothesis, we used a unique experimental setup with a transgenerational selective breeding scheme for cold tolerance in tropical tilapias. We tested the effects of the selection on the gut microbiome and on host transcriptomic response. Interestingly, we found that host genetic selection for thermal tolerance shapes the microbiome composition and its response to cold. The microbiomes of cold-resistant fish showed higher resilience to temperature changes, indicating that the microbiome is shaped by its host's selection. These findings are consistent with the hologenome concept and highlight the connection between the host and its microbiome's response to the environment.}, }
@article {pmid30443242, year = {2018}, author = {O'Brien, PA and Smith, HA and Fallon, S and Fabricius, K and Willis, BL and Morrow, KM and Bourne, DG}, title = {Elevated CO2 Has Little Influence on the Bacterial Communities Associated With the pH-Tolerant Coral, Massive Porites spp.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2621}, pmid = {30443242}, issn = {1664-302X}, abstract = {Ocean acidification (OA) as a result of increased anthropogenic CO2 input into the atmosphere carries consequences for all ocean life. Low pH can cause a shift in coral-associated microbial communities of pCO2-sensitive corals, however, it remains unknown whether the microbial community is also influenced in corals known to be more tolerant to high pCO2/low pH. This study profiles the bacterial communities associated with the tissues of the pCO2-tolerant coral, massive Porites spp., from two natural CO2 seep sites in Papua New Guinea. Amplicon sequencing of the hypervariable V3-V4 regions of the 16S rRNA gene revealed that microbial communities remained stable across CO2 seep sites (pH = 7.44-7.85) and adjacent control sites (ambient pH = 8.0-8.1). Microbial communities were more significantly influenced by reef location than pH, with the relative abundance of dominant microbial taxa differing between reefs. These results directly contrast with previous findings that increased CO2 has a strong effect on structuring microbial communities. The stable structure of microbial communities associated with the tissues of massive Porites spp. under high pCO2/low pH conditions confirms a high degree of tolerance by the whole Porites holobiont to OA, and suggest that pH tolerant corals such as Porites may dominate reef assemblages in an increasingly acidic ocean.}, }
@article {pmid30427096, year = {2018}, author = {Goüy de Bellocq, J and Wasimuddin,  and Ribas, A and Bryja, J and Piálek, J and Baird, SJE}, title = {Holobiont suture zones: Parasite evidence across the European house mouse hybrid zone.}, journal = {Molecular ecology}, volume = {27}, number = {24}, pages = {5214-5227}, doi = {10.1111/mec.14938}, pmid = {30427096}, issn = {1365-294X}, support = {14-35009S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; 15-13265S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; 16-20049S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; 16-23773S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/International ; //Czech Science Foundation is the english translation of Grantova Agentura Ceske Republiky/International ; }, mesh = {Animals ; Czech Republic ; DNA, Mitochondrial/genetics ; Genetic Markers ; *Genetics, Population ; Genotype ; Germany ; *Hybridization, Genetic ; Mice/genetics/*parasitology ; Nematoda/genetics ; Parasites/*genetics ; Phylogeny ; Pneumocystis/genetics ; }, abstract = {Parasite hybrid zones resulting from host secondary contact have never been described in nature although parasite hybridization is well known and secondary contact should affect them similarly to free-living organisms. When host populations are isolated, diverge and recontact, intimate parasites (host specific, direct life cycle) carried during isolation will also meet and so may form parasite hybrid zones. If so, we hypothesize these should be narrower than the host's hybrid zone as shorter parasite generation time allows potentially higher divergence. We investigate multilocus genetics of two parasites across the European house mouse hybrid zone. We find each host taxon harbours its own parasite taxa. These also hybridize: Parasite hybrid zones are significantly narrower than the host's. Here, we show a host hybrid zone is a suture zone for a subset of its parasite community and highlight the potential of such systems as windows on the evolutionary processes of host-parasite interactions and recombinant pathogen emergence.}, }
@article {pmid30424933, year = {2019}, author = {Castillo-Álvarez, F and Marzo-Sola, ME}, title = {Disease of the holobiont, the example of multiple sclerosis.}, journal = {Medicina clinica}, volume = {152}, number = {4}, pages = {147-153}, doi = {10.1016/j.medcli.2018.08.019}, pmid = {30424933}, issn = {1578-8989}, mesh = {Animals ; Disease Models, Animal ; Encephalomyelitis, Autoimmune, Experimental/immunology/*microbiology/prevention &amp; control ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Immunity, Cellular ; Male ; Multiple Sclerosis/*microbiology ; Sex Factors ; Symbiosis ; }, abstract = {In recent years there has been a revolution regarding the role of the microbiota in different diseases, most of them within the spectrum of inflammatory and autoimmune diseases, associated with the development of metagenomics and the concept of holobiont, a large organism together with its microbiota. Specifically, in Multiple Sclerosis, multiple evidence points to the role of the microbiota in experimental autoimmune encephalomyelitis, animal model of the disease, and several articles have been published in recent years about differences in intestinal microbiota among patients with multiple sclerosis and control subjects. We review in this article the concept of holobiont and the gut microbiota functions, as well as the evidence accumulated about the role of the microbiota in experimental autoimmune encephalomyelitis and multiple sclerosis. Nowadays, there is a lot of evidence showing the role of the microbiota in the genesis, prevention and treatment of experimental autoimmune encephalomyelitis based mainly on three immunological pillars, the Th1-Th17 / Th2 balance, the Treg cells and the humoral immunity. It is also well documented that there are differences in the microbiota of patients with MS that are associated with a different expression of genes related to inflammation.}, }
@article {pmid30420844, year = {2018}, author = {Galand, PE and Chapron, L and Meistertzheim, AL and Peru, E and Lartaud, F}, title = {The Effect of Captivity on the Dynamics of Active Bacterial Communities Differs Between Two Deep-Sea Coral Species.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2565}, pmid = {30420844}, issn = {1664-302X}, abstract = {Microbes play a crucial role in sustaining the coral holobiont's functions and in particular under the pressure of environmental stressors. The effect of a changing environment on coral health is now a major branch of research that relies heavily on aquarium experiments. However, the effect of captivity on the coral microbiome remains poorly known. Here we show that different cold-water corals species have different microbiome responses to captivity. For both the DNA and the RNA fraction, Madrepora oculata bacterial communities were maintained for at least 6 months of aquarium rearing, while Lophelia pertusa bacteria changed within a day. Interestingly, bacteria from the genus Endozoicomonas, a ubiquitous symbiont of numerous marine hosts, were resilient and remained active in M. oculata for several months. Our results demonstrate that a good knowledge of the coral microbiome and an understanding of the ecological strategy of the holobiont is needed before designing aquarium experiments.}, }
@article {pmid30417121, year = {2018}, author = {Ochsenkühn, MA and Schmitt-Kopplin, P and Harir, M and Amin, SA}, title = {Coral metabolite gradients affect microbial community structures and act as a disease cue.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {184}, pmid = {30417121}, issn = {2399-3642}, abstract = {Corals are threatened worldwide due to prevalence of disease and bleaching. Recent studies suggest the ability of corals to resist disease is dependent on maintaining healthy microbiomes that span coral tissues and surfaces, the holobiont. Although our understanding of the role endosymbiotic microbes play in coral health has advanced, the role surface-associated microbes and their chemical signatures play in coral health is limited. Using minimally invasive water sampling, we show that the corals Acropora and Platygyra harbor unique bacteria and metabolites at their surface, distinctly different from surrounding seawater. The surface metabolites released by the holobiont create concentration gradients at 0-5 cm away from the coral surface. These molecules are identified as chemo-attractants, antibacterials, and infochemicals, suggesting they may structure coral surface-associated microbes. Further, we detect surface-associated metabolites characteristic of healthy or white syndrome disease infected corals, a finding which may aid in describing effects of diseases.}, }
@article {pmid30417109, year = {2018}, author = {Mazel, F and Davis, KM and Loudon, A and Kwong, WK and Groussin, M and Parfrey, LW}, title = {Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?.}, journal = {mSystems}, volume = {3}, number = {5}, pages = {}, pmid = {30417109}, issn = {2379-5077}, abstract = {Host-associated microbiota composition can be conserved over evolutionary time scales. Indeed, closely related species often host similar microbiota; i.e., the composition of their microbiota harbors a phylogenetic signal, a pattern sometimes referred to as "phylosymbiosis." Elucidating the origins of this pattern is important to better understand microbiota ecology and evolution. However, this is hampered by our lack of theoretical expectations and a comprehensive overview of phylosymbiosis prevalence in nature. Here, we use simulations to provide a simple expectation for when we should expect this pattern to occur and then review the literature to document the prevalence and strength of phylosymbiosis across the host tree of life. We demonstrate that phylosymbiosis can readily emerge from a simple ecological filtering process, whereby a given host trait (e.g., gut pH) that varies with host phylogeny (i.e., harbors a phylogenetic signal) filters preadapted microbes. We found marked differences between methods used to detect phylosymbiosis, so we proposed a series of practical recommendations based on using multiple best-performing approaches. Importantly, we found that, while the prevalence of phylosymbiosis is mixed in nature, it appears to be stronger for microbiotas living in internal host compartments (e.g., the gut) than those living in external compartments (e.g., the rhizosphere). We show that phylosymbiosis can theoretically emerge without any intimate, long-term coevolutionary mechanisms and that most phylosymbiosis patterns observed in nature are compatible with a simple ecological process. Deviations from baseline ecological expectations might be used to further explore more complex hypotheses, such as codiversification. IMPORTANCE Phylosymbiosis is a pattern defined as the tendency of closely related species to host microbiota whose compositions resemble each other more than host species drawn at random from the same tree. Understanding the mechanisms behind phylosymbiosis is important because it can shed light on rules governing the assembly of host-associated microbiotas and, potentially, their coevolutionary dynamics with hosts. For example, is phylosymbiosis a result of coevolution, or can it be generated by simple ecological filtering processes? Beyond qualitative theoretical models, quantitative theoretical expectations can provide new insights. For example, deviations from a simple baseline of ecological filtering may be used to test more-complex hypotheses (e.g., coevolution). Here, we use simulations to provide evidence that simple host-related ecological filtering can readily generate phylosymbiosis, and we contrast these predictions with real-world data. We find that while phylosymbiosis is widespread in nature, phylosymbiosis patterns are compatible with a simple ecological model in the majority of taxa. Internal compartments of hosts, such as the animal gut, often display stronger phylosymbiosis than expected from a purely ecological filtering process, suggesting that other mechanisms are also involved.}, }
@article {pmid30413836, year = {2019}, author = {Villegas-Plazas, M and Wos-Oxley, ML and Sanchez, JA and Pieper, DH and Thomas, OP and Junca, H}, title = {Variations in Microbial Diversity and Metabolite Profiles of the Tropical Marine Sponge Xestospongia muta with Season and Depth.}, journal = {Microbial ecology}, volume = {78}, number = {1}, pages = {243-256}, pmid = {30413836}, issn = {1432-184X}, support = {KBBE-2009-245226//MAGICPAH/ ; 652-2014//EcosNord-Colciencias/ ; JI-2012//J&#xf3;ven Investigador - Colciencias/ ; MSc scholarship//Universidad de los Andes/ ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Caribbean Region ; Coral Reefs ; *Microbiota ; Panama ; Phylogeny ; Seasons ; Seawater/*chemistry/microbiology ; Symbiosis ; Xestospongia/*microbiology/physiology ; }, abstract = {Xestospongia muta is among the most emblematic sponge species inhabiting coral reefs of the Caribbean Sea. Besides being the largest sponge species growing in the Caribbean, it is also known to produce secondary metabolites. This study aimed to assess the effect of depth and season on the symbiotic bacterial dynamics and major metabolite profiles of specimens of X. muta thriving in a tropical marine biome (Portobelo Bay, Panamá), which allow us to determine whether variability patterns are similar to those reported for subtropical latitudes. The bacterial assemblages were characterized using Illumina deep-sequencing and metabolomic profiles using UHPLC-DAD-ELSD from five depths (ranging 9-28 m) across two seasons (spring and autumn). Diverse symbiotic communities, representing 24 phyla with a predominance of Proteobacteria and Chloroflexi, were found. Although several thousands of OTUs were determined, most of them belong to the rare biosphere and only 23 to a core community. There was a significant difference between the structure of the microbial communities in respect to season (autumn to spring), with a further significant difference between depths only in autumn. This was partially mirrored in the metabolome profile, where the overall metabolite composition did not differ between seasons, but a significant depth gradient was observed in autumn. At the phyla level, Cyanobacteria, Firmicutes, Actinobacteria, and Spirochaete showed a mild-moderate correlation with the metabolome profile. The metabolomic profiles were mainly characterized by known brominated polyunsaturated fatty acids. This work presents findings about the composition and dynamics of the microbial assemblages of X. muta expanding and confirming current knowledge about its remarkable diversity and geographic variability as observed in this tropical marine biome.}, }
@article {pmid30410727, year = {2018}, author = {Morris, JJ}, title = {What is the hologenome concept of evolution?.}, journal = {F1000Research}, volume = {7}, number = {}, pages = {}, pmid = {30410727}, issn = {2046-1402}, mesh = {Animals ; *Biological Evolution ; Biota ; Genome ; Humans ; Microbiota/*genetics ; Phenotype ; Selection, Genetic ; }, abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a "holobiont". Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the "hologenome", or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.}, }
@article {pmid30405652, year = {2018}, author = {Backer, R and Rokem, JS and Ilangumaran, G and Lamont, J and Praslickova, D and Ricci, E and Subramanian, S and Smith, DL}, title = {Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {1473}, pmid = {30405652}, issn = {1664-462X}, abstract = {Microbes of the phytomicrobiome are associated with every plant tissue and, in combination with the plant form the holobiont. Plants regulate the composition and activity of their associated bacterial community carefully. These microbes provide a wide range of services and benefits to the plant; in return, the plant provides the microbial community with reduced carbon and other metabolites. Soils are generally a moist environment, rich in reduced carbon which supports extensive soil microbial communities. The rhizomicrobiome is of great importance to agriculture owing to the rich diversity of root exudates and plant cell debris that attract diverse and unique patterns of microbial colonization. Microbes of the rhizomicrobiome play key roles in nutrient acquisition and assimilation, improved soil texture, secreting, and modulating extracellular molecules such as hormones, secondary metabolites, antibiotics, and various signal compounds, all leading to enhancement of plant growth. The microbes and compounds they secrete constitute valuable biostimulants and play pivotal roles in modulating plant stress responses. Research has demonstrated that inoculating plants with plant-growth promoting rhizobacteria (PGPR) or treating plants with microbe-to-plant signal compounds can be an effective strategy to stimulate crop growth. Furthermore, these strategies can improve crop tolerance for the abiotic stresses (e.g., drought, heat, and salinity) likely to become more frequent as climate change conditions continue to develop. This discovery has resulted in multifunctional PGPR-based formulations for commercial agriculture, to minimize the use of synthetic fertilizers and agrochemicals. This review is an update about the role of PGPR in agriculture, from their collection to commercialization as low-cost commercial agricultural inputs. First, we introduce the concept and role of the phytomicrobiome and the agricultural context underlying food security in the 21st century. Next, mechanisms of plant growth promotion by PGPR are discussed, including signal exchange between plant roots and PGPR and how these relationships modulate plant abiotic stress responses via induced systemic resistance. On the application side, strategies are discussed to improve rhizosphere colonization by PGPR inoculants. The final sections of the paper describe the applications of PGPR in 21st century agriculture and the roadmap to commercialization of a PGPR-based technology.}, }
@article {pmid30404178, year = {2018}, author = {Pasquaretta, C and Gómez-Moracho, T and Heeb, P and Lihoreau, M}, title = {Exploring Interactions between the Gut Microbiota and Social Behavior through Nutrition.}, journal = {Genes}, volume = {9}, number = {11}, pages = {}, pmid = {30404178}, issn = {2073-4425}, support = {ANR-16-CE02-0002-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-41//Laboratoire d'Excellence (LABEX)' TULIP/ ; }, abstract = {Microbes influence a wide range of host social behaviors and vice versa. So far, however, the mechanisms underpinning these complex interactions remain poorly understood. In social animals, where individuals share microbes and interact around foods, the gut microbiota may have considerable consequences on host social interactions by acting upon the nutritional behavior of individual animals. Here we illustrate how conceptual advances in nutritional ecology can help the study of these processes and allow the formulation of new empirically testable predictions. First, we review key evidence showing that gut microbes influence the nutrition of individual animals, through modifications of their nutritional state and feeding decisions. Next, we describe how these microbial influences and their social consequences can be studied by modelling populations of hosts and their gut microbiota into a single conceptual framework derived from nutritional geometry. Our approach raises new perspectives for the study of holobiont nutrition and will facilitate theoretical and experimental research on the role of the gut microbiota in the mechanisms and evolution of social behavior.}, }
@article {pmid30386791, year = {2018}, author = {Sewell, AK and Han, M and Qi, B}, title = {An unexpected benefit from E. coli: how enterobactin benefits host health.}, journal = {Microbial cell (Graz, Austria)}, volume = {5}, number = {10}, pages = {469-471}, doi = {10.15698/mic2018.10.653}, pmid = {30386791}, issn = {2311-2638}, abstract = {Iron plays many critical roles in human biology, such as aiding the transport of oxygen and mediating redox reactions. Iron is essential for life, yet little is known about how iron is taken up into mitochondria to impact the labile iron pool. Iron deficiency is one of the most prevalent human nutrient-deficiency diseases in the world and is a major cause of anemia that affects >25% of the world's population, but unfortunately the current treatment (oral iron supplementation) is inefficient and has many side effects. A greater understanding of iron uptake, and discovery of molecules that aid in this process, may lead to more effective treatments for iron deficiency. In this study, we uncovered a unique and surprising role for an Escherichia coli-produced siderophore enterobactin (Ent) that facilitates iron uptake by the host, observed in both C. elegans and mammalian cells. Although siderophores are well-known Fe[+3] scavengers, this activity has previously been described to only benefit iron acquisition by bacteria, not the host. This unexpected function is dependent on the binding of Ent to the host's ATP synthase α-subunit but is independent of other subunits of the ATP synthase. This finding marks a major shift regarding the role of this siderophore in the "iron tug-of-war" paradigm, which is often used to describe the fight between the bacteria and the host for this essential micronutrient. Instead, this study presents E. coli as a commensal "friend" that provides a molecule that supports the host's iron homeostasis. This work reveals a novel, beneficial role of a bacteria-generated molecule in aiding the host's iron homeostasis, and points to surprising new benefits from commensal bacteria.}, }
@article {pmid30358445, year = {2018}, author = {Sigwart, JD and Chen, C}, title = {Comparative Oxygen Consumption of Gastropod Holobionts from Deep-Sea Hydrothermal Vents in the Indian Ocean.}, journal = {The Biological bulletin}, volume = {235}, number = {2}, pages = {102-112}, doi = {10.1086/699326}, pmid = {30358445}, issn = {1939-8697}, mesh = {Animals ; Gastropoda/*metabolism ; *Hydrothermal Vents ; Indian Ocean ; Oxygen Consumption/*physiology ; Symbiosis/*physiology ; Temperature ; }, abstract = {Physiological traits are the foundation of an organism's success in a dynamic environment, yet basic measurements are unavailable for many taxa and even ecosystems. We measured routine metabolism in two hydrothermal vent gastropods, Alviniconcha marisindica (n = 40) and the scaly-foot gastropod Chrysomallon squamiferum (n = 18), from Kairei and Edmond vent fields on the Central Indian Ridge (23-25°S, about 3000 meter depth). No previous studies have measured metabolism in any Indian Ocean vent animals. After recovering healthy animals to the surface, we performed shipboard closed-chamber respirometry experiments to compare oxygen uptake at different temperatures (10, 16, and 25 °C) at surface pressure (1 atm). The physiology of these species is driven by the demands of their chemoautotrophic symbionts. Chrysomallon has very enlarged respiratory and circulatory systems, and endosymbionts are housed in its trophosome-like internal esophageal gland. By contrast, Alviniconcha has chemoautotrophic bacteria within the gill and less extensive associated anatomical adaptations. Thus, we predicted that routine oxygen consumption of Chrysomallon might be higher than that of Alviniconcha. However, oxygen consumption of Chrysomallon was not higher than that of Alviniconcha, and, further, Chrysomallon maintained a steady metabolic demand in two widely separated experimental temperatures, while Alviniconcha did not. We interpret that these findings indicate that (1) the "trophosome" does not fundamentally increase oxygen requirement compared to other gastropod holobionts, and (2) cold temperatures (10 °C) induce a stress response in Alviniconcha, resulting in aberrantly high uptake. While these two large gastropod species co-occur, differences in oxygen consumption may reflect the separate niches they occupy in the vent ecosystem.}, }
@article {pmid30336184, year = {2019}, author = {Miller, WB and Torday, JS and Baluška, F}, title = {Biological evolution as defense of 'self'.}, journal = {Progress in biophysics and molecular biology}, volume = {142}, number = {}, pages = {54-74}, doi = {10.1016/j.pbiomolbio.2018.10.002}, pmid = {30336184}, issn = {1873-1732}, mesh = {*Biological Evolution ; Cell Physiological Phenomena ; Cells/metabolism ; Cognition/physiology ; Consciousness/*physiology ; Emotions/physiology ; Homeostasis/physiology ; Humans ; Intelligence/physiology ; Signal Transduction ; }, abstract = {Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement of the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference. The means by which these states are attained and maintained is through self-referential measurement of information and its communication. The multicellular forms, either as biofilms or holobionts, represent the cellular attempt to achieve maximum states of informational distinction and energy efficiency through individual and collective means. In this frame, consciousness, self-consciousness and intelligence can be identified as forms of collective cellular phenotype directed towards the defense of fundamental cellular self-reference.}, }
@article {pmid30328280, year = {2019}, author = {Thomashow, LS and LeTourneau, MK and Kwak, YS and Weller, DM}, title = {The soil-borne legacy in the age of the holobiont.}, journal = {Microbial biotechnology}, volume = {12}, number = {1}, pages = {51-54}, pmid = {30328280}, issn = {1751-7915}, mesh = {Agriculture/*methods ; *Plant Development ; Plant Diseases/microbiology/*prevention &amp; control ; Plants/immunology/*microbiology ; *Soil Microbiology ; Symbiosis ; }, abstract = {Future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated microflora in the context of the various environments in which they are grown. It is suggested that future efforts to increase agricultural productivity will focus on crops as functional units comprised of plants and their associated beneficial microorganisms in the context in which they are grown. Scientists, industry, and farmers must work closely together to develop, adapt, and apply new technologies to a wide range of cropping systems. Consumer education is needed help grow public awareness that 'plant probiotics' offer a safe and environmentally friendly alternative to dependence on the use of chemical pesticides.}, }
@article {pmid30311675, year = {2018}, author = {Leftwich, PT and Hutchings, MI and Chapman, T}, title = {Diet, Gut Microbes and Host Mate Choice: Understanding the significance of microbiome effects on host mate choice requires a case by case evaluation.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {12}, pages = {e1800053}, doi = {10.1002/bies.201800053}, pmid = {30311675}, issn = {1521-1878}, support = {BB/K000489/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Alleles ; Animals ; Biological Evolution ; *Diet ; Drosophila melanogaster/physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Male ; Mating Preference, Animal/*physiology ; Symbiosis ; Wolbachia/physiology ; }, abstract = {All organisms live in close association with microbes. However, not all such associations are meaningful in an evolutionary context. Current debate concerns whether hosts and microbes are best described as communities of individuals or as holobionts (selective units of hosts plus their microbes). Recent reports that assortative mating of hosts by diet can be mediated by commensal gut microbes have attracted interest as a potential route to host reproductive isolation (RI). Here, the authors discuss logical problems with this line of argument. The authors briefly review how microbes can affect host mating preferences and evaluate recent findings from fruitflies. Endosymbionts can potentially influence host RI given stable and recurrent co-association of hosts and microbes over evolutionary time. However, observations of co-occurrence of microbes and hosts are ripe for misinterpretation and such associations will rarely represent a meaningful holobiont. A framework in which hosts and their microbes are independent evolutionary units provides the only satisfactory explanation for the observed range of effects and associations.}, }
@article {pmid30310167, year = {2019}, author = {Cernava, T and Aschenbrenner, IA and Soh, J and Sensen, CW and Grube, M and Berg, G}, title = {Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota.}, journal = {The ISME journal}, volume = {13}, number = {2}, pages = {547-556}, pmid = {30310167}, issn = {1751-7370}, support = {I 882/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ascomycota/genetics/*physiology ; Bacteria/genetics/*metabolism ; Dehydration ; Gene Expression Regulation, Bacterial ; Lichens/*microbiology ; Microbiota/*physiology ; Water ; }, abstract = {The role of host-associated microbiota in enduring dehydration and drought is largely unknown. We have used lichens to study this increasingly important problem because they are the organisms that are optimally adapted to reoccurring hydration/dehydration cycles, and they host a defined and persistent bacterial community. The analysis of metatranscriptomic datasets from bacterial communities of the lung lichen (Lobaria pulmonaria (L.) Hoffm.), sampled under representative hydration stages, revealed significant structural shifts and functional specialization to host conditions. The hydrated samples showed upregulated transcription of transport systems, tRNA modification and various porins (Omp2b by Rhizobiales), whereas the desiccated samples showed different functions related to stress adaption prominently. Carbohydrate metabolism was activated under both conditions. Under dry conditions, upregulation of a specialized ketone metabolism indicated a switch to lipid-based nutrition. Several bacterial lineages were involved in a functional transition that was reminiscent of a 'fasting metaorganism'. Similar functional adaptions were assigned to taxonomically unrelated groups, indicating hydration-related specialization of the microbiota. We were able to show that host-associated bacterial communities are well adapted to dehydration by stress protection and changes of the metabolism. Moreover, our results indicate an intense interplay in holobiont functioning under drought stress.}, }
@article {pmid30309375, year = {2018}, author = {Zepeda Mendoza, ML and Roggenbuck, M and Manzano Vargas, K and Hansen, LH and Brunak, S and Gilbert, MTP and Sicheritz-Pontén, T}, title = {Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging.}, journal = {Acta veterinaria Scandinavica}, volume = {60}, number = {1}, pages = {61}, pmid = {30309375}, issn = {1751-0147}, support = {R52-A5062//Lundbeckfonden/ ; }, mesh = {Adaptation, Biological ; Animals ; Animals, Wild/microbiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Falconiformes/*microbiology/physiology ; *Feeding Behavior ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Skin/*microbiology ; }, abstract = {BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut.<br><br>RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut.<br><br>CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging.}, }
@article {pmid30305166, year = {2018}, author = {Guyomar, C and Legeai, F and Jousselin, E and Mougel, C and Lemaitre, C and Simon, JC}, title = {Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {181}, pmid = {30305166}, issn = {2049-2618}, mesh = {Animals ; Aphids/*microbiology ; Buchnera/classification/genetics/*isolation &amp; purification ; Genome, Bacterial/genetics ; Metagenome/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Rickettsia/classification/genetics/*isolation &amp; purification ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Most metazoans are involved in durable relationships with microbes which can take several forms, from mutualism to parasitism. The advances of NGS technologies and bioinformatics tools have opened opportunities to shed light on the diversity of microbial communities and to give some insights into the functions they perform in a broad array of hosts. The pea aphid is a model system for the study of insect-bacteria symbiosis. It is organized in a complex of biotypes, each adapted to specific host plants. It harbors both an obligatory symbiont supplying key nutrients and several facultative symbionts bringing additional functions to the host, such as protection against biotic and abiotic stresses. However, little is known on how the symbiont genomic diversity is structured at different scales: across host biotypes, among individuals of the same biotype, or within individual aphids, which limits our understanding on how these multi-partner symbioses evolve and interact.<br><br>RESULTS: We present a framework well adapted to the study of genomic diversity and evolutionary dynamics of the pea aphid holobiont from metagenomic read sets, based on mapping to reference genomes and whole genome variant calling. Our results revealed that the pea aphid microbiota is dominated by a few heritable bacterial symbionts reported in earlier works, with no discovery of new microbial associates. However, we detected a large and heterogeneous genotypic diversity associated with the different symbionts of the pea aphid. Partitioning analysis showed that this fine resolution diversity is distributed across the three considered scales. Phylogenetic analyses highlighted frequent horizontal transfers of facultative symbionts between host lineages, indicative of flexible associations between the pea aphid and its microbiota. However, the evolutionary dynamics of symbiotic associations strongly varied depending on the symbiont, reflecting different histories and possible constraints. In addition, at the intra-host scale, we showed that different symbiont strains may coexist inside the same aphid host.<br><br>CONCLUSIONS: We present a methodological framework for the detailed analysis of NGS data from microbial communities of moderate complexity and gave major insights into the extent of diversity in pea aphid-symbiont associations and the range of evolutionary trajectories they could take.}, }
@article {pmid30301849, year = {2018}, author = {Hernandez-Agreda, A and Leggat, W and Bongaerts, P and Herrera, C and Ainsworth, TD}, title = {Rethinking the Coral Microbiome: Simplicity Exists within a Diverse Microbial Biosphere.}, journal = {mBio}, volume = {9}, number = {5}, pages = {}, pmid = {30301849}, issn = {2150-7511}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification ; Genetic Variation ; *Host Microbial Interactions ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; Symbiosis ; }, abstract = {Studies of the coral microbiome predominantly characterize the microbial community of the host species as a collective, rather than that of the individual. This ecological perspective on the coral microbiome has led to the conclusion that the coral holobiont is the most diverse microbial biosphere studied thus far. However, investigating the microbiome of the individual, rather than that of the species, highlights common and conserved community attributes which can provide insights into the significance of microbial associations to the host. Here, we show there are consistent characteristics between individuals in the proposed three components of the coral microbiome (i.e., "environmentally responsive community," "resident or individual microbiome," and "core microbiome"). We found that the resident microbiome of a photoendosymbiotic coral harbored <3% (∼605 phylotypes) of the 16S rRNA phylotypes associated with all investigated individuals of that species ("species-specific microbiome") (∼21,654 phylotypes; individuals from Pachyseris speciosa [n = 123], Mycedium elephantotus [n = 95], and Acropora aculeus [n = 91] from 10 reef locations). The remaining bacterial phylotypes (>96%) (environmentally responsive community) of the species-specific microbiome were in fact not found in association with the majority of individuals of the species. Only 0.1% (∼21 phylotypes) of the species-specific microbiome of each species was shared among all individuals of the species (core microbiome), equating to ∼3.4% of the resident microbiome. We found taxonomic redundancy and consistent patterns of composition, structure, and taxonomic breadth across individual microbiomes from the three coral species. Our results demonstrate that the coral microbiome is structured at the individual level.IMPORTANCE We propose that the coral holobiont should be conceptualized as a diverse transient microbial community that is responsive to the surrounding environment and encompasses a simple, redundant, resident microbiome and a small conserved core microbiome. Most importantly, we show that the coral microbiome is comparable to the microbiomes of other organisms studied thus far. Accurately characterizing the coral-microbe interactions provides an important baseline from which the functional roles and the functional niches within which microbes reside can be deciphered.}, }
@article {pmid30286722, year = {2018}, author = {Mancini, MV and Damiani, C and Accoti, A and Tallarita, M and Nunzi, E and Cappelli, A and Bozic, J and Catanzani, R and Rossi, P and Valzano, M and Serrao, A and Ricci, I and Spaccapelo, R and Favia, G}, title = {Estimating bacteria diversity in different organs of nine species of mosquito by next generation sequencing.}, journal = {BMC microbiology}, volume = {18}, number = {1}, pages = {126}, pmid = {30286722}, issn = {1471-2180}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Biodiversity ; Culicidae/classification/*microbiology ; DNA, Bacterial/genetics ; Female ; High-Throughput Nucleotide Sequencing ; Male ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Symbiosis in insects is accumulating significant amount of studies: the description of a wide array of mutualistic associations across the evolutionary history of insects suggests that resident microbiota acts as a driving force by affecting several aspects of hosts biology. Among arthropods, mosquito midgut microbiota has been largely investigated, providing crucial insights on the role and implications of host-symbiont relationships. However, limited amount of studies addressed their efforts on the investigation of microbiota colonizing salivary glands and reproductive tracts, crucial organs for pathogen invasion and vertical transmission of symbiotic microorganisms. Using 16S rRNA gene sequencing-based approach, we analysed the microbiota of gut, salivary glands and reproductive tracts of several mosquito species, representing some of the main vectors of diseases, aiming at describing the dynamics of bacterial communities within the individual.<br><br>RESULTS: We identified a shared core microbiota between different mosquito species, although interesting inter- and intra-species differences were detected. Additionally, our results showed deep divergences between genera, underlining microbiota specificity and adaptation to their host.<br><br>CONCLUSIONS: The comprehensive landscape of the bacterial microbiota components may ultimately provide crucial insights and novel targets for possible application of symbionts in innovative strategies for the control of vector borne diseases, globally named Symbiotic Control (SC), and suggesting that the holobiont of different mosquito species may significantly vary. Moreover, mosquito species are characterized by distinctive microbiota in different organs, likely reflecting different functions and/or adaptation processes.}, }
@article {pmid30274716, year = {2018}, author = {Batista, D and Costa, R and Carvalho, AP and Batista, WR and Rua, CPJ and de Oliveira, L and Leomil, L and Fróes, AM and Thompson, FL and Coutinho, R and Dobretsov, S}, title = {Environmental conditions affect activity and associated microorganisms of marine sponges.}, journal = {Marine environmental research}, volume = {142}, number = {}, pages = {59-68}, doi = {10.1016/j.marenvres.2018.09.020}, pmid = {30274716}, issn = {1879-0291}, mesh = {Animals ; Aquatic Organisms/chemistry/drug effects/microbiology ; *Environment ; Microbiota/*drug effects ; Porifera/chemistry/drug effects/*microbiology ; Water Pollutants/*toxicity ; }, abstract = {Changes in environmental conditions can influence sponges and their holobionts. The present study investigated the effect of upwelling and anthropogenic pollution on the bioactivity of marine sponges, microbial communities and functional genes, and composition of their chemical compounds. The species Dysidea etheria, Darwinella sp., Hymeniacidon heliophila and Tedania ignis were collected from areas with distinct influence of upwelling and low anthropogenic impact and from areas without influence of upwelling but affected by sewage and the port. In most cases, the same sponge species collected from areas with distinct environmental conditions had a different chemical composition, antifouling activity, composition and diversity of associated microorganisms. Antimicrobial, quorum sensing inhibitory and anti-larval activities of sponge extracts were more pronounced in the area without upwelling showing higher level of anthropogenic pollution. This study suggests that upwelling and anthropogenic pollution affect the chemical activity and holobiome composition of sponges.}, }
@article {pmid30271972, year = {2018}, author = {Palmer, CV}, title = {Immunity and the coral crisis.}, journal = {Communications biology}, volume = {1}, number = {}, pages = {91}, pmid = {30271972}, issn = {2399-3642}, abstract = {Climate change is killing coral at an unprecedented rate. As immune systems promote homeostasis and survival of adverse conditions I propose we explore coral health in the context of holobiont immunity.}, }
@article {pmid30255826, year = {2018}, author = {Løvendahl, P and Difford, GF and Li, B and Chagunda, MGG and Huhtanen, P and Lidauer, MH and Lassen, J and Lund, P}, title = {Review: Selecting for improved feed efficiency and reduced methane emissions in dairy cattle.}, journal = {Animal : an international journal of animal bioscience}, volume = {12}, number = {s2}, pages = {s336-s349}, doi = {10.1017/S1751731118002276}, pmid = {30255826}, issn = {1751-732X}, mesh = {Animal Feed/*analysis ; Animals ; Cattle/genetics/*physiology ; Dairying ; Diet/veterinary ; *Eating ; *Energy Metabolism ; Female ; Fermentation ; Lactation ; Methane/*metabolism ; Milk/*metabolism ; Rumen/metabolism/microbiology ; }, abstract = {It may be possible for dairy farms to improve profitability and reduce environmental impacts by selecting for higher feed efficiency and lower methane (CH4) emission traits. It remains to be clarified how CH4 emission and feed efficiency traits are related to each other, which will require direct and accurate measurements of both of these traits in large numbers of animals under the conditions in which they are expected to perform. The ranking of animals for feed efficiency and CH4 emission traits can differ depending upon the type and duration of measurement used, the trait definitions and calculations used, the period in lactation examined and the production system, as well as interactions among these factors. Because the correlation values obtained between feed efficiency and CH4 emission data are likely to be biased when either or both are expressed as ratios, therefore researchers would be well advised to maintain weighted components of the ratios in the selection index. Nutrition studies indicate that selecting low emitting animals may result in reduced efficiency of cell wall digestion, that is NDF, a key ruminant characteristic in human food production. Moreover, many interacting biological factors that are not measured directly, including digestion rate, passage rate, the rumen microbiome and rumen fermentation, may influence feed efficiency and CH4 emission. Elucidating these mechanisms may improve dairy farmers ability to select for feed efficiency and reduced CH4 emission.}, }
@article {pmid30249182, year = {2018}, author = {Cavalcanti, GS and Shukla, P and Morris, M and Ribeiro, B and Foley, M and Doane, MP and Thompson, CC and Edwards, MS and Dinsdale, EA and Thompson, FL}, title = {Rhodoliths holobionts in a changing ocean: host-microbes interactions mediate coralline algae resilience under ocean acidification.}, journal = {BMC genomics}, volume = {19}, number = {1}, pages = {701}, pmid = {30249182}, issn = {1471-2164}, mesh = {Biodiversity ; Hydrogen-Ion Concentration ; Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Photosynthesis ; Rhodophyta/metabolism/*microbiology/physiology ; Seawater/chemistry/microbiology ; Stress, Physiological ; }, abstract = {BACKGROUND: Life in the ocean will increasingly have to contend with a complex matrix of concurrent shifts in environmental properties that impact their physiology and control their life histories. Rhodoliths are coralline red algae (Corallinales, Rhodophyta) that are photosynthesizers, calcifiers, and ecosystem engineers and therefore represent important targets for ocean acidification (OA) research. Here, we exposed live rhodoliths to near-future OA conditions to investigate responses in their photosynthetic capacity, calcium carbonate production, and associated microbiome using carbon uptake, decalcification assays, and whole genome shotgun sequencing metagenomic analysis, respectively. The results from our live rhodolith assays were compared to similar manipulations on dead rhodolith (calcareous skeleton) biofilms and water column microbial communities, thereby enabling the assessment of host-microbiome interaction under climate-driven environmental perturbations.<br><br>RESULTS: Under high pCO2 conditions, live rhodoliths exhibited positive physiological responses, i.e. increased photosynthetic activity, and no calcium carbonate biomass loss over time. Further, whereas the microbiome associated with live rhodoliths remained stable and resembled a healthy holobiont, the microbial community associated with the water column changed after exposure to elevated pCO2.<br><br>CONCLUSIONS: Our results suggest that a tightly regulated microbial-host interaction, as evidenced by the stability of the rhodolith microbiome recorded here under OA-like conditions, is important for host resilience to environmental stress. This study extends the scarce comprehension of microbes associated with rhodolith beds and their reaction to increased pCO2, providing a more comprehensive approach to OA studies by assessing the host holobiont.}, }
@article {pmid30238406, year = {2018}, author = {Stencel, A and Wloch-Salamon, DM}, title = {Correction to: Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {137}, number = {2}, pages = {207-208}, pmid = {30238406}, issn = {1611-7530}, abstract = {The original version of this article unfortunately contained a mistake.}, }
@article {pmid30233528, year = {2018}, author = {Clerissi, C and Brunet, S and Vidal-Dupiol, J and Adjeroud, M and Lepage, P and Guillou, L and Escoubas, JM and Toulza, E}, title = {Protists Within Corals: The Hidden Diversity.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {2043}, pmid = {30233528}, issn = {1664-302X}, abstract = {Previous observations suggested that microbial communities contribute to coral health and the ecological resilience of coral reefs. However, most studies of coral microbiology focused on prokaryotes and the endosymbiotic algae Symbiodinium. In contrast, knowledge concerning diversity of other protists is still lacking, possibly due to methodological constraints. As most eukaryotic DNA in coral samples was derived from hosts, protist diversity was missed in metagenome analyses. To tackle this issue, we designed blocking primers for Scleractinia sequences amplified with two primer sets that targeted variable loops of the 18S rRNA gene (18SV1V2 and 18SV4). These blocking primers were used on environmental colonies of Pocillopora damicornis sensu lato from two regions with contrasting thermal regimes (Djibouti and New Caledonia). In addition to Symbiodinium clades A/C/D, Licnophora and unidentified coccidia genera were found in many samples. In particular, coccidian sequences formed a robust monophyletic clade with other protists identified in Agaricia, Favia, Montastraea, Mycetophyllia, Porites, and Siderastrea coral colonies. Moreover, Licnophora and coccidians had different distributions between the two geographic regions. A similar pattern was observed between Symbiodinium clades C and A/D. Although we were unable to identify factors responsible for this pattern, nor were we able to confirm that these taxa were closely associated with corals, we believe that these primer sets and the associated blocking primers offer new possibilities to describe the hidden diversity of protists within different coral species.}, }
@article {pmid30224089, year = {2018}, author = {Carthey, AJR and Gillings, MR and Blumstein, DT}, title = {The Extended Genotype: Microbially Mediated Olfactory Communication.}, journal = {Trends in ecology &amp; evolution}, volume = {33}, number = {11}, pages = {885-894}, doi = {10.1016/j.tree.2018.08.010}, pmid = {30224089}, issn = {1872-8383}, mesh = {Animals ; Bacteria/genetics ; Bacterial Physiological Phenomena ; Cues ; Genotype ; Microbiota/genetics/*physiology ; *Odorants ; *Pheromones ; }, abstract = {Microbes are now known to influence inter- and intraspecific olfactory signaling systems. They do so by producing metabolites that function as odorants. A unique attribute of such odorants is that they arise as a product of microbial-host interactions. These interactions need not be mutualistic, and indeed can be antagonistic. We develop an integrated ecoevolutionary model to explore microbially mediated olfactory communication and a process model that illustrates the various ways that microbial products might contribute to odorants. This novel approach generates testable predictions, including that selection to incorporate microbial products should be a common feature of infochemicals that communicate identity but not those that communicate fitness or quality. Microbes extend an individual's genotype, but also enhance vulnerability to environmental change.}, }
@article {pmid30223906, year = {2018}, author = {Bredon, M and Dittmer, J and Noël, C and Moumen, B and Bouchon, D}, title = {Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {162}, pmid = {30223906}, issn = {2049-2618}, mesh = {Animals ; Bacteria/enzymology/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; Isopoda/*metabolism/*microbiology/physiology ; Lignin/*metabolism ; Phylogeny ; Soil/parasitology ; *Symbiosis ; }, abstract = {BACKGROUND: Woodlice are recognized as keystone species in terrestrial ecosystems due to their role in the decomposition of organic matter. Thus, they contribute to lignocellulose degradation and nutrient cycling in the environment together with other macroarthropods. Lignocellulose is the main component of plants and is composed of cellulose, lignin and hemicellulose. Its digestion requires the action of multiple Carbohydrate-Active enZymes (called CAZymes), typically acting together as a cocktail with complementary, synergistic activities and modes of action. Some invertebrates express a few endogenous lignocellulose-degrading enzymes but in most species, an efficient degradation and digestion of lignocellulose can only be achieved through mutualistic associations with endosymbionts. Similar to termites, it has been suspected that several bacterial symbionts may be involved in lignocellulose degradation in terrestrial isopods, by completing the CAZyme repertoire of their hosts.<br><br>RESULTS: To test this hypothesis, host transcriptomic and microbiome shotgun metagenomic datasets were obtained and investigated from the pill bug Armadillidium vulgare. Many genes of bacterial and archaeal origin coding for CAZymes were identified in the metagenomes of several host tissues and the gut content of specimens from both laboratory lineages and a natural population of A. vulgare. Some of them may be involved in the degradation of cellulose, hemicellulose, and lignin. Reconstructing a lignocellulose-degrading microbial community based on the prokaryotic taxa contributing relevant CAZymes revealed two taxonomically distinct but functionally redundant microbial communities depending on host origin. In parallel, endogenous CAZymes were identified from the transcriptome of the host and their expression in digestive tissues was demonstrated by RT-qPCR, demonstrating a complementary enzyme repertoire for lignocellulose degradation from both the host and the microbiome in A. vulgare.<br><br>CONCLUSIONS: Our results provide new insights into the role of the microbiome in the evolution of terrestrial isopods and their adaptive radiation in terrestrial habitats.}, }
@article {pmid30223892, year = {2018}, author = {Sitaraman, R}, title = {Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {163}, pmid = {30223892}, issn = {2049-2618}, mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biological Evolution ; *Gene Transfer, Horizontal ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.}, }
@article {pmid30218130, year = {2019}, author = {Bernasconi, R and Stat, M and Koenders, A and Huggett, MJ}, title = {Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.}, journal = {Microbial ecology}, volume = {77}, number = {3}, pages = {794-807}, pmid = {30218130}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/classification/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; Coral Reefs ; Microbiota ; Phylogeny ; *Symbiosis ; }, abstract = {Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.}, }
@article {pmid30157257, year = {2018}, author = {Wenzel, MA and Douglas, A and Piertney, SB}, title = {Microbiome composition within a sympatric species complex of intertidal isopods (Jaera albifrons).}, journal = {PloS one}, volume = {13}, number = {8}, pages = {e0202212}, pmid = {30157257}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Ecosystem ; Female ; Genetic Speciation ; Genetic Variation ; Host Microbial Interactions/genetics ; Isopoda/*microbiology ; Male ; Microbiota/*genetics ; Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Scotland ; Sex Factors ; Sympatry ; }, abstract = {The increasingly recognised effects of microbiomes on the eco-evolutionary dynamics of their hosts are promoting a view of the "hologenome" as an integral host-symbiont evolutionary entity. For example, sex-ratio distorting reproductive parasites such as Wolbachia are well-studied pivotal drivers of invertebrate reproductive processes, and more recent work is highlighting novel effects of microbiome assemblages on host mating behaviour and developmental incompatibilities that underpin or reinforce reproductive isolation processes. However, examining the hologenome and its eco-evolutionary effects in natural populations is challenging because microbiome composition is considerably influenced by environmental factors. Here we illustrate these challenges in a sympatric species complex of intertidal isopods (Jaera albifrons spp.) with pervasive sex-ratio distortion and ecological and behavioural reproductive isolation mechanisms. We deep-sequence the bacterial 16S rRNA gene among males and females collected in spring and summer from two coasts in north-east Scotland, and examine microbiome composition with a particular focus on reproductive parasites. Microbiomes of all species were diverse (overall 3,317 unique sequences among 3.8 million reads) and comprised mainly Proteobacteria and Bacteroidetes taxa typical of the marine intertidal zone, in particular Vibrio spp. However, we found little evidence of the reproductive parasites Wolbachia, Rickettsia, Spiroplasma and Cardinium, suggesting alternative causes of sex-ratio distortion. Notwithstanding, a significant proportion of the variance in microbiome composition among samples was explained by sex (14.1 %), nested within geographic (26.9 %) and seasonal (39.6 %) variance components. The functional relevance of this sex signal was difficult to ascertain given the absence of reproductive parasites, the ephemeral nature of the species assemblages and substantial environmental variability. These results establish the Jaera albifrons species complex as an intriguing system for examining the effects of microbiomes on reproductive processes and speciation, and highlight the difficulties associated with snapshot assays of microbiome composition in dynamic and complex environments.}, }
@article {pmid30156020, year = {2018}, author = {Basso, V and De Freitas Pereira, M and Maillard, F and Mallerman, J and Mangeot-Peter, L and Zhang, F and Bonnot, C}, title = {Facing global change: the millennium challenge for plant scientists: 41[st] New Phytologist Symposium 'Plant sciences for the future', Nancy, France, April 2018.}, journal = {The New phytologist}, volume = {220}, number = {1}, pages = {25-29}, doi = {10.1111/nph.15376}, pmid = {30156020}, issn = {1469-8137}, mesh = {Adaptation, Physiological ; *Botany ; *Climate Change ; Plant Physiological Phenomena ; *Plants ; *Research Personnel ; }, }
@article {pmid30147222, year = {2018}, author = {Takagi, H and Kimoto, K and Fujiki, T and Moriya, K}, title = {Effect of nutritional condition on photosymbiotic consortium of cultured Globigerinoides sacculifer (Rhizaria, Foraminifera).}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {76}, number = {1}, pages = {25-39}, pmid = {30147222}, issn = {0334-5114}, abstract = {Several foraminifers found in warm and low-nutrient ocean surface water have photosynthetic algae as endosymbionts (photosymbiosis). To understand the trophic interactions, we studied Globigerinoides sacculifer, a spinose planktic foraminifer that has a dinoflagellate endosymbiont. We controlled two nutritional factors, feeding and inorganic nutrients in the seawater. The growth of the host and the symbionts and the photophysiological parameters were monitored under four experimental conditions. The results demonstrated that the holobionts primarily relied on phagotrophy for growth. The foraminifers grew considerably, and the chlorophyll a content per foraminifer, which is an indicator of the symbiont population, increased in the fed groups, but not in the unfed groups. The nutrient-rich seawater used for some of the cultures made no difference in either the growth or photophysiology of the holobionts. These observations indicated that the symbionts mainly utilized metabolites from the hosts for photosynthesis rather than inorganic nutrients in the seawater. Additionally, we observed that the symbionts in the starved hosts maintained their photosynthetic capability for at least 12 days, and that the hosts maintained at least some symbionts until gametogenesis was achieved. This suggests that the hosts have to retain the symbionts as an energy source for reproduction. The symbionts may also play an indispensable role in the metabolic activities of the hosts including waste transport or essential compound synthesis. Overall, our results revealed a novel mode of photosymbiosis in planktic foraminifers which contrasts with that found in benthic photosymbiotic foraminifers and corals.}, }
@article {pmid30146755, year = {2018}, author = {Allard, SM and Ottesen, AR and Brown, EW and Micallef, SA}, title = {Insect exclusion limits variation in bacterial microbiomes of tomato flowers and fruit.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14087}, pmid = {30146755}, issn = {1365-2672}, support = {2014-68003-21588//National Institute of Food and Agriculture, U.S. Department of Agriculture/ ; }, abstract = {AIMS: The effect of insect exclusion via netting on bacterial microbiota associated with field-grown tomato fruit and flowers was evaluated.<br><br>METHODS AND RESULTS: Amplicon-based bacterial community profiling from insect-exposed plants and plants wrapped in nylon mosquito netting was conducted on total DNA extracted from tomato flower and mature unripe fruit washes. The V1-V3 region of the 16S rRNA gene was sequenced using Illumina MiSeq and analysed using qiime ver. 1.8. The carposphere supported significantly more phylogenetic diversity (PD) compared to the anthosphere, as measured by operational taxonomic unit richness (P&#xa0;=&#xa0;0&#xb7;001) and Faith's PD (P&#xa0;=&#xa0;0&#xb7;004). Flowers and fruit hosted distinct bacterial community structures (R[2] = 0&#xb7;27, P&#xa0;=&#xa0;0&#xb7;001), with specific taxonomic differences in taxa that included the Xanthomonadaceae (higher in flowers), and the Pseudomonadaceae, Methylobacteriaceae and Rhizobiales (higher in fruit) (FDR-P&#xa0;<&#xa0;0&#xb7;05). Bacterial community profiles of netted plants were overall statistically similar to non-netted plants for both flowers and fruit (P&#xa0;>&#xa0;0&#xb7;10). However, less variation between samples was observed among flowers (~50% less, P&#xa0;=&#xa0;0&#xb7;004) and green fruit (~10% less, P&#xa0;=&#xa0;0&#xb7;038) collected from netted than non-netted plants.<br><br>CONCLUSION: Insects may introduce or augment variability in bacterial diversity associated with tomato flowers and potentially green fruit surfaces.<br><br>This work contributes to knowledge on microbiome dynamics of the tomato holobiont. Deciphering drivers of bacterial diversity and community structure of fruit crops could reveal processes important to agricultural management, such as competitive exclusion of pathogens and priming of plant defense mechanisms.}, }
@article {pmid30142922, year = {2018}, author = {Stabili, L and Parisi, MG and Parrinello, D and Cammarata, M}, title = {Cnidarian Interaction with Microbial Communities: From Aid to Animal's Health to Rejection Responses.}, journal = {Marine drugs}, volume = {16}, number = {9}, pages = {}, pmid = {30142922}, issn = {1660-3397}, mesh = {Animals ; Biotechnology/methods ; Cnidaria/microbiology/*physiology ; Homeostasis/immunology ; *Immunity, Innate ; Microbiota/*immunology ; Mucous Membrane/immunology/microbiology ; Phylogeny ; Symbiosis/*immunology ; }, abstract = {The phylum Cnidaria is an ancient branch in the tree of metazoans. Several species exert a remarkable longevity, suggesting the existence of a developed and consistent defense mechanism of the innate immunity capable to overcome the potential repeated exposure to microbial pathogenic agents. Increasing evidence indicates that the innate immune system in Cnidarians is not only involved in the disruption of harmful microorganisms, but also is crucial in structuring tissue-associated microbial communities that are essential components of the Cnidarian holobiont and useful to the animal's health for several functions, including metabolism, immune defense, development, and behavior. Sometimes, the shifts in the normal microbiota may be used as "early" bio-indicators of both environmental changes and/or animal disease. Here the Cnidarians relationships with microbial communities and the potential biotechnological applications are summarized and discussed.}, }
@article {pmid30128208, year = {2018}, author = {Van Duyl, FC and Mueller, B and Meesters, EH}, title = {Spatio-temporal variation in stable isotope signatures (δ[13]C and δ[15]N) of sponges on the Saba Bank.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e5460}, pmid = {30128208}, issn = {2167-8359}, abstract = {Sponges are ubiquitous on coral reefs, mostly long lived and therefore adaptive to changing environmental conditions. They feed on organic matter withdrawn from the passing water and they may harbor microorganisms (endosymbionts), which contribute to their nutrition. Their diets and stable isotope (SI) fractionation determine the SI signature of the sponge holobiont. Little is known of spatio-temporal variations in SI signatures of δ[13]C and δ[15]N in tropical sponges and whether they reflect variations in the environment. We investigated the SI signatures of seven common sponge species with different functional traits and their potential food sources between 15 and 32 m depth along the S-SE and E-NE side of the Saba Bank, Eastern Caribbean, in October 2011 and October 2013. SI signatures differed significantly between most sponge species, both in mean values and in variation, indicating different food preferences and/or fractionation, inferring sponge species-specific isotopic niche spaces. In 2011, all sponge species at the S-SE side were enriched in d[13]C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ[13]C and δ[15]N than in 2011. Observed spatio-temporal changes in SI in sponges could not be attributed to changes in the SI signatures of their potential food sources, which remained stable with different SI signatures of pelagic (particulate organic matter (POM): δ[13]C -24.9‰, δ[15]N +4.3‰) and benthic-derived food (macroalgae: δ[13]C -15.4‰, δ[15]N +0.8‰). Enriched δ[13]C signatures in sponges at the S-SE side in 2011 are proposed to be attributed to predominantly feeding on benthic-derived C. This interpretation was supported by significant differences in water mass constituents between sides in October 2011. Elevated NO3 and dissolved organic matter concentrations point toward a stronger reef signal in reef overlying water at the S-SE than N-NE side of the Bank in 2011. The depletions of δ[13]C and δ[15]N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ[15]N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ[15]N than pelagic food. Average proportional feeding on available sources varied between sponge species and ranged from 20% to 50% for benthic and 50% to 80% for pelagic-derived food, assuming trophic enrichment factors of 0.5‰ ± sd 0.5 for δ[13]C and 3‰ ± sd 0.5 for δ[15]N for sponges. We suggest that observed variation of SI in sponges between sides and years were the result of shifts in the proportion of ingested benthic- and pelagic-derived organic matter driven by environmental changes. We show that sponge SI signatures reflect environmental variability in space and time on the Saba Bank and that SI of sponges irrespective of their species-specific traits move in a similar direction in response to these environmental changes.}, }
@article {pmid30084239, year = {2019}, author = {Kranabetter, JM and Harman-Denhoed, R and Hawkins, BJ}, title = {Saprotrophic and ectomycorrhizal fungal sporocarp stoichiometry (C : N : P) across temperate rainforests as evidence of shared nutrient constraints among symbionts.}, journal = {The New phytologist}, volume = {221}, number = {1}, pages = {482-492}, doi = {10.1111/nph.15380}, pmid = {30084239}, issn = {1469-8137}, support = {//British Columbia Ministry of Forests, Lands and Natural Resource Operations/International ; }, mesh = {British Columbia ; Carbon/analysis ; Ecosystem ; Fruiting Bodies, Fungal/*chemistry ; Mycorrhizae/*physiology ; Nitrogen/analysis ; Phosphorus/analysis ; Plant Leaves/chemistry ; Pseudotsuga ; *Rainforest ; Soil/*chemistry ; *Soil Microbiology ; Symbiosis ; }, abstract = {Quantifying nutritional dynamics of free-living saprotrophs and symbiotic ectomycorrhizal fungi in the field is challenging, but the stoichiometry of fruiting bodies (sporocarps) may be an effective methodology for this purpose. Carbon (C), nitrogen (N) and phosphorus (P) concentrations of soils, foliage and 146 sporocarp collections were analyzed from 14 Pseudotsuga menziesii var. menziesii stands across a podzolization gradient on Vancouver Island (Canada). N and P concentrations were considerably higher in saprotrophic fungi. Fungal N% increased with soil N content at a greater rate for saprotrophs than ectomycorrhizal fungi, while fungal P% of saprotrophs was more constrained. Fungal N : P was more responsive to soil N : P for ectomycorrhizal fungi (homeostatic regulation coefficient 'H' = 2.9) than saprotrophs (H = 5.9), while N : P of ectomycorrhizal fungi and host tree foliage scaled almost identically. Results underscore the role of ectomycorrhizal fungi as nutrient conduits, supporting host trees, whereas saprotrophs maintain a greater degree of nutritional homeostasis. Site nutrient constraints were shared in equal measure between ectomycorrhizal fungi and host trees, particularly for P, suggesting neither partner benefits from enhanced nutrition at the expense of the other. Sporocarp stoichiometry provides new insights into mycorrhizal relationships and illustrates pervasive P deficiencies across temperate rainforests of the Pacific Northwest.}, }
@article {pmid30083934, year = {2018}, author = {Godoy-Vitorino, F and Toledo-Hernandez, C}, title = {Reef-Building Corals as a Tool for Climate Change Research in the Genomics Era.}, journal = {Results and problems in cell differentiation}, volume = {65}, number = {}, pages = {529-546}, doi = {10.1007/978-3-319-92486-1_23}, pmid = {30083934}, issn = {0080-1844}, mesh = {Animals ; Anthozoa/*genetics/microbiology/*physiology ; Biodiversity ; *Climate Change ; *Coral Reefs ; *Ecosystem ; *Genomics ; Humans ; *Research ; }, abstract = {Coral reef ecosystems are among the most biodiverse habitats in the marine realm. They not only contribute with a plethora of ecosystem services, but they also are beneficial to humankind via nurturing marine fisheries and sustaining recreational activities. We will discuss the biology of coral reefs and their ecophysiology including the complex bacterial microbiota associated with them.}, }
@article {pmid30066215, year = {2018}, author = {Stencel, A and Wloch-Salamon, DM}, title = {Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {137}, number = {2}, pages = {197-206}, pmid = {30066215}, issn = {1611-7530}, support = {2018/28/T/HS1/00201//Narodowe Centrum Nauki/ ; Opus 2017/25/B/NZ8/01035//Narodowe Centrum Nauki/ ; DS/762 - K/ZDS/007338//Uniwersytet Jagiello&#x144;ski w Krakowie/ ; }, mesh = {*Adaptation, Biological ; Adaptation, Physiological/genetics ; Animals ; *Genetic Speciation ; Host-Parasite Interactions/genetics ; Microbiota ; Philosophy ; Plants ; Species Specificity ; *Symbiosis ; }, abstract = {Research on symbiotic communities (microbiomes) of multicellular organisms seems to be changing our understanding of how species of plants and animals have evolved over millions of years. The quintessence of these discoveries is the emergence of the hologenome theory of evolution, founded on the concept that a holobiont (a host along with all of its associated symbiotic microorganisms) acts a single unit of selection in the process of evolution. Although the hologenome theory has become very popular among certain scientific circles, its principles are still being debated. In this paper, we argue, firstly, that only a very small number of symbiotic microorganisms are sufficiently integrated into multicellular organisms to act in concert with them as units of selection, thus rendering claims that holobionts are units of selection invalid. Secondly, even though holobionts are not units of selection, they can still constitute genuine units from an evolutionary perspective, provided we accept certain constraints: mainly, they should be considered units of co-operation. Thirdly, we propose a reconciliation of the role of symbiotic microorganisms with the theory of speciation through the use of a developed framework. Mainly, we will argue that, in order to understand the role of microorganisms in the speciation of multicellular organisms, it is not necessary to consider holobionts units of selection; it is sufficient to consider them units of co-operation.}, }
@article {pmid30065035, year = {2018}, author = {Armstrong, EJ and Roa, JN and Stillman, JH and Tresguerres, M}, title = {Symbiont photosynthesis in giant clams is promoted by V-type H[+]-ATPase from host cells.}, journal = {The Journal of experimental biology}, volume = {221}, number = {Pt 18}, pages = {}, doi = {10.1242/jeb.177220}, pmid = {30065035}, issn = {1477-9145}, mesh = {Algal Proteins/*metabolism ; Animals ; Cardiidae/*physiology ; Dinoflagellida/*metabolism ; Energy Metabolism ; *Photosynthesis ; Protozoan Proteins/*metabolism ; Symbiosis/*physiology ; Vacuolar Proton-Translocating ATPases/*metabolism ; }, abstract = {Giant clams (genus Tridacna) are the largest living bivalves and, like reef-building corals, host symbiotic dinoflagellate algae (Symbiodinium) that significantly contribute to their energy budget. In turn, Symbiodinium rely on the host to supply inorganic carbon (Ci) for photosynthesis. In corals, host 'proton pump' vacuolar-type H[+]-ATPase (VHA) is part of a carbon-concentrating mechanism (CCM) that promotes Symbiodinium photosynthesis. Here, we report that VHA in the small giant clam (Tridacna maxima) similarly promotes Symbiodinium photosynthesis. VHA was abundantly expressed in the apical membrane of epithelial cells of T. maxima's siphonal mantle tubule system, which harbors Symbiodinium Furthermore, application of the highly specific pharmacological VHA inhibitors bafilomycin A1 and concanamycin A significantly reduced photosynthetic O2 production by ∼40%. Together with our observation that exposure to light increased holobiont aerobic metabolism ∼5-fold, and earlier estimates that translocated fixed carbon exceeds metabolic demand, we conclude that VHA activity in the siphonal mantle confers strong energetic benefits to the host clam through increased supply of Ci to algal symbionts and subsequent photosynthetic activity. The convergent role of VHA in promoting Symbiodinium photosynthesis in the giant clam siphonal mantle tubule system and coral symbiosome suggests that VHA-driven CCM is a common exaptation in marine photosymbioses that deserves further investigation in other taxa.}, }
@article {pmid30057302, year = {2018}, author = {Berg, M and Koskella, B}, title = {Nutrient- and Dose-Dependent Microbiome-Mediated Protection against a Plant Pathogen.}, journal = {Current biology : CB}, volume = {28}, number = {15}, pages = {2487-2492.e3}, doi = {10.1016/j.cub.2018.05.085}, pmid = {30057302}, issn = {1879-0445}, mesh = {Solanum lycopersicum/*microbiology ; *Microbiota ; Nutrients/physiology ; Plant Diseases/*microbiology ; Plant Leaves/*microbiology ; Pseudomonas syringae/*physiology ; }, abstract = {Plant-associated microbial communities can promote plant nutrient uptake, growth, and resistance to pathogens [1-3]. Host resistance to infection can increase directly through commensal-pathogen interactions or indirectly through modulation of host defenses [4-6], the mechanisms of which are best described for rhizosphere-associated bacteria. For example, Arabidopsis plants infected with the foliar pathogen, Pseudomonas syringae pathovar tomato (Pst), increase their root secretion of malate, which attracts Bacillus subtillis to the roots and leads to a stronger host response against Pst [7]. Although there are numerous examples of individual defensive symbionts (e.g., [8]), it is less clear whether this type of protection is an emergent property of whole microbial communities. In particular, relatively little is known about whether and how the presence of phyllosphere (above-ground) microbial communities can increase host resistance against pathogens. In this study, we examined the ability of augmented tomato phyllosphere microbiomes to confer resistance against the causal agent of bacterial speck, Pst. Across five independent experiments, the augmented phyllosphere microbiome was found to decrease pathogen colonization. Furthermore, the dose of commensal bacteria applied affected the degree of protection conferred, and although the effect is dependent on microbial composition, it is not clearly related to overall bacterial diversity. Finally, our results suggest that resources available to the phyllosphere microbial community may play an important role in protection, as the addition of fertilizer abolished the observed microbiome-mediated protection. Together, these results have clear relevance to microbiome-mediated protection within agricultural settings and the use of plant probiotics to increase disease resistance.}, }
@article {pmid30050510, year = {2018}, author = {Garcia, J and Kao-Kniffin, J}, title = {Microbial Group Dynamics in Plant Rhizospheres and Their Implications on Nutrient Cycling.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1516}, pmid = {30050510}, issn = {1664-302X}, abstract = {Plant rhizospheres encompass a dynamic zone of interactions between microorganisms and their respective plant hosts. For decades, researchers have worked to understand how these complex interactions influence different aspects of plant growth, development, and evolution. Studies of plant-microbial interactions in the root zone have typically focused on the effect of single microbial species or strains on a plant host. These studies, however, provide only a snapshot of the complex interactions that occur in the rhizosphere, leaving researchers with a limited understanding of how the complex microbiome influences the biology of the plant host. To better understand how rhizosphere interactions influence plant growth and development, novel frameworks and research methodologies could be implemented. In this perspective, we propose applying concepts in evolutionary biology to microbiome experiments for improved understanding of group-to-group and community-level microbial interactions influencing soil nutrient cycling. We also put forth simple experimental designs utilizing -omics techniques that can reveal important changes in the rhizosphere impacting the plant host. A greater focus on the components of complexity of the microbiome and how these impact plant host biology could yield more insight into previously unexplored aspects of host-microbe biology relevant to crop production and protection.}, }
@article {pmid30046174, year = {2018}, author = {Klassen, JL}, title = {Defining microbiome function.}, journal = {Nature microbiology}, volume = {3}, number = {8}, pages = {864-869}, doi = {10.1038/s41564-018-0189-4}, pmid = {30046174}, issn = {2058-5276}, mesh = {*Bacterial Physiological Phenomena ; Evolution, Molecular ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Host Microbial Interactions ; Humans ; Microbiota ; }, abstract = {Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.}, }
@article {pmid30041377, year = {2018}, author = {Bielmyer-Fraser, GK and Patel, P and Capo, T and Grosell, M}, title = {Physiological responses of corals to ocean acidification and copper exposure.}, journal = {Marine pollution bulletin}, volume = {133}, number = {}, pages = {781-790}, doi = {10.1016/j.marpolbul.2018.06.048}, pmid = {30041377}, issn = {1879-3363}, mesh = {Animals ; Anthozoa/chemistry/classification/*metabolism ; Carbon Dioxide/analysis/metabolism ; Copper/analysis/*metabolism ; Coral Reefs ; Glutathione Reductase/metabolism ; Hydrogen-Ion Concentration ; Oceans and Seas ; Photosynthesis ; Seawater/*chemistry ; Water Pollutants, Chemical/analysis/metabolism ; }, abstract = {Acidification and land-based sources of pollution have been linked to widespread declines of coral cover in coastal reef ecosystems. In this study, two coral species, Acropora cervicornis and Pocillopora damicornis were exposed to increased copper at two CO2 levels for 96 h. Copper accumulation and anti-oxidant enzyme activities were measured. Copper accumulation only increased in A. cervicornis zooxanthellae and corresponded with photosynthetic toxicity. Enzyme activities in both coral species were affected; however, A. cervicornis was more sensitive than P. damicornis, and zooxanthellae were more affected than animal fractions of holobionts. Generally, activities of all anti-oxidant enzymes increased, with copper exposure in corals; whereas, activities of glutathione reductase and to some degree glutathione peroxidase were observed due to increasing CO2 exposure alone. Exposure to copper in combination with higher CO2 resulted in a synergistic response in some cases. These results provide insight into mechanisms of copper and CO2 impacts in corals.}, }
@article {pmid30038485, year = {2018}, author = {Karimi, K and Wuitchik, DM and Oldach, MJ and Vize, PD}, title = {Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences.}, journal = {Evolutionary bioinformatics online}, volume = {14}, number = {}, pages = {1176934318788866}, pmid = {30038485}, issn = {1176-9343}, support = {P41 HD064556/HD/NICHD NIH HHS/United States ; }, abstract = {With the advent of whole transcriptome and genome analysis methods, classifying samples containing multiple origins has become a significant task. Nucleotide sequences can be allocated to a genome or transcriptome by aligning sequences to multiple target sequence sets, but this approach requires extensive computational resources and also depends on target sequence sets lacking contaminants, which is often not the case. Here, we demonstrate that raw sequences can be rapidly sorted into groups, in practice corresponding to genera, by exploiting differences in nucleotide GC content. To do so, we introduce GCSpeciesSorter, which uses classification, specifically Support Vector Machines (SVM) and the C4.5 decision tree generator, to differentiate sequences. It also implements a secondary BLAST feature to identify known outliers. In the test case presented, a hermatypic coral holobiont, the cnidarian host includes various endosymbionts. The best characterized and most common of these symbionts are zooxanthellae of the genus Symbiodinium. GCSpeciesSorter separates cnidarian from Symbiodinium sequences with a high degree of accuracy. We show that if the GC contents of the species differ enough, this method can be used to accurately distinguish the sequences of different species when using high-throughput sequencing technologies.}, }
@article {pmid30022157, year = {2018}, author = {Li, Y and Liles, MR and Halanych, KM}, title = {Endosymbiont genomes yield clues of tubeworm success.}, journal = {The ISME journal}, volume = {12}, number = {11}, pages = {2785-2795}, pmid = {30022157}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics/metabolism ; Carbon Cycle ; Chemoautotrophic Growth ; Ecosystem ; Hydrogen/metabolism ; Hydrothermal Vents ; Photosynthesis ; Polychaeta/*microbiology ; *Symbiosis ; }, abstract = {Forty years after discovery of chemosynthetic symbiosis in the tubeworm Riftia pachyptila, how organisms maintain their unique host-symbiont associations at the cellular level is still largely unknown. Previous studies primarily focus on symbionts associated with host lineages living in hydrothermal vents. To understand physiological adaptations and evolution in these holobiont systems in markedly different habitats, we characterized four novel siboglinid-symbiont genomes spanning deep-sea seep and sedimented environments. Our comparative analyses suggest that all sampled siboglinid chemoautotrophic symbionts, except for frenulate symbionts, can use both rTCA and Calvin cycle for carbon fixation. We hypothesize that over evolutionary time siboglinids have been able to utilize different bacterial lineages allowing greater metabolic flexibility of carbon fixation (e.g., rTCA) enabling tubeworms to thrive in more reducing habitats, such as vents and seeps. Moreover, we show that sulfur metabolism and molecular mechanisms related to initial infection are remarkably conserved across chemoautotrophic symbionts in different habitats. Unexpectedly, we find that the ability to use hydrogen, as an additional energy source, is potentially more widespread than previously recognized. Our comparative genomic results help elucidate potential mechanisms used to allow chemosynthetically dependent holobionts adapt to, and evolve in, different environments.}, }
@article {pmid30003599, year = {2019}, author = {Lorimer, J}, title = {Hookworms Make Us Human: The Microbiome, Eco-immunology, and a Probiotic Turn in Western Health Care.}, journal = {Medical anthropology quarterly}, volume = {33}, number = {1}, pages = {60-79}, doi = {10.1111/maq.12466}, pmid = {30003599}, issn = {0745-5194}, mesh = {Ancylostomatoidea ; Animals ; Anthropology, Medical ; *Ecology ; *Hookworm Infections ; Humans ; Infectious Disease Medicine ; *Microbiota ; Probiotics/*therapeutic use ; }, abstract = {Historians of science have identified an ecological turn underway in immunology, driven by the mapping of the human microbiome and wider environmentalist anxieties. A figure is emerging of the human as a holobiont, composed of microbes and threatened by both microbial excess and microbial absence. Antimicrobial approaches to germ warfare are being supplemented by probiotic approaches to restoring microbial life. This article examines the political ecology of this probiotic turn in Western health care. It focuses on Necator americanus-a species of human hookworm-and its relations with immunologists. The analysis moves from a history of human disentanglement from hookworm, to contemporary anxieties about their absence. It examines the reintroduction of worms for helminthic therapy and explores emerging trajectories for probiotic health care involving the synthesis, modification, and/or restoration of worms and their salutary ecologies. The conclusion differentiates these trajectories and identifies an emerging model of "post-paleo" microbiopolitics.}, }
@article {pmid29989180, year = {2018}, author = {Klimovich, AV and Bosch, TCG}, title = {Rethinking the Role of the Nervous System: Lessons From the Hydra Holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {9}, pages = {e1800060}, doi = {10.1002/bies.201800060}, pmid = {29989180}, issn = {1521-1878}, mesh = {Animals ; Host Microbial Interactions/physiology ; Humans ; Hydra/microbiology/*physiology ; Microbiota/physiology ; Nervous System/microbiology/*physiopathology ; Neuropeptides/metabolism ; }, abstract = {Here we evaluate our current understanding of the function of the nervous system in Hydra, a non-bilaterian animal which is among the first metazoans that contain neurons. We highlight growing evidence that the nervous system, with its rich repertoire of neuropeptides, is involved in controlling resident beneficial microbes. We also review observations that indicate that microbes affect the animal's behavior by directly interfering with neuronal receptors. These findings provide new insight into the original role of the nervous system, and suggest that it emerged to orchestrate multiple functions including host-microbiome interactions. The excitement of future research in the Hydra model now relies on uncovering the common rules and principles that govern the interaction between neurons and microbes and the extent to which such laws might apply to other and more complex organisms.}, }
@article {pmid29978601, year = {2018}, author = {Lian, J and Wijffels, RH and Smidt, H and Sipkema, D}, title = {The effect of the algal microbiome on industrial production of microalgae.}, journal = {Microbial biotechnology}, volume = {11}, number = {5}, pages = {806-818}, pmid = {29978601}, issn = {1751-7915}, mesh = {Biotechnology/methods ; Microalgae/*growth &amp; development/*microbiology ; *Microbial Interactions ; *Microbiota ; }, abstract = {Microbes are ubiquitously distributed, and they are also present in algae production systems. The algal microbiome is a pivotal part of the alga holobiont and has a key role in modulating algal populations in nature. However, there is a lack of knowledge on the role of bacteria in artificial systems ranging from laboratory flasks to industrial ponds. Coexisting microorganisms, and predominantly bacteria, are often regarded as contaminants in algal research, but recent studies manifested that many algal symbionts not only promote algal growth but also offer advantages in downstream processing. Because of the high expectations for microalgae in a bio-based economy, better understanding of benefits and risks of algal-microbial associations is important for the algae industry. Reducing production cost may be through applying specific bacteria to enhance algae growth at large scale as well as through preventing the growth of a broad spectrum of algal pathogens. In this review, we highlight the latest studies of algae-microbial interactions and their underlying mechanisms, discuss advantages of large-scale algal-bacterial cocultivation and extend such knowledge to a broad range of biotechnological applications.}, }
@article {pmid29948922, year = {2018}, author = {Kutschera, U}, title = {Systems biology of eukaryotic superorganisms and the holobiont concept.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {137}, number = {2}, pages = {117-131}, pmid = {29948922}, issn = {1611-7530}, support = {Stanford U. Kut. 2013/14//Alexander von Humboldt-Stiftung/ ; }, mesh = {Animals ; Bacterial Physiological Phenomena ; *Biological Evolution ; Biology/history ; Biomass ; Eukaryota ; Genotype ; History, 19th Century ; History, 20th Century ; History, Ancient ; Homeostasis ; Humans ; Philosophy, Medical ; Plants/genetics ; *Selection, Genetic ; Symbiosis ; *Systems Biology ; Systems Theory ; }, abstract = {The founders of modern biology (Jean Lamarck, Charles Darwin, August Weismann etc.) were organismic life scientists who attempted to understand the morphology and evolution of living beings as a whole (i.e., the phenotype). However, with the emergence of the study of animal and plant physiology in the nineteenth century, this "holistic view" of the living world changed and was ultimately replaced by a reductionistic perspective. Here, I summarize the history of systems biology, i.e., the modern approach to understand living beings as integrative organisms, from genotype to phenotype. It is documented that the physiologists Claude Bernard and Julius Sachs, who studied humans and plants, respectively, were early pioneers of this discipline, which was formally founded 50 years ago. In 1968, two influential monographs, authored by Ludwig von Bertalanffy and Mihajlo D. Mesarović, were published, wherein a "systems theory of biology" was outlined. Definitions of systems biology are presented with reference to metabolic or cell signaling networks, analyzed via genomics, proteomics, and other methods, combined with computer simulations/mathematical modeling. Then, key insights of this discipline with respect to epiphytic microbes (Methylobacterium sp.) and simple bacteria (Mycoplasma sp.) are described. The principles of homeostasis, molecular systems energetics, gnotobiology, and holobionts (i.e., complexities of host-microbiota interactions) are outlined, and the significance of systems biology for evolutionary theories is addressed. Based on the microbe-Homo sapiens-symbiosis, it is concluded that human biology and health should be interpreted in light of a view of the biomedical sciences that is based on the holobiont concept.}, }
@article {pmid29946243, year = {2018}, author = {Münger, E and Montiel-Castro, AJ and Langhans, W and Pacheco-López, G}, title = {Reciprocal Interactions Between Gut Microbiota and Host Social Behavior.}, journal = {Frontiers in integrative neuroscience}, volume = {12}, number = {}, pages = {21}, pmid = {29946243}, issn = {1662-5145}, abstract = {Animals harbor an extensive, dynamic microbial ecosystem in their gut. Gut microbiota (GM) supposedly modulate various host functions including fecundity, metabolism, immunity, cognition and behavior. Starting by analyzing the concept of the holobiont as a unit of selection, we highlight recent findings suggesting an intimate link between GM and animal social behavior. We consider two reciprocal emerging themes: (i) that GM influence host social behavior; and (ii) that social behavior and social structure shape the composition of the GM across individuals. We propose that, throughout a long history of coevolution, GM may have become involved in the modulation of their host's sociality to foster their own transmission, while in turn social organization may have fine-tuned the transmission of beneficial endosymbionts and prevented pathogen infection. We suggest that investigating these reciprocal interactions can advance our understanding of sociality, from healthy and impaired social cognition to the evolution of specific social behaviors and societal structure.}, }
@article {pmid29943448, year = {2018}, author = {Marchesi, JR}, title = {Advancing microbiome research.}, journal = {Immunology}, volume = {154}, number = {4}, pages = {535-536}, pmid = {29943448}, issn = {1365-2567}, }
@article {pmid29941067, year = {2018}, author = {Marchesi, JR}, title = {Advancing microbiome research.}, journal = {Microbiology (Reading, England)}, volume = {164}, number = {8}, pages = {1005-1006}, doi = {10.1099/mic.0.000688}, pmid = {29941067}, issn = {1465-2080}, mesh = {Biomedical Research/*methods ; High-Throughput Nucleotide Sequencing ; Humans ; Microbiota/*physiology ; }, }
@article {pmid29938062, year = {2018}, author = {Bellis, ES and Edlund, RB and Berrios, HK and Lessios, HA and Denver, DR}, title = {Molecular signatures of host specificity linked to habitat specialization in Exaiptasia sea anemones.}, journal = {Ecology and evolution}, volume = {8}, number = {11}, pages = {5413-5426}, pmid = {29938062}, issn = {2045-7758}, abstract = {Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between coelenterates and photosynthetic microalgae of the genus Symbiodinium. Association with more thermotolerant partners could contribute to resilience, but the genetic mechanisms controlling specificity of hosts for particular Symbiodinium types are poorly known. Here, we characterize wild populations of a sea anemone laboratory model system for anthozoan symbiosis, from contrasting environments in Caribbean Panama. Patterns of anemone abundance and symbiont diversity were consistent with specialization of holobionts for particular habitats, with Exaiptasia pallida/S. minutum (ITS2 type B1) abundant on vertical substrate in thermally stable, shaded environments but E. brasiliensis/Symbiodinium sp. (ITS2 clade A) more common in shallow areas subject to high temperature and irradiance. Population genomic sequencing revealed a novel E. pallida population from the Bocas del Toro Archipelago that only harbors S. minutum. Loci most strongly associated with divergence of the Bocas-specific population were enriched in genes with putative roles in cnidarian symbiosis, including activators of the complement pathway of the innate immune system, thrombospondin-type-1 repeat domain proteins, and coordinators of endocytic recycling. Our findings underscore the importance of unmasking cryptic diversity in natural populations and the role of long-term evolutionary history in mediating interactions with Symbiodinium.}, }
@article {pmid29922264, year = {2018}, author = {Yurgel, SN and Douglas, GM and Dusault, A and Percival, D and Langille, MGI}, title = {Dissecting Community Structure in Wild Blueberry Root and Soil Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {1187}, pmid = {29922264}, issn = {1664-302X}, abstract = {A complex network of functions and symbiotic interactions between a eukaryotic host and its microbiome is a the foundation of the ecological unit holobiont. However, little is known about how the non-fungal eukaryotic microorganisms fit in this complex network of host-microbiome interactions. In this study, we employed a unique wild blueberry ecosystem to evaluate plant-associated microbiota, encompassing both eukaryotic and bacterial communities. We found that, while soil microbiome serves as a foundation for root microbiome, plant-influenced species sorting had stronger effect on eukaryotes than on bacteria. Our study identified several fungal and protist taxa, which are correlated with decreased fruit production in wild blueberry agricultural ecosystems. The specific effect of species sorting in root microbiome resulted in an increase in relative abundance of fungi adapted to plant-associated life-style, while the relative abundance of non-fungal eukaryotes was decreased along the soil-endosphere continuum in the root, probably because of low adaptation of these microorganisms to host-plant defense responses. Analysis of community correlation networks indicated that bacterial and eukaryotic interactions became more complex along the soil-endosphere continuum and, in addition to extensive mutualistic interactions, co-exclusion also played an important role in shaping wild blueberry associated microbiome. Our study identified several potential hub taxa with important roles in soil fertility and/or plant-microbe interaction, suggesting the key role of these taxa in the interconnection between soils and plant health and overall microbial community structure. This study also provides a comprehensive view of the role of non-fungal eukaryotes in soil ecosystem.}, }
@article {pmid29917104, year = {2018}, author = {Celis, JS and Wibberg, D and Ramírez-Portilla, C and Rupp, O and Sczyrba, A and Winkler, A and Kalinowski, J and Wilke, T}, title = {Binning enables efficient host genome reconstruction in cnidarian holobionts.}, journal = {GigaScience}, volume = {7}, number = {7}, pages = {}, pmid = {29917104}, issn = {2047-217X}, mesh = {Algorithms ; Animals ; Anthozoa/*physiology ; Cnidaria/*genetics ; Computational Biology ; Coral Reefs ; DNA/analysis ; Ecology ; *Genome ; Genomics/*methods ; High-Throughput Nucleotide Sequencing ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/analysis ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: Many cnidarians, including stony corals, engage in complex symbiotic associations, comprising the eukaryotic host, photosynthetic algae, and highly diverse microbial communities-together referred to as holobiont. This taxonomic complexity makes sequencing and assembling coral host genomes extremely challenging. Therefore, previous cnidarian genomic projects were based on symbiont-free tissue samples. However, this approach may not be applicable to the majority of cnidarian species for ecological reasons. We therefore evaluated the performance of an alternative method based on sequence binning for reconstructing the genome of the stony coral Porites rus from a hologenomic sample and compared it to traditional approaches.<br><br>RESULTS: Our results demonstrate that binning performs well for hologenomic data, producing sufficient reads for assembling the draft genome of P. rus. An assembly evaluation based on operational criteria showed results that were comparable to symbiont-free approaches in terms of completeness and usefulness, despite a high degree of fragmentation in our assembly. In addition, we found that binning provides sufficient data for exploratory k-mer estimation of genomic features, such as genome size and heterozygosity.<br><br>CONCLUSIONS: Binning constitutes a powerful approach for disentangling taxonomically complex coral hologenomes. Considering the recent decline of coral reefs on the one hand and previous limitations to coral genome sequencing on the other hand, binning may facilitate rapid and reliable genome assembly. This study also provides an important milestone in advancing binning from the metagenomic to the hologenomic and from the prokaryotic to the eukaryotic level.}, }
@article {pmid29902263, year = {2018}, author = {Bednarz, VN and Naumann, MS and Cardini, U and van Hoytema, N and Rix, L and Al-Rshaidat, MMD and Wild, C}, title = {Contrasting seasonal responses in dinitrogen fixation between shallow and deep-water colonies of the model coral Stylophora pistillata in the northern Red Sea.}, journal = {PloS one}, volume = {13}, number = {6}, pages = {e0199022}, pmid = {29902263}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*metabolism ; Indian Ocean ; *Nitrogen Fixation ; Photosynthesis ; *Seasons ; }, abstract = {Tropical corals are often associated with dinitrogen (N2)-fixing bacteria (diazotrophs), and seasonal changes in key environmental parameters, such as dissolved inorganic nitrogen (DIN) availability and seawater temperature, are known to affect N2 fixation in coral-microbial holobionts. Despite, then, such potential for seasonal and depth-related changes in N2 fixation in reef corals, such variation has not yet been investigated. Therefore, this study quantified seasonal (winter vs. summer) N2 fixation rates associated with the reef-building coral Stylophora pistillata collected from depths of 5, 10 and 20 m in the northern Gulf of Aqaba (Red Sea). Findings revealed that corals from all depths exhibited the highest N2 fixation rates during the oligotrophic summer season, when up to 11% of their photo-metabolic nitrogen demand (CPND) could be met by N2 fixation. While N2 fixation remained seasonally stable for deep corals (20 m), it significantly decreased for the shallow corals (5 and 10 m) during the DIN-enriched winter season, accounting for less than 2% of the corals' CPND. This contrasting seasonal response in N2 fixation across corals of different depths could be driven by 1) release rates of coral-derived organic matter, 2) the community composition of the associated diazotrophs, and/or 3) nutrient acquisition by the Symbiodinium community.}, }
@article {pmid29900626, year = {2018}, author = {van Oppen, MJH and Bongaerts, P and Frade, P and Peplow, LM and Boyd, SE and Nim, HT and Bay, LK}, title = {Adaptation to reef habitats through selection on the coral animal and its associated microbiome.}, journal = {Molecular ecology}, volume = {27}, number = {14}, pages = {2956-2971}, doi = {10.1111/mec.14763}, pmid = {29900626}, issn = {1365-294X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; Anthozoa/*genetics/growth &amp; development/microbiology ; *Coral Reefs ; Dinoflagellida/*genetics/growth &amp; development ; Ecosystem ; Gene Flow ; Genetics, Population ; Genome/genetics ; Microbiota/genetics ; Photosynthesis/genetics ; Symbiosis/*genetics ; }, abstract = {Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction site-associated sequencing) and characterized both the dinoflagellate photosymbiont- and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically, and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. The prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intraspecific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations.}, }
@article {pmid29900606, year = {2018}, author = {Vančurová, L and Muggia, L and Peksa, O and Řídká, T and Škaloud, P}, title = {The complexity of symbiotic interactions influences the ecological amplitude of the host: A case study in Stereocaulon (lichenized Ascomycota).}, journal = {Molecular ecology}, volume = {27}, number = {14}, pages = {3016-3033}, doi = {10.1111/mec.14764}, pmid = {29900606}, issn = {1365-294X}, mesh = {Ascomycota/genetics/*growth &amp; development ; Biological Evolution ; Chlorophyta/genetics/*growth &amp; development ; DNA, Ribosomal Spacer/genetics ; Ecology ; Ecosystem ; Genetic Variation ; Lichens/genetics/*growth &amp; development/microbiology ; Symbiosis/*genetics ; }, abstract = {Symbiosis plays a fundamental role in nature. Lichens are among the best known, globally distributed symbiotic systems whose ecology is shaped by the requirements of all symbionts forming the holobiont. The widespread lichen-forming fungal genus Stereocaulon provides a suitable model to study the ecology of microscopic green algal symbionts (i.e., phycobionts) within the lichen symbiosis. We analysed 282 Stereocaulon specimens, collected in diverse habitats worldwide, using the algal ITS rDNA and actin gene sequences and fungal ITS rDNA sequences. Phylogenetic analyses revealed a great diversity among the predominant phycobionts. The algal genus Asterochloris (Trebouxiophyceae) was recovered in most sampled thalli, but two additional genera, Vulcanochloris and Chloroidium, were also found. We used variation-partitioning analyses to investigate the effects of climatic conditions, substrate/habitat characteristic, spatial distribution and mycobionts on phycobiont distribution. Based on an analogy, we examined the effects of climate, substrate/habitat, spatial distribution and phycobionts on mycobiont distribution. According to our analyses, the distribution of phycobionts is primarily driven by mycobionts and vice versa. Specificity and selectivity of both partners, as well as their ecological requirements and the width of their niches, vary significantly among the species-level lineages. We demonstrated that species-level lineages, which accept more symbiotic partners, have wider climatic niches, overlapping with the niches of their partners. Furthermore, the survival of lichens on substrates with high concentrations of heavy metals appears to be supported by their association with toxicity-tolerant phycobionts. In general, low specificity towards phycobionts allows the host to associate with ecologically diversified algae, thereby broadening its ecological amplitude.}, }
@article {pmid29899267, year = {2018}, author = {R L Morlighem, J&#xc9; and Huang, C and Liao, Q and Braga Gomes, P and Daniel Pérez, C and de Brandão Prieto-da-Silva, &#xc1;R and Ming-Yuen Lee, S and Rádis-Baptista, G}, title = {The Holo-Transcriptome of the Zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa): A Plentiful Source of Enzymes for Potential Application in Green Chemistry, Industrial and Pharmaceutical Biotechnology.}, journal = {Marine drugs}, volume = {16}, number = {6}, pages = {}, pmid = {29899267}, issn = {1660-3397}, mesh = {Animals ; Anthozoa/*enzymology/genetics ; Aquatic Organisms/*enzymology/genetics ; Biocatalysis ; *Biological Products ; Biotechnology/methods ; Enzymes/*genetics/metabolism ; Green Chemistry Technology/methods ; Industry/methods ; Transcriptome ; }, abstract = {Marine invertebrates, such as sponges, tunicates and cnidarians (zoantharians and scleractinian corals), form functional assemblages, known as holobionts, with numerous microbes. This type of species-specific symbiotic association can be a repository of myriad valuable low molecular weight organic compounds, bioactive peptides and enzymes. The zoantharian Protopalythoa variabilis (Cnidaria: Anthozoa) is one such example of a marine holobiont that inhabits the coastal reefs of the tropical Atlantic coast and is an interesting source of secondary metabolites and biologically active polypeptides. In the present study, we analyzed the entire holo-transcriptome of P. variabilis, looking for enzyme precursors expressed in the zoantharian-microbiota assemblage that are potentially useful as industrial biocatalysts and biopharmaceuticals. In addition to hundreds of predicted enzymes that fit into the classes of hydrolases, oxidoreductases and transferases that were found, novel enzyme precursors with multiple activities in single structures and enzymes with incomplete Enzyme Commission numbers were revealed. Our results indicated the predictive expression of thirteen multifunctional enzymes and 694 enzyme sequences with partially characterized activities, distributed in 23 sub-subclasses. These predicted enzyme structures and activities can prospectively be harnessed for applications in diverse areas of industrial and pharmaceutical biotechnology.}, }
@article {pmid29888140, year = {2018}, author = {Nguyen, MTHD and Thomas, T}, title = {Diversity, host-specificity and stability of sponge-associated fungal communities of co-occurring sponges.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4965}, pmid = {29888140}, issn = {2167-8359}, abstract = {Fungi play a critical role in a range of ecosystems; however, their interactions and functions in marine hosts, and particular sponges, is poorly understood. Here we assess the fungal community composition of three co-occurring sponges (Cymbastela concentrica, Scopalina sp., Tedania anhelans) and the surrounding seawater over two time points to help elucidate host-specificity, stability and potential core members, which may shed light into the ecological function of fungi in sponges. The results showed that ITS-amplicon-based community profiling likely provides a more realistic assessment of fungal diversity in sponges than cultivation-dependent approaches. The sponges studied here were found to contain phylogenetically diverse fungi (eight fungal classes were observed), including members of the family Togniniaceae and the genus Acrostalagmus, that have so far not been reported to be cultured from sponges. Fungal communities within any given sponge species were found to be highly variable compared to bacterial communities, and influenced in structure by the community of the surrounding seawater, especially considering temporal variation. Nevertheless, the sponge species studied here contained a few "variable/core" fungi that appeared in multiple biological replicates and were enriched in their relative abundance compared to seawater communities. These fungi were the same or highly similar to fungal species detected in sponges around the world, which suggests a prevalence of horizontal transmission where selectivity and enrichment of some fungi occur for those that can survive and/or exploit the sponge environment. Our current sparse knowledge about sponge-associated fungi thus indicate that fungal communities may perhaps not play as an important ecological role in the sponge holobiont compared to bacterial or archaeal symbionts.}, }
@article {pmid29886997, year = {2018}, author = {Hall, ER and Muller, EM and Goulet, T and Bellworthy, J and Ritchie, KB and Fine, M}, title = {Eutrophication may compromise the resilience of the Red Sea coral Stylophora pistillata to global change.}, journal = {Marine pollution bulletin}, volume = {131}, number = {Pt A}, pages = {701-711}, doi = {10.1016/j.marpolbul.2018.04.067}, pmid = {29886997}, issn = {1879-3363}, mesh = {Animals ; Anthozoa/*physiology ; Climate Change ; Coral Reefs ; Ecosystem ; *Eutrophication ; Indian Ocean ; }, abstract = {Environmental stressors are adversely affecting coral reef ecosystems. There is ample evidence that scleractinian coral growth and physiology may be compromised by reduced pH, and elevated temperature, and that this is exacerbated by local environmental stressors. The Gulf of Aqaba is considered a coral reef refuge from acidification and warming but coastal development and nutrient effluent may pose a local threat. This study examined the effects of select forecasted environmental changes (acidification, warming, and increased nutrients) individually and in combination on the coral holobiont Stylophora pistillata from the Gulf of Aqaba to understand how corals in a potential global climate change refugia may fare in the face of local eutrophication. The results indicate interactions between all stressors, with elevated nutrient concentrations having the broadest individual and additive impacts upon the performance of S. pistillata. These findings highlight the importance of maintaining oligotrophic conditions to secure these reefs as potential refugia.}, }
@article {pmid29885666, year = {2018}, author = {Meng, A and Marchet, C and Corre, E and Peterlongo, P and Alberti, A and Da Silva, C and Wincker, P and Pelletier, E and Probert, I and Decelle, J and Le Crom, S and Not, F and Bittner, L}, title = {A de novo approach to disentangle partner identity and function in holobiont systems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {105}, pmid = {29885666}, issn = {2049-2618}, support = {ANR-15-CE02-0011//Agence Nationale de la Recherche (FR)/International ; }, mesh = {Animals ; Cnidaria/*parasitology ; Computational Biology ; *Coral Reefs ; Microalgae/metabolism ; Plankton/parasitology ; Porifera/*microbiology ; Rhizaria/*parasitology ; Symbiosis/*physiology ; Transcriptome/genetics ; }, abstract = {BACKGROUND: Study of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. As the study of holobiont meta-transcriptomes is affected by challenges invoked above, we propose an innovative bioinformatic approach to tackle such difficulties and tested it on marine models as a proof of concept.<br><br>RESULTS: We considered three holobiont models, of which two transcriptomes were previously published and a yet unpublished transcriptome, to analyze and sort their raw reads using Short Read Connector, a k-mer based similarity method. Before assembly, we thus defined four distinct categories for each holobiont meta-transcriptome: host reads, symbiont reads, shared reads, and unassigned reads. Afterwards, we observed that independent de novo assemblies for each category led to a diminution of the number of chimeras compared to classical assembly methods. Moreover, the separation of each partner's transcriptome offered the independent and comparative exploration of their functional diversity in the holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts (a Cnidaria-Dinophyta, a Porifera-Bacteria) and a first meta-transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is considerably limited.<br><br>CONCLUSIONS: In contrast to classical assembly approaches, our bioinformatic strategy generates less de novo assembled chimera and allows biologists to study separately host and symbiont data from a holobiont mixture. The pre-assembly separation of reads using an efficient tool as Short Read Connector is an effective way to tackle meta-transcriptomic challenges and offers bright perpectives to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages and ultimately expand our knowledge about these associations.}, }
@article {pmid29849034, year = {2018}, author = {Glasl, B and Smith, CE and Bourne, DG and Webster, NS}, title = {Exploring the diversity-stability paradigm using sponge microbial communities.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {8425}, pmid = {29849034}, issn = {2045-2322}, mesh = {Animals ; *Biodiversity ; Host-Pathogen Interactions ; *Microbiota/genetics ; Pigmentation ; Porifera/metabolism/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Symbiosis ; }, abstract = {A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.}, }
@article {pmid29795808, year = {2018}, author = {Rädecker, N and Raina, JB and Pernice, M and Perna, G and Guagliardo, P and Kilburn, MR and Aranda, M and Voolstra, CR}, title = {Corrigendum: Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {449}, doi = {10.3389/fphys.2018.00449}, pmid = {29795808}, issn = {1664-042X}, abstract = {[This corrects the article on p. 214 in vol. 9, PMID: 29615919.].}, }
@article {pmid29766224, year = {2019}, author = {García-Bonilla, E and Brandão, PFB and Pérez, T and Junca, H}, title = {Stable and Enriched Cenarchaeum symbiosum and Uncultured Betaproteobacteria HF1 in the Microbiome of the Mediterranean Sponge Haliclona fulva (Demospongiae: Haplosclerida).}, journal = {Microbial ecology}, volume = {77}, number = {1}, pages = {25-36}, pmid = {29766224}, issn = {1432-184X}, support = {Doctoral Grant (Convocatoria 528-2011)//Colciencias-Colfuturo/ ; Projects (2012-2014 and 2015-2017//EcosNord-Colciencias/ ; }, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification/physiology ; Bacteria ; Betaproteobacteria/*classification/genetics/isolation &amp; purification/physiology ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; France ; Haliclona/*microbiology ; Mediterranean Sea ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Water Microbiology ; }, abstract = {Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.}, }
@article {pmid29765310, year = {2018}, author = {Houdek, P}, title = {Economic Holobiont: Influence of Parasites, Microbiota and Chemosignals on Economic Behavior.}, journal = {Frontiers in behavioral neuroscience}, volume = {12}, number = {}, pages = {77}, pmid = {29765310}, issn = {1662-5153}, abstract = {The article is a perspective on utilization of microorganisms and chemosignals in studying human economic behavior. Research in biological roots of economic development has already confirmed that parasitic pressure influenced the creation and development of cultural norms and institutions. However, other effects of microorganisms on human groups and individual decision-making and behavior are heavily understudied. The perspective discusses how parasitic infections, sexually transmitted organisms and microbiota (i.e., "human holobiont") could causally influence risk-seeking behavior, impulsivity, social dominance, empathy, political views and gender differences. As a case study, the parasite Toxoplasma gondii and its influence on economic preferences, personal characteristics and human appearance are examined. I also briefly review how chemosignals influence decision-making, particularly in the social preferences domain. I mention some predictions that arise from the paradigm of economic holobiont for the economic science. The conclusion summarizes limitations of the discussed findings and the stated speculations.}, }
@article {pmid29761370, year = {2018}, author = {Bourrat, P and Griffiths, PE}, title = {Multispecies individuals.}, journal = {History and philosophy of the life sciences}, volume = {40}, number = {2}, pages = {33}, doi = {10.1007/s40656-018-0194-1}, pmid = {29761370}, issn = {0391-9714}, support = {DP0878650//Australian Research Council (AU)/ ; }, mesh = {Alismatales/growth &amp; development/physiology ; Animals ; Biological Evolution ; Bivalvia/*microbiology/physiology ; Humans ; Individuality ; Life History Traits ; *Microbiota ; Oligochaeta/*microbiology/physiology ; *Symbiosis ; }, abstract = {We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called 'holobionts'. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of ecological dependence between separate individuals. Some widely used arguments in support of the 'holobiont' concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality.}, }
@article {pmid29745450, year = {2018}, author = {Sivakumar, S and Vimal, S and Abdul Majeed, S and Santhosh Kumar, S and Taju, G and Madan, N and Rajkumar, T and Thamizhvanan, S and Shamsudheen, KV and Scaria, V and Sivasubbu, S and Sahul Hameed, AS}, title = {A new strain of white spot syndrome virus affecting Litopenaeus vannamei in Indian shrimp farms.}, journal = {Journal of fish diseases}, volume = {41}, number = {7}, pages = {1129-1146}, doi = {10.1111/jfd.12811}, pmid = {29745450}, issn = {1365-2761}, mesh = {Animals ; DNA, Viral/*analysis ; Gene Deletion ; *Genome, Viral ; High-Throughput Nucleotide Sequencing ; India ; Penaeidae/*virology ; White spot syndrome virus 1/genetics/*physiology ; }, abstract = {White spot syndrome virus (WSSV)-infected shrimp samples collected from grow-out ponds located at Nellore, Andhra Pradesh, India, showed WSSV negative and positive by PCR using primer sets specific to ORF119 and VP28 gene of WSSV, respectively. This indicated the deletion of genetic fragments in the genome of WSSV. The WSSV isolate along with lab strain of WSSV was subjected to next-generation sequencing. The sequence analysis revealed a deletion of 13,170 bp at five positions in the genome of WSSV-NS (new strain) relative to WSSV-TH and WSSV-LS (lab strain). The PCR analysis using the ORF's specific primer sets revealed the complete deletion of 10 ORFs in the genome of WSSV-NS strain. The primer set was designed based on sequence covering ORF161/162/163 to amplify a product of 2,748 bp for WSSV-LS and 402 bp for WSSV-NS. Our surveillance programme carried out since 2002 revealed the replacement of WSSV-LS by WSSV-NS in Indian shrimp culture system.}, }
@article {pmid29742123, year = {2018}, author = {León-Palmero, E and Joglar, V and Álvarez, PA and Martín-Platero, A and Llamas, I and Reche, I}, title = {Diversity and antimicrobial potential in sea anemone and holothurian microbiomes.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196178}, pmid = {29742123}, issn = {1932-6203}, mesh = {Animals ; Bacteria/isolation &amp; purification ; *Biodiversity ; Holothuria/*microbiology/*physiology ; *Microbiota ; Sea Anemones/*microbiology/*physiology ; Symbiosis ; }, abstract = {Marine invertebrates, as holobionts, contain symbiotic bacteria that coevolve and develop antimicrobial substances. These symbiotic bacteria are an underexplored source of new bioactive molecules to face the emerging antibiotic resistance in pathogens. Here, we explored the antimicrobial activity of bacteria retrieved from the microbiota of two sea anemones (Anemonia sulcata, Actinia equina) and two holothurians (Holothuria tubulosa, Holothuria forskali). We tested the antimicrobial activity of the isolated bacteria against pathogens with interest for human health, agriculture and aquaculture. We isolated 27 strains with antibacterial activity and 12 of these isolates also showed antifungal activity. We taxonomically identified these strains being Bacillus and Vibrio species the most representative producers of antimicrobial substances. Microbiome species composition of the two sea anemones was similar between them but differed substantially of seawater bacteria. In contrast, microbiome species composition of the two holothurian species was different between them and in comparison with the bacteria in holothurian feces and seawater. In all the holobiont microbiomes Bacteroidetes was the predominant phylum. For each microbiome, we determined diversity and the rank-abundance dominance using five fitted models (null, pre-emption, log-Normal, Zipf and Zipf-Mandelbrot). The models with less evenness (i.e. Zipf and Zipf-Mandelblot) showed the best fits in all the microbiomes. Finally, we tracked (using the V4 hypervariable region of 16S rRNA gene) the relative abundance of these 27 isolates with antibacterial activity in the total pool of sequences obtained for the microbiome of each holobiont. Coincidences, although with extremely low frequencies, were detected only in the microbiome of H. forskali. This fact suggests that these isolated bacteria belong to the long tail of rare symbiotic bacteria. Therefore, more and more sophisticated culture techniques are necessary to explore this apparently vast pool of rare symbiontic bacteria and to determine their biotechnological potentiality.}, }
@article {pmid29740401, year = {2018}, author = {Domin, H and Zurita-Gutiérrez, YH and Scotti, M and Buttlar, J and Hentschel Humeida, U and Fraune, S}, title = {Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {728}, pmid = {29740401}, issn = {1664-302X}, abstract = {The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria-bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria-bacteria interactions through co-occurrence networks. The analysis indicates that bacteria-bacteria interactions are dynamic during host colonization and change according to the host's developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.}, }
@article {pmid29739445, year = {2018}, author = {Sorek, M and Schnytzer, Y and Waldman Ben-Asher, H and Caspi, VC and Chen, CS and Miller, DJ and Levy, O}, title = {Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {83}, pmid = {29739445}, issn = {2049-2618}, support = {1294//Taiwan-Israel cooperative program/International ; }, mesh = {Animals ; Biological Clocks/*physiology ; Circadian Rhythm/genetics/*physiology ; Dinoflagellida/*metabolism ; Gene Expression Regulation/*genetics ; Oxygen/metabolism ; Sea Anemones/*genetics/parasitology ; Symbiosis/physiology ; }, abstract = {BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana.<br><br>RESULTS: The results showed that whereas circatidal (approx. 12-h) cycles of activity and gene expression predominated in aposymbiotic morphs, circadian (approx. 24-h) patterns were the more common in symbiotic morphs, where the expression of a significant number of genes shifted from a 12- to 24-h rhythm. The behavioural experiments on symbiotic A. diaphana displayed diel (24-h) rhythmicity in body and tentacle contraction under the light/dark cycles, whereas aposymbiotic morphs showed approximately 12-h (circatidal) rhythmicity. Reinfection experiments represent an important step in understanding the hierarchy of endogenous clocks in symbiotic associations, where the aposymbiotic Aiptasia morphs returned to a 24-h behavioural rhythm after repopulation with algae.<br><br>CONCLUSION: Whilst some modification of host metabolism is to be expected, the extent to which the presence of the algae modified host endogenous behavioural and transcriptional rhythms implies that it is the symbionts that influence the pace. Our results clearly demonstrate the importance of the endosymbiotic algae in determining the timing and the duration of the extension and contraction of the body and tentacles and temporal gene expression.}, }
@article {pmid29738088, year = {2018}, author = {Faure, D and Simon, JC and Heulin, T}, title = {Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.}, journal = {The New phytologist}, volume = {218}, number = {4}, pages = {1321-1324}, doi = {10.1111/nph.15199}, pmid = {29738088}, issn = {1469-8137}, mesh = {*Biological Evolution ; *Ecosystem ; Genomics ; *Host Microbial Interactions/genetics ; Metagenome ; Research Personnel ; }, }
@article {pmid29716650, year = {2018}, author = {van de Guchte, M and Blottière, HM and Doré, J}, title = {Humans as holobionts: implications for prevention and therapy.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {81}, pmid = {29716650}, issn = {2049-2618}, mesh = {Bacteria/classification/*immunology ; Bacterial Physiological Phenomena/*immunology ; Dysbiosis/microbiology ; Gastrointestinal Microbiome/*immunology ; Host Microbial Interactions/*immunology/physiology ; Humans ; Inflammation/microbiology ; Inflammatory Bowel Diseases/microbiology ; Obesity/microbiology ; Symbiosis/*physiology ; }, abstract = {The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maintained and serves health, but signs are that perturbation of this equilibrium beyond the limits of resilience can propel the system into an alternative stable state, a pre-disease state, more susceptible to the development of chronic diseases. The microbiota-host equilibrium of a large and growing proportion of individuals in Western society may represent such a pre-disease state and explain the explosive development of chronic diseases such as inflammatory bowel disease, obesity, and other inflammatory diseases. These diseases themselves represent other alternative stable states again and are therefore hard to cure. The holistic view of the microbiota-host association where feedback loops between microbiota and host are thought to maintain the system in a stable state-be it a healthy, pre-disease, or disease state-implies that integrated approaches, addressing host processes and microbiota, should be used to treat or prevent (pre-)disease.}, }
@article {pmid29714033, year = {2018}, author = {Nobori, T and Mine, A and Tsuda, K}, title = {Molecular networks in plant-pathogen holobiont.}, journal = {FEBS letters}, volume = {592}, number = {12}, pages = {1937-1953}, doi = {10.1002/1873-3468.13071}, pmid = {29714033}, issn = {1873-3468}, mesh = {Bacteria/immunology/*pathogenicity ; Gene Regulatory Networks ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; Plant Immunity ; Plant Proteins/*metabolism ; Plants/metabolism/*microbiology ; Signal Transduction ; Virulence Factors/*immunology ; }, abstract = {Plant immune receptors enable detection of a multitude of microbes including pathogens. The recognition of microbes activates various plant signaling pathways, such as those mediated by phytohormones. Over the course of coevolution with microbes, plants have expanded their repertoire of immune receptors and signaling components, resulting in highly interconnected plant immune networks. These immune networks enable plants to appropriately respond to different types of microbes and to coordinate immune responses with developmental programs and environmental stress responses. However, the interconnectivity in plant immune networks is exploited by microbial pathogens to promote pathogen fitness in plants. Analogous to plant immune networks, virulence-related pathways in bacterial pathogens are also interconnected. Accumulating evidence implies that some plant-derived compounds target bacterial virulence networks. Thus, the plant immune and bacterial virulence networks intimately interact with each other. Here, we highlight recent insights into the structures of the plant immune and bacterial virulence networks and the interactions between them. We propose that small molecules derived from plants and/or bacterial pathogens connect the two molecular networks, forming supernetworks in the plant-bacterial pathogen holobiont.}, }
@article {pmid29701776, year = {2018}, author = {Karimi, E and Slaby, BM and Soares, AR and Blom, J and Hentschel, U and Costa, R}, title = {Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy074}, pmid = {29701776}, issn = {1574-6941}, mesh = {Animals ; Carbon/metabolism ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Rhodospirillaceae/genetics/*metabolism ; Sulfur/metabolism ; Symbiosis/*physiology ; }, abstract = {Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.}, }
@article {pmid29695294, year = {2018}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution after 10 years.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {78}, pmid = {29695294}, issn = {2049-2618}, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome/genetics ; Humans ; Microbiota/*genetics ; Plants ; Symbiosis/*physiology ; }, abstract = {The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution. The hologenome is comprised of two complimentary parts: host and microbiome genomes. Changes in either genome can result in variations that can be selected for or against. The host genome is highly conserved, and genetic changes within it occur slowly, whereas the microbiome genome is dynamic and can change rapidly in response to the environment by increasing or reducing particular microbes, by acquisition of novel microbes, by horizontal gene transfer, and by mutation. Recent experiments showing that microbiota can play an initial role in speciation have been suggested as an additional mode of enhancing evolution. Some of the genetic variations can be transferred to offspring by a variety of mechanisms. Strain-specific DNA analysis has shown that at least some of the microbiota can be maintained across hundreds of thousands of host generations, implying the existence of a microbial core. We argue that rapid changes in the microbiome genome could allow holobionts to adapt and survive under changing environmental conditions thus providing the time necessary for the host genome to adapt and evolve. As Darwin wrote, "It is not the strongest of the species that survives but the most adaptable".}, }
@article {pmid29695286, year = {2018}, author = {Vannier, N and Mony, C and Bittebiere, AK and Michon-Coudouel, S and Biget, M and Vandenkoornhuyse, P}, title = {A microorganisms' journey between plant generations.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {79}, pmid = {29695286}, issn = {2049-2618}, support = {EC2CO program (MIME project)//Centre National de la Recherche Scientifique/International ; PEPS program (MYCOLAND project)//Centre National de la Recherche Scientifique/International ; }, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics/isolation &amp; purification ; Lamiaceae/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network.<br><br>METHODS: We used the clonal plant Glechoma hederacea as plant model and forced newly emitted clonal progeny to root in separated pots while controlling the presence of microorganisms. We used an amplicon sequencing approach of 16S and 18S rRNA targeting bacteria/archaea and fungi respectively to describe the root microbiota of mother and clonal-plant offspring.<br><br>RESULTS: We demonstrated the vertical transmission of a significant proportion of the mother plants' symbiotic bacteria and fungi to the daughters. Interestingly, archaea were not transmitted to the daughter plants. Transmitted communities had lower richness, suggesting a filtration during transmission. We found that the transmitted pool of microorganisms was similar among daughters, constituting the heritability of a specific cohort of microorganisms, opening a new understanding of the plant holobiont. We also found significant effects of distance to the mother plant and of growth time on the richness of the microbiota transmitted.<br><br>CONCLUSIONS: In this clonal plant, microorganisms are transmitted between individuals through connections, thereby ensuring the availability of microbe partners for the newborn plants as well as the dispersion between hosts for the microorganisms. This previously undescribed ecological process allows the dispersal of microorganisms in space and across plant generations. As the vast majority of plants are clonal, this process might be therefore a strong driver of ecosystem functioning and assembly of plant and microorganism communities in a wide range of ecosystems.}, }
@article {pmid29685747, year = {2018}, author = {Miller, WB and Torday, JS}, title = {Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {140}, number = {}, pages = {49-73}, doi = {10.1016/j.pbiomolbio.2018.04.006}, pmid = {29685747}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Cells/*cytology ; *Cognition ; Humans ; Signal Transduction ; }, abstract = {Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.}, }
@article {pmid29666616, year = {2018}, author = {Mortzfeld, BM and Taubenheim, J and Fraune, S and Klimovich, AV and Bosch, TCG}, title = {Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {629}, pmid = {29666616}, issn = {1664-302X}, abstract = {The aging process is considered to be the result of accumulating cellular deterioration in an individual organism over time. It can be affected by the combined influence of genetic, epigenetic, and environmental factors including life-style-associated events. In the non-senescent freshwater polyp Hydra, one of the classical model systems for evolutionary developmental biology and regeneration, transcription factor FoxO modulates both stem cell proliferation and innate immunity. This provides strong support for the role of FoxO as a critical rate-of-aging regulator. However, how environmental factors interact with FoxO remains unknown. Here, we find that deficiency in FoxO signaling in Hydra leads to dysregulation of antimicrobial peptide expression and that FoxO loss-of-function polyps are impaired in selection for bacteria resembling the native microbiome and more susceptible to colonization of foreign bacteria. These findings reveal a key role of FoxO signaling in the communication between host and microbiota and embed the evolutionary conserved longevity factor FoxO into the holobiont concept.}, }
@article {pmid29657963, year = {2018}, author = {Theis, KR}, title = {Hologenomics: Systems-Level Host Biology.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29657963}, issn = {2379-5077}, abstract = {The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.}, }
@article {pmid29651978, year = {2018}, author = {Vigliotti, C and Bicep, C and Bapteste, E and Lopez, P and Corel, E}, title = {Tracking the Rules of Transmission and Introgression with Networks.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, pmid = {29651978}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*microbiology ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Interspersed Repetitive Sequences ; Metagenome/genetics ; Microbiota/*genetics/physiology ; Plasmids/genetics ; *Recombination, Genetic ; Sequence Homology ; Viruses/genetics ; }, abstract = {Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of "gene externalization," which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an "externalized gut metagenome" is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.}, }
@article {pmid29650460, year = {2018}, author = {Allemand, D and Furla, P}, title = {How does an animal behave like a plant? Physiological and molecular adaptations of zooxanthellae and their hosts to symbiosis.}, journal = {Comptes rendus biologies}, volume = {341}, number = {5}, pages = {276-280}, doi = {10.1016/j.crvi.2018.03.007}, pmid = {29650460}, issn = {1768-3238}, mesh = {Acclimatization ; Adaptation, Physiological/*physiology ; Animals ; Anthozoa/physiology ; Dinoflagellida/*physiology ; Ecology ; Photosynthesis/physiology ; Sea Anemones/physiology ; Symbiosis/*physiology ; }, abstract = {Cnidarians (corals and sea anemones) harbouring photosynthetic microalgae derive several benefits from their association. To allow this association, numerous symbiotic-dependent adaptations in both partners, resulting from evolutionary pressures, have been selected. The dinoflagellate symbionts (zooxanthellae) are located inside a vesicle in the cnidarian host cell and are therefore exposed to a very different environment compared to the free-living state of these microalgae in terms of ion concentration and carbon content and speciation. In addition, this intracellular localization imposes that they rely completely upon the host for their nutrient supply (nitrogen, CO2). Symbiotic-dependent adaptations imposed to the animal host by phototrophic symbiosis are more relevant to photosynthetic organisms than to metazoans: indeed, the cnidarian host often harbours diurnal changes of morphology to adapt itself to the amount of light and possesses carbon-concentrating mechanisms, antioxidative defences and UV sunscreens similar to that present in phototrophs. These adaptations and the contrasting fragility of the association are discussed from both ecological and evolutionary points of view.}, }
@article {pmid29645277, year = {2019}, author = {Wille, L and Messmer, MM and Studer, B and Hohmann, P}, title = {Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.}, journal = {Plant, cell &amp; environment}, volume = {42}, number = {1}, pages = {20-40}, doi = {10.1111/pce.13214}, pmid = {29645277}, issn = {1365-3040}, mesh = {*Disease Resistance ; Edible Grain/*microbiology ; Fabaceae/*microbiology ; *Host Microbial Interactions ; Host-Pathogen Interactions ; *Plant Breeding/methods ; Plant Diseases/immunology/*microbiology ; Plant Roots/*microbiology ; }, abstract = {Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.}, }
@article {pmid29615919, year = {2018}, author = {Rädecker, N and Raina, JB and Pernice, M and Perna, G and Guagliardo, P and Kilburn, MR and Aranda, M and Voolstra, CR}, title = {Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {214}, pmid = {29615919}, issn = {1664-042X}, abstract = {The symbiosis between cnidarian hosts and microalgae of the genus Symbiodinium provides the foundation of coral reefs in oligotrophic waters. Understanding the nutrient-exchange between these partners is key to identifying the fundamental mechanisms behind this symbiosis, yet has proven difficult given the endosymbiotic nature of this relationship. In this study, we investigated the respective contribution of host and symbiont to carbon and nitrogen assimilation in the coral model anemone Aiptaisa. For this, we combined traditional measurements with nanoscale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling to investigate patterns of nutrient uptake and translocation both at the organismal scale and at the cellular scale. Our results show that the rate of carbon and nitrogen assimilation in Aiptasia depends on the identity of the host and the symbiont. NanoSIMS analysis confirmed that both host and symbiont incorporated carbon and nitrogen into their cells, implying a rapid uptake and cycling of nutrients in this symbiotic relationship. Gross carbon fixation was highest in Aiptasia associated with their native Symbiodinium communities. However, differences in fixation rates were only reflected in the δ[13]C enrichment of the cnidarian host, whereas the algal symbiont showed stable enrichment levels regardless of host identity. Thereby, our results point toward a "selfish" character of the cnidarian-Symbiodinium association in which both partners directly compete for available resources. Consequently, this symbiosis may be inherently instable and highly susceptible to environmental change. While questions remain regarding the underlying cellular controls of nutrient exchange and the nature of metabolites involved, the approach outlined in this study constitutes a powerful toolset to address these questions.}, }
@article {pmid29611114, year = {2018}, author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B}, title = {Of genes and microbes: solving the intricacies in host genomes.}, journal = {Protein &amp; cell}, volume = {9}, number = {5}, pages = {446-461}, pmid = {29611114}, issn = {1674-8018}, mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a "hologenome", that is, the organized, closely interacting genome of the host and the microbiome.}, }
@article {pmid29609655, year = {2018}, author = {van de Water, JAJM and Allemand, D and Ferrier-Pagès, C}, title = {Host-microbe interactions in octocoral holobionts - recent advances and perspectives.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {64}, pmid = {29609655}, issn = {2049-2618}, mesh = {Animal Diseases/microbiology ; Animals ; Anthozoa/*microbiology ; Bacteria/classification ; Biological Products ; Coral Reefs ; Drug Discovery ; Ecosystem ; Fungi/classification ; *Host Microbial Interactions ; Host-Pathogen Interactions/immunology ; *Microbiota ; Spatio-Temporal Analysis ; Symbiosis ; Viruses/classification/genetics ; }, abstract = {Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.}, }
@article {pmid29599012, year = {2018}, author = {Bang, C and Dagan, T and Deines, P and Dubilier, N and Duschl, WJ and Fraune, S and Hentschel, U and Hirt, H and Hülter, N and Lachnit, T and Picazo, D and Pita, L and Pogoreutz, C and Rädecker, N and Saad, MM and Schmitz, RA and Schulenburg, H and Voolstra, CR and Weiland-Bräuer, N and Ziegler, M and Bosch, TCG}, title = {Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?.}, journal = {Zoology (Jena, Germany)}, volume = {127}, number = {}, pages = {1-19}, doi = {10.1016/j.zool.2018.02.004}, pmid = {29599012}, issn = {1873-2720}, mesh = {*Adaptation, Physiological/physiology ; Animals ; Ecosystem ; *Extreme Environments ; Microbiota/genetics/*physiology ; Phylogeny ; Symbiosis/physiology ; }, abstract = {From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.}, }
@article {pmid29587885, year = {2018}, author = {Hassani, MA and Durán, P and Hacquard, S}, title = {Microbial interactions within the plant holobiont.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {58}, pmid = {29587885}, issn = {2049-2618}, support = {758003/ERC_/European Research Council/International ; }, mesh = {Bacteria/classification ; Biodiversity ; Biological Evolution ; Fungi/classification ; Microbial Consortia ; *Microbial Interactions ; *Microbiota ; Plant Development ; Plants/*microbiology ; }, abstract = {Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a "holobiont." Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.}, }
@article {pmid29587830, year = {2018}, author = {Gobet, A and Mest, L and Perennou, M and Dittami, SM and Caralp, C and Coulombet, C and Huchette, S and Roussel, S and Michel, G and Leblanc, C}, title = {Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {60}, pmid = {29587830}, issn = {2049-2618}, support = {ANR-10-BTBR-02-04-11//Agence Nationale de la Recherche/International ; }, mesh = {Animal Feed ; Animals ; Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Gastropoda/*microbiology ; *Herbivory ; Polysaccharides ; *Seasons ; }, abstract = {BACKGROUND: Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding.<br><br>RESULTS: Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides.<br><br>CONCLUSIONS: This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.}, }
@article {pmid29581311, year = {2018}, author = {Doolittle, WF and Inkpen, SA}, title = {Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {16}, pages = {4006-4014}, pmid = {29581311}, issn = {1091-6490}, mesh = {Adaptation, Physiological ; Animals ; Biological Variation, Individual ; Cell Lineage ; Ecology ; Gene Regulatory Networks ; Genes ; Genetic Linkage ; Genetic Variation ; *Genetics, Population ; Metaphysics ; Microbial Interactions ; Microbiota ; *Models, Genetic ; Plants/genetics ; Reproduction ; Selection, Genetic/*genetics ; Symbiosis/genetics ; }, abstract = {Many practicing biologists accept that nothing in their discipline makes sense except in the light of evolution, and that natural selection is evolution's principal sense-maker. But what natural selection actually is (a force or a statistical outcome, for example) and the levels of the biological hierarchy (genes, organisms, species, or even ecosystems) at which it operates directly are still actively disputed among philosophers and theoretical biologists. Most formulations of evolution by natural selection emphasize the differential reproduction of entities at one or the other of these levels. Some also recognize differential persistence, but in either case the focus is on lineages of material things: even species can be thought of as spatiotemporally restricted, if dispersed, physical beings. Few consider-as "units of selection" in their own right-the processes implemented by genes, cells, species, or communities. "It's the song not the singer" (ITSNTS) theory does that, also claiming that evolution by natural selection of processes is more easily understood and explained as differential persistence than as differential reproduction. ITSNTS was formulated as a response to the observation that the collective functions of microbial communities (the songs) are more stably conserved and ecologically relevant than are the taxa that implement them (the singers). It aims to serve as a useful corrective to claims that "holobionts" (microbes and their animal or plant hosts) are aggregate "units of selection," claims that often conflate meanings of that latter term. But ITSNS also seems broadly applicable, for example, to the evolution of global biogeochemical cycles and the definition of ecosystem function.}, }
@article {pmid29573244, year = {2018}, author = {Pootakham, W and Mhuantong, W and Putchim, L and Yoocha, T and Sonthirod, C and Kongkachana, W and Sangsrakru, D and Naktang, C and Jomchai, N and Thongtham, N and Tangphatsornruang, S}, title = {Dynamics of coral-associated microbiomes during a thermal bleaching event.}, journal = {MicrobiologyOpen}, volume = {7}, number = {5}, pages = {e00604}, pmid = {29573244}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology/*radiation effects ; Bacteria/*classification/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Dinoflagellida/*classification/genetics ; Microbiota/*radiation effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Temperature ; }, abstract = {Coral-associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral-associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea-associated bacterial and algal communities throughout a natural bleaching event, using full-length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral-associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress.}, }
@article {pmid29567394, year = {2018}, author = {Rahman, MM and Flory, E and Koyro, HW and Abideen, Z and Schikora, A and Suarez, C and Schnell, S and Cardinale, M}, title = {Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.).}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {386-398}, doi = {10.1016/j.syapm.2018.02.003}, pmid = {29567394}, issn = {1618-0984}, mesh = {Endophytes/growth &amp; development ; Hordeum/growth &amp; development/*microbiology ; Microbiota ; Paenibacillus/classification/growth &amp; development/*isolation &amp; purification ; Pantoea/classification/growth &amp; development/*isolation &amp; purification ; Plant Roots/*microbiology ; Pseudomonas/classification/growth &amp; development/*isolation &amp; purification ; Seeds/*microbiology ; Symbiosis ; }, abstract = {The importance of the plant microbiome for host fitness has led to the concept of the "plant holobiont". Seeds are reservoirs and vectors for beneficial microbes, which are very intimate partners of higher plants with the potential to connect plant generations. In this study, the endophytic seed microbiota of numerous barley samples, representing different cultivars, geographical sites and harvest years, was investigated. Cultivation-dependent and -independent analyses, microscopy, functional plate assays, greenhouse assays and functional prediction were used, with the aim of assessing the composition, stability and function of the barley seed endophytic bacterial microbiota. Associations were consistently detected in the seed endosphere with Paenibacillus, Pantoea and Pseudomonas spp., which were able to colonize the root with a notable rhizocompetence after seed germination. In greenhouse assays, enrichment with these bacteria promoted barley growth, improved mineral nutrition and induced resistance against the fungal pathogen Blumeria graminis. We demonstrated here that barley, an important crop plant, was consistently associated with beneficial bacteria inside the seeds. The results have relevant implications for plant microbiome ecology and for the holobiont concept, as well as opening up new possibilities for research and application of seed endophytes as bioinoculants in sustainable agriculture.}, }
@article {pmid29566771, year = {2018}, author = {Callens, M and Watanabe, H and Kato, Y and Miura, J and Decaestecker, E}, title = {Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {56}, pmid = {29566771}, issn = {2049-2618}, support = {FWO G060216N//FWO/International ; BOF C16/17/002//KU Leuven/International ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Load ; Biodiversity ; Daphnia/drug effects/growth &amp; development/*microbiology/*physiology ; *Host Microbial Interactions/drug effects ; *Microbiota/drug effects ; }, abstract = {BACKGROUND: Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota.<br><br>RESULTS: Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth.<br><br>CONCLUSIONS: These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.}, }
@article {pmid29562933, year = {2018}, author = {Ravanbakhsh, M and Sasidharan, R and Voesenek, LACJ and Kowalchuk, GA and Jousset, A}, title = {Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {52}, pmid = {29562933}, issn = {2049-2618}, mesh = {Bacteria/*metabolism ; Environment ; Ethylenes/*metabolism ; Gene Expression Regulation, Plant/*genetics ; Microbiota/physiology ; Plants/*microbiology ; Signal Transduction ; Stress, Physiological/physiology ; Symbiosis/*physiology ; }, abstract = {The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.}, }
@article {pmid29556542, year = {2018}, author = {Wegley Kelly, L and Haas, AF and Nelson, CE}, title = {Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29556542}, issn = {2379-5077}, abstract = {Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to broaden our understanding of the ecological roles of environmental microbes. Studies on coral reefs are actively integrating these data streams at multiple levels, from the symbiotic habitat of the coral holobiont to microbially mediated interactions between corals and algae to the effects of these interactions on the microbial community structure, metabolism, and organic geochemistry of the reef ecosystem. Coral reefs endure multiple anthropogenic impacts, including pollution, overfishing, and global change. In this context, we must develop ecosystem microbiology with an eye to providing managers with microbial indicators of reef ecosystem processes, coral health, and resilience to both local and global stressors.}, }
@article {pmid29556373, year = {2018}, author = {Hornung, B and Martins Dos Santos, VAP and Smidt, H and Schaap, PJ}, title = {Studying microbial functionality within the gut ecosystem by systems biology.}, journal = {Genes &amp; nutrition}, volume = {13}, number = {}, pages = {5}, pmid = {29556373}, issn = {1555-8932}, abstract = {Humans are not autonomous entities. We are all living in a complex environment, interacting not only with our peers, but as true holobionts; we are also very much in interaction with our coexisting microbial ecosystems living on and especially within us, in the intestine. Intestinal microorganisms, often collectively referred to as intestinal microbiota, contribute significantly to our daily energy uptake by breaking down complex carbohydrates into simple sugars, which are fermented to short-chain fatty acids and subsequently absorbed by human cells. They also have an impact on our immune system, by suppressing or enhancing the growth of malevolent and beneficial microbes. Our lifestyle can have a large influence on this ecosystem. What and how much we consume can tip the ecological balance in the intestine. A "western diet" containing mainly processed food will have a different effect on our health than a balanced diet fortified with pre- and probiotics. In recent years, new technologies have emerged, which made a more detailed understanding of microbial communities and ecosystems feasible. This includes progress in the sequencing of PCR-amplified phylogenetic marker genes as well as the collective microbial metagenome and metatranscriptome, allowing us to determine with an increasing level of detail, which microbial species are in the microbiota, understand what these microorganisms do and how they respond to changes in lifestyle and diet. These new technologies also include the use of synthetic and in vitro systems, which allow us to study the impact of substrates and addition of specific microbes to microbial communities at a high level of detail, and enable us to gather quantitative data for modelling purposes. Here, we will review the current state of microbiome research, summarizing the computational methodologies in this area and highlighting possible outcomes for personalized nutrition and medicine.}, }
@article {pmid29554951, year = {2018}, author = {Guégan, M and Zouache, K and Démichel, C and Minard, G and Tran Van, V and Potier, P and Mavingui, P and Valiente Moro, C}, title = {The mosquito holobiont: fresh insight into mosquito-microbiota interactions.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {49}, pmid = {29554951}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*metabolism ; Culicidae/*microbiology ; Host-Pathogen Interactions/*physiology ; Microbiota/*physiology ; Mosquito Vectors/*microbiology ; Symbiosis/*physiology ; }, abstract = {The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced strong evidence that symbiotic bacteria play a major role in host biology. However, the understanding of these symbiotic relationships has mainly been limited to phytophagous insects, while the role of host-associated microbiota in haematophagous insect vectors remains largely unexplored. Mosquitoes are a major global public health concern, with a concomitant increase in people at risk of infection. The global emergence and re-emergence of mosquito-borne diseases has led many researchers to study both the mosquito host and its associated microbiota. Although most of these studies have been descriptive, they have led to a broad description of the bacterial communities hosted by mosquito populations. This review describes key advances and progress in the field of the mosquito microbiota research while also encompassing other microbes and the environmental factors driving their composition and diversity. The discussion includes recent findings on the microbiota functional roles and underlines their interactions with the host biology and pathogen transmission. Insight into the ecology of multipartite interactions, we consider that conferring the term holobiont to the mosquito and its microbiota is useful to get a comprehensive understanding of the vector pathosystem functioning so as to be able to develop innovative and efficient novel vector control strategies.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2014/17616- 7//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29540239, year = {2018}, author = {Sevellec, M and Derome, N and Bernatchez, L}, title = {Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {47}, pmid = {29540239}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Intestines/*microbiology ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salmonidae/*classification/*microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: It is well established that symbionts have considerable impact on their host, yet the investigation of the possible role of the holobiont in the host's speciation process is still in its infancy. In this study, we compared the intestinal microbiota among five sympatric pairs of dwarf (limnetic) and normal (benthic) lake whitefish Coregonus clupeaformis representing a continuum in the early stage of ecological speciation. We sequenced the 16s rRNA gene V3-V4 regions of the intestinal microbiota present in a total of 108 wild sympatric dwarf and normal whitefish as well as the water bacterial community from five lakes to (i) test for differences between the whitefish intestinal microbiota and the water bacterial community and (ii) test for parallelism in the intestinal microbiota of dwarf and normal whitefish.<br><br>RESULTS: The water bacterial community was distinct from the intestinal microbiota, indicating that intestinal microbiota did not reflect the environment, but rather the intrinsic properties of the host microbiota. Our results revealed a strong influence of the host (dwarf or normal) on the intestinal microbiota with pronounced conservation of the core intestinal microbiota (mean ~&#x2009;44% of shared genera). However, no clear evidence for parallelism was observed, whereby non-parallel differences between dwarf and normal whitefish were observed in three of the lakes while similar taxonomic composition was observed for the two other species pairs.<br><br>CONCLUSIONS: This absence of parallelism across dwarf vs. normal whitefish microbiota highlighted the complexity of the holobiont and suggests that the direction of selection could be different between the host and its microbiota.}, }
@article {pmid29523192, year = {2018}, author = {Pita, L and Rix, L and Slaby, BM and Franke, A and Hentschel, U}, title = {The sponge holobiont in a changing ocean: from microbes to ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {46}, pmid = {29523192}, issn = {2049-2618}, support = {679849//Horizon 2020/International ; 679849//Horizon 2020/International ; CRC1182-TPB1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*metabolism ; Carbon/metabolism ; Climate Change ; Dysbiosis/*pathology ; Ecosystem ; Microbiota/*physiology ; Nitrogen/metabolism ; Oceans and Seas ; Phosphorus/metabolism ; Porifera/*metabolism/*microbiology ; Symbiosis/*physiology ; }, abstract = {The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as "nested ecosystems." In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.}, }
@article {pmid29507840, year = {2018}, author = {Brüwer, JD and Voolstra, CR}, title = {First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4449}, pmid = {29507840}, issn = {2167-8359}, abstract = {Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.}, }
@article {pmid29505062, year = {2018}, author = {Haag, KL}, title = {Holobionts and their hologenomes: Evolution with mixed modes of inheritance.}, journal = {Genetics and molecular biology}, volume = {41}, number = {1 suppl 1}, pages = {189-197}, pmid = {29505062}, issn = {1415-4757}, abstract = {Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and its associated microbiota constitute a biological entity called holobiont, and that regarding it as a higher-level unit of selection is unavoidable to understand phenotypic evolution. Novel extended phenotypes are often built through symbiotic interactions, allowing the holobiont to explore and survive in distinct environmental conditions, and may evolve in a Lamarckian fashion.}, }
@article {pmid29503179, year = {2018}, author = {Lee, KA and Cho, KC and Kim, B and Jang, IH and Nam, K and Kwon, YE and Kim, M and Hyeon, DY and Hwang, D and Seol, JH and Lee, WJ}, title = {Inflammation-Modulated Metabolic Reprogramming Is Required for DUOX-Dependent Gut Immunity in Drosophila.}, journal = {Cell host &amp; microbe}, volume = {23}, number = {3}, pages = {338-352.e5}, doi = {10.1016/j.chom.2018.01.011}, pmid = {29503179}, issn = {1934-6069}, mesh = {AMP-Activated Protein Kinases/metabolism ; Animals ; Autophagy-Related Protein-1 Homolog/metabolism ; CRISPR-Cas Systems/genetics ; Cell Culture Techniques ; Digestive System/*immunology ; Drosophila/genetics/*immunology ; Drosophila Proteins/genetics/metabolism ; Dual Oxidases/*metabolism ; Enterocytes/metabolism ; Female ; Gastrointestinal Microbiome ; Gene Editing ; Gene Expression Regulation ; Homeostasis ; Host-Pathogen Interactions/*immunology ; Immunity, Innate ; Inflammation/*metabolism ; Lipid Metabolism ; Lipolysis ; MAP Kinase Kinase Kinase 1/metabolism ; Male ; Pectobacterium carotovorum/pathogenicity ; Reactive Oxygen Species/metabolism ; Sequence Analysis, RNA ; Signal Transduction ; TNF Receptor-Associated Factor 3/metabolism ; }, abstract = {DUOX, a member of the NADPH oxidase family, acts as the first line of defense against enteric pathogens by producing microbicidal reactive oxygen species. DUOX is activated upon enteric infection, but the mechanisms regulating DUOX activity remain incompletely understood. Using Drosophila genetic tools, we show that enteric infection results in "pro-catabolic" signaling that initiates metabolic reprogramming of enterocytes toward lipid catabolism, which ultimately governs DUOX homeostasis. Infection induces signaling cascades involving TRAF3 and kinases AMPK and WTS, which regulate TOR kinase to control the balance of lipogenesis versus lipolysis. Enhancing lipogenesis blocks DUOX activity, whereas stimulating lipolysis via ATG1-dependent lipophagy is required for DUOX activation. Drosophila with altered activity in TRAF3-AMPK/WTS-ATG1 pathway components exhibit abolished infection-induced lipolysis, reduced DUOX activation, and enhanced susceptibility to enteric infection. Thus, this work uncovers signaling cascades governing inflammation-induced metabolic reprogramming and provides insight into the pathophysiology of immune-metabolic interactions in the microbe-laden gut epithelia.}, }
@article {pmid29499735, year = {2018}, author = {Tetreau, G and Grizard, S and Patil, CD and Tran, FH and Tran Van, V and Stalinski, R and Laporte, F and Mavingui, P and Després, L and Valiente Moro, C}, title = {Bacterial microbiota of Aedes aegypti mosquito larvae is altered by intoxication with Bacillus thuringiensis israelensis.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {121}, pmid = {29499735}, issn = {1756-3305}, support = {ANR-13-EBID-0007-01//Agence Nationale de la Recherche/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacillus thuringiensis/*physiology ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; Gram-Positive Bacterial Infections ; Larva/*microbiology ; Microbiota/*genetics ; Mosquito Control/methods ; Pest Control, Biological/methods ; }, abstract = {BACKGROUND: Insect microbiota is a dynamic microbial community that can actively participate in defense against pathogens. Bacillus thuringiensis (Bt) is a natural entomopathogen widely used as a bioinsecticide for pest control. Although Bt's mode of action has been extensively studied, whether the presence of microbiota is mandatory for Bt to effectively kill the insect is still under debate. An association between a higher tolerance and a modified microbiota was already evidenced but a critical point remained to be solved: is the modified microbiota a cause or a consequence of a higher tolerance to Bt?<br><br>METHODS: In this study we focused on the mosquito species Aedes aegypti, as no work has been performed on Diptera on this topic to date, and on B. thuringiensis israelensis (Bti), which is used worldwide for mosquito control. To avoid using antibiotics to cure bacterial microbiota, mosquito larvae were exposed to an hourly increasing dose of Bti during 25 hours to separate the most susceptible larvae dying quickly from more tolerant individuals, with longer survival.<br><br>RESULTS: Denaturing gradient gel electrophoresis (DGGE) fingerprinting revealed that mosquito larval bacterial microbiota was strongly affected by Bti infection after only a few hours of exposure. Bacterial microbiota from the most tolerant larvae showed the lowest diversity but the highest inter-individual differences. The proportion of Bti in the host tissue was reduced in the most tolerant larvae as compared to the most susceptible ones, suggesting an active control of Bti infection by the host.<br><br>CONCLUSIONS: Here we show that a modified microbiota is associated with a higher tolerance of mosquitoes to Bti, but that it is rather a consequence of Bti infection than the cause of the higher tolerance. This study paves the way to future investigations aiming at unraveling the role of host immunity, inter-species bacterial competition and kinetics of host colonization by Bti that could be at the basis of the phenotype observed in this study.}, }
@article {pmid29492882, year = {2018}, author = {Grasis, JA}, title = {Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1746}, number = {}, pages = {1-25}, doi = {10.1007/978-1-4939-7683-6_1}, pmid = {29492882}, issn = {1940-6029}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics/isolation &amp; purification ; Computational Biology ; Genome, Viral ; *Host-Pathogen Interactions ; *Metagenomics ; }, abstract = {Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.}, }
@article {pmid29473977, year = {2018}, author = {Ramsby, BD and Hoogenboom, MO and Whalan, S and Webster, NS}, title = {Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {2124-2137}, doi = {10.1111/mec.14544}, pmid = {29473977}, issn = {1365-294X}, mesh = {Animals ; *Ecology ; Microbiota/*genetics/physiology ; Porifera/genetics/growth &amp; development/*microbiology ; Seawater/microbiology ; Temperature ; }, abstract = {Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The "core" microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.}, }
@article {pmid29468040, year = {2018}, author = {Pogoreutz, C and Rädecker, N and Cárdenas, A and Gärdes, A and Wild, C and Voolstra, CR}, title = {Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome.}, journal = {Ecology and evolution}, volume = {8}, number = {4}, pages = {2240-2252}, pmid = {29468040}, issn = {2045-7758}, abstract = {The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.}, }
@article {pmid29463295, year = {2018}, author = {Brener-Raffalli, K and Clerissi, C and Vidal-Dupiol, J and Adjeroud, M and Bonhomme, F and Pratlong, M and Aurelle, D and Mitta, G and Toulza, E}, title = {Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {39}, pmid = {29463295}, issn = {2049-2618}, support = {ANR-12-ADAP-0016//Agence Nationale de la Recherche/International ; }, mesh = {Acinetobacter/genetics/*isolation &amp; purification ; Animals ; Anthozoa/*microbiology/*parasitology ; Arcobacter/genetics/*isolation &amp; purification ; DNA, Intergenic/genetics ; Dinoflagellida/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Oceanospirillaceae/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis/physiology ; }, abstract = {BACKGROUND: Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues.<br><br>RESULTS: We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions <&#x2009;1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures.<br><br>CONCLUSION: Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.}, }
@article {pmid29459707, year = {2018}, author = {Zepeda Mendoza, ML and Xiong, Z and Escalera-Zamudio, M and Runge, AK and Thézé, J and Streicker, D and Frank, HK and Loza-Rubio, E and Liu, S and Ryder, OA and Samaniego Castruita, JA and Katzourakis, A and Pacheco, G and Taboada, B and Löber, U and Pybus, OG and Li, Y and Rojas-Anaya, E and Bohmann, K and Carmona Baez, A and Arias, CF and Liu, S and Greenwood, AD and Bertelsen, MF and White, NE and Bunce, M and Zhang, G and Sicheritz-Pontén, T and Gilbert, MPT}, title = {Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat.}, journal = {Nature ecology &amp; evolution}, volume = {2}, number = {4}, pages = {659-668}, pmid = {29459707}, issn = {2397-334X}, support = {/WT_/Wellcome Trust/United Kingdom ; 681396/ERC_/European Research Council/International ; MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; *Biological Evolution ; Blood ; Chiroptera/genetics/microbiology/*physiology ; *Diet ; *Gastrointestinal Microbiome ; *Genome ; Phylogeny ; }, abstract = {Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.}, }
@article {pmid29453252, year = {2018}, author = {Romano, S}, title = {Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29453252}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/microbiology ; Biotechnology ; Environment ; Porifera/microbiology ; Rhodobacteraceae/growth &amp; development/metabolism/*physiology ; *Symbiosis ; }, abstract = {Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.}, }
@article {pmid29441234, year = {2018}, author = {Bonthond, G and Merselis, DG and Dougan, KE and Graff, T and Todd, W and Fourqurean, JW and Rodriguez-Lanetty, M}, title = {Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4323}, pmid = {29441234}, issn = {2167-8359}, abstract = {Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.}, }
@article {pmid29435256, year = {2018}, author = {Leite, DCA and Salles, JF and Calderon, EN and van Elsas, JD and Peixoto, RS}, title = {Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont.}, journal = {Ecology and evolution}, volume = {8}, number = {3}, pages = {1818-1832}, pmid = {29435256}, issn = {2045-7758}, abstract = {Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad-host-range (BHR) plasmid groups, IncP-1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co-occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host-specific bacteriome and co-occurrence (and potential symbioses or niche space co-dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host-specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.}, }
@article {pmid29433554, year = {2018}, author = {Cregger, MA and Veach, AM and Yang, ZK and Crouch, MJ and Vilgalys, R and Tuskan, GA and Schadt, CW}, title = {The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {31}, pmid = {29433554}, issn = {2049-2618}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Organ Specificity ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Populus/*genetics/microbiology ; Rhizosphere ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; }, abstract = {BACKGROUND: Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses.<br><br>RESULTS: Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa &#xd7; deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils.<br><br>CONCLUSIONS: This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.}, }
@article {pmid29430857, year = {2018}, author = {Voss, JD and Goodson, MS and Leon, JC}, title = {Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species.}, journal = {Zoonoses and public health}, volume = {65}, number = {3}, pages = {279-290}, doi = {10.1111/zph.12445}, pmid = {29430857}, issn = {1863-2378}, mesh = {Animals ; *Epidemics ; Humans ; Obesity/epidemiology/*veterinary ; *One Health ; }, abstract = {We propose the idea of "phenotype diffusion," which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and "obesogens"), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so identification of phenotype diffusion is highly relevant for practitioners (public health officials, physicians and veterinarians) in this field.}, }
@article {pmid29423641, year = {2018}, author = {Feng, G and Sun, W and Zhang, F and Orlić, S and Li, Z}, title = {Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {20}, number = {2}, pages = {131-143}, pmid = {29423641}, issn = {1436-2236}, mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Glutamate-Ammonia Ligase/genetics ; Microbiota/genetics/*physiology ; Oxidoreductases/genetics ; Phylogeny ; Porifera/*physiology ; Seawater ; Symbiosis ; Transcriptome ; }, abstract = {Symbiotic ammonia scavengers contribute to effective removal of ammonia in sponges. However, the phylogenetic diversity and in situ activity of ammonia-scavenging microbiota between different sponge species are poorly addressed. Here, transcribed ammonia monooxygenase genes (amoA), hydrazine synthase genes (hzsA), and glutamine synthetase genes (glnA) were analyzed to reveal the active ammonia-scavenging microbiota in the sympatric sponges Theonella swinhoei, Plakortis simplex, and Phakellia fusca, and seawater. Archaeal amoA and bacterial glnA transcripts rather than bacterial amoA, hzsA, and archaeal glnA transcripts were detected in the investigated sponges and seawater. The transcribed amoA genes were ascribed to two Thaumarchaeota ecotypes, while the transcribed glnA genes were interspersed among the lineages of Cyanobacteria, Tectomicrobia, Poribacteria, Alpha-, Beta-, Gamma-, and Epsilonproteobacteria. In addition, transcribed abundances of archaeal amoA and bacterial glnA genes in these sponges have been quantified, showing significant variation among the investigated sponges and seawater. The transcriptome-based qualitative and quantitative analyses clarified the different phylogenetic diversity and transcription expression of functional genes related to microbially mediated ammonia scavenging in different sympatric sponges, contributing to the understanding of in situ active ecological functions of sponge microbial symbionts in holobiont nitrogen cycling.}, }
@article {pmid29410656, year = {2018}, author = {Rubio-Portillo, E and Kersting, DK and Linares, C and Ramos-Esplá, AA and Antón, J}, title = {Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {22}, pmid = {29410656}, issn = {1664-302X}, abstract = {The endemic Mediterranean zooxanthellate scleractinian reef-builder Cladocora caespitosa is among the organisms most affected by warming-related mass mortality events in the Mediterranean Sea. Corals are known to contain a diverse microbiota that plays a key role in their physiology and health. Here we report the first study that examines the microbiome and pathobiome associated with C. caespitosa in three different Mediterranean locations (i.e., Genova, Columbretes Islands, and Tabarca Island). The microbial communities associated with this species showed biogeographical differences, but shared a common core microbiome that probably plays a key role in the coral holobiont. The putatively pathogenic microbial assemblage (i.e., pathobiome) of C. caespitosa also seemed to depend on geographic location and the human footprint. In locations near the coast and with higher human influence, the pathobiome was entirely constituted by Vibrio species, including the well-known coral pathogens Vibrio coralliilyticus and V. mediterranei. However, in the Columbretes Islands, located off the coast and the most pristine of the analyzed locations, no changes among microbial communities associated to healthy and necrosed samples were detected. Hence, our results provide new insights into the microbiome of the temperate corals and its role in coral health status, highlighting its dependence on the local environmental conditions and the human footprint.}, }
@article {pmid29403516, year = {2018}, author = {Saminathan, T and García, M and Ghimire, B and Lopez, C and Bodunrin, A and Nimmakayala, P and Abburi, VL and Levi, A and Balagurusamy, N and Reddy, UK}, title = {Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {4}, pmid = {29403516}, issn = {1664-462X}, abstract = {The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.}, }
@article {pmid29396559, year = {2018}, author = {Massé, A and Domart-Coulon, I and Golubic, S and Duché, D and Tribollet, A}, title = {Early skeletal colonization of the coral holobiont by the microboring Ulvophyceae Ostreobium sp.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2293}, pmid = {29396559}, issn = {2045-2322}, mesh = {Animal Shells/*microbiology ; Animals ; Anthozoa/*microbiology ; Chlorophyta/classification/genetics/*growth &amp; development ; Genetic Variation ; Metagenome ; Ribulose-Bisphosphate Carboxylase/genetics ; *Symbiosis ; }, abstract = {Ostreobium sp. (Bryopsidales, Ulvophyceae) is a major microboring alga involved in tropical reef dissolution, with a proposed symbiotic lifestyle in living corals. However, its diversity and colonization dynamics in host's early life stages remained unknown. Here, we mapped microborer distribution and abundance in skeletons of the branching coral Pocillopora damicornis from the onset of calcification in primary polyps (7 days) to budding juvenile colonies (1 and 3 months) growing on carbonate and non-carbonate substrates pre-colonized by natural biofilms, and compared them to adult colonies (in aquarium settings). Primary polyps were surprisingly already colonized by microboring filaments and their level of invasion depended on the nature of settlement substrate and the extent of its pre-colonization by microborers. Growth of early coral recruits was unaffected even when microborers were in close vicinity to the polyp tissue. In addition to morphotype observations, chloroplast-encoded rbcL gene sequence analyses revealed nine new Ostreobium clades (OTU99%) in Pocillopora coral. Recruits and adults shared one dominant rbcL clade, undetected in larvae, but also present in aquarium seawater, carbonate and non-carbonate settlement substrates, and in corals from reef settings. Our results show a substratum-dependent colonization by Ostreobium clades, and indicate horizontal transmission of Ostreobium-coral associations.}, }
@article {pmid29395346, year = {2018}, author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP}, title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {252-264}, doi = {10.1016/j.tibtech.2017.12.006}, pmid = {29395346}, issn = {1879-3096}, support = {681396/ERC_/European Research Council/International ; }, mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.}, }
@article {pmid29386628, year = {2018}, author = {Achlatis, M and Pernice, M and Green, K and Guagliardo, P and Kilburn, MR and Hoegh-Guldberg, O and Dove, S}, title = {Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1308-1318}, pmid = {29386628}, issn = {1751-7370}, mesh = {Ammonium Compounds/*metabolism ; Animals ; Bicarbonates/*metabolism ; Coral Reefs ; Dinoflagellida/*metabolism ; Ecosystem ; Porifera/*metabolism ; Single-Cell Analysis ; *Symbiosis ; }, abstract = {Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of [15]N-ammonium and [13]C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially [13]C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.}, }
@article {pmid29382945, year = {2018}, author = {Frischkorn, KR and Haley, ST and Dyhrman, ST}, title = {Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {997-1007}, pmid = {29382945}, issn = {1751-7370}, mesh = {Carbon/metabolism ; *Gene Expression Regulation, Bacterial ; Heterotrophic Processes ; *Microbial Interactions ; Microbiota/*genetics ; Nitrogen/metabolism ; Oceans and Seas ; Periodicity ; Seawater/microbiology ; Transcriptome ; Trichodesmium/*genetics/metabolism ; }, abstract = {Trichodesmium is a widespread, N2 fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmium ubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmium holobiont could influence the fate of fixed carbon and nitrogen. Metatranscriptome sequencing was performed on Trichodesmium colonies collected during high-frequency Lagrangian sampling in the North Pacific Subtropical Gyre (NPSG) to identify possible interactions between the Trichodesmium host and microbiome over day-night cycles. Here we show significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day-night periodicity. The functions of the co-expressed genes suggested a suite of interactions within the holobiont linked to key resources including nitrogen, carbon, and iron. Evidence of microbiome reliance on Trichodesmium-derived vitamin B12 was also detected in co-expression patterns, highlighting a dependency that could shape holobiont community structure. Collectively, these patterns of expression suggest that biotic interactions could influence colony cycling of resources like nitrogen and vitamin B12, and decouple activities, like N2 fixation, from typical abiotic drivers of Trichodesmium physiological ecology.}, }
@article {pmid29379177, year = {2018}, author = {Baker, DM and Freeman, CJ and Wong, JCY and Fogel, ML and Knowlton, N}, title = {Climate change promotes parasitism in a coral symbiosis.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {921-930}, pmid = {29379177}, issn = {1751-7370}, mesh = {Acclimatization/*physiology ; Animals ; Anthozoa/metabolism/*physiology ; Carbon/metabolism ; *Climate Change ; *Coral Reefs ; Cyanobacteria/metabolism/*physiology ; Dinoflagellida/metabolism/*physiology ; Nitrogen/metabolism ; Symbiosis/*physiology ; *Temperature ; }, abstract = {Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change.}, }
@article {pmid29378627, year = {2018}, author = {Broberg, M and Doonan, J and Mundt, F and Denman, S and McDonald, JE}, title = {Integrated multi-omic analysis of host-microbiota interactions in acute oak decline.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {21}, pmid = {29378627}, issn = {2049-2618}, support = {TH0108//Department for Environment, Food and Rural Affairs/International ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/genetics/metabolism/*pathogenicity ; Gene Expression Profiling ; Genomics/*methods ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/*microbiology ; Proteomics ; Quercus/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Virulence Factors/*genetics/*metabolism ; }, abstract = {BACKGROUND: Britain's native oak species are currently under threat from acute oak decline (AOD), a decline-disease where stem bleeds overlying necrotic lesions in the inner bark and larval galleries of the bark-boring beetle, Agrilus biguttatus, represent the primary symptoms. It is known that complex interactions between the plant host and its microbiome, i.e. the holobiont, significantly influence the health status of the plant. In AOD, necrotic lesions are caused by a microbiome shift to a pathobiome consisting predominantly of Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and potentially other bacteria. However, the specific mechanistic processes of the microbiota causing tissue necrosis, and the host response, have not been established and represent a barrier to understanding and managing this decline.<br><br>RESULTS: We profiled the metagenome, metatranscriptome and metaproteome of inner bark tissue from AOD symptomatic and non-symptomatic trees to characterise microbiota-host interactions. Active bacterial virulence factors such as plant cell wall-degrading enzymes, reactive oxygen species defence and flagella in AOD lesions, along with host defence responses including reactive oxygen species, cell wall modification and defence regulators were identified. B. goodwinii dominated the lesion microbiome, with significant expression of virulence factors such as the phytopathogen effector avrE. A smaller proportion of microbiome activity was attributed to G. quercinecans and R. victoriana. In addition, we describe for the first time the potential role of two previously uncharacterised Gram-positive bacteria predicted from metagenomic binning and identified as active in the AOD lesion metatranscriptome and metaproteome, implicating them in lesion formation.<br><br>CONCLUSIONS: This multi-omic study provides novel functional insights into microbiota-host interactions in AOD, a complex arboreal decline disease where polymicrobial-host interactions result in lesion formation on tree stems. We present the first descriptions of holobiont function in oak health and disease, specifically, the relative lesion activity of B. goodwinii, G. quercinecans, Rahnella victoriana and other bacteria. Thus, the research presented here provides evidence of some of the mechanisms used by members of the lesion microbiome and a template for future multi-omic research into holobiont characterisation, plant polymicrobial diseases and pathogen defence in trees.}, }
@article {pmid29374490, year = {2018}, author = {Liu, J and Abdelfattah, A and Norelli, J and Burchard, E and Schena, L and Droby, S and Wisniewski, M}, title = {Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {18}, pmid = {29374490}, issn = {2049-2618}, support = {2017YFD0201100//National Key Research and Development Program of China/International ; IS 2513-16//U.S. - Israel Binational Agricultural Research and Development Fund/International ; R2016LX01//Foundation for High-level Talents of Chongqing University of Arts and Sciences/International ; }, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Ascomycota/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Basidiomycota/classification/genetics/isolation &amp; purification ; Endophytes ; Firmicutes/classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics/isolation &amp; purification ; Fusobacteria/classification/genetics/isolation &amp; purification ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Malus/*genetics/microbiology ; Microbiota ; Phylogeny ; Plant Roots/microbiology ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component.<br><br>RESULTS: Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9).<br><br>CONCLUSIONS: The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.}, }
@article {pmid29367878, year = {2018}, author = {Marzinelli, EM and Qiu, Z and Dafforn, KA and Johnston, EL and Steinberg, PD and Mayer-Pinto, M}, title = {Coastal urbanisation affects microbial communities on a dominant marine holobiont.}, journal = {NPJ biofilms and microbiomes}, volume = {4}, number = {}, pages = {1}, pmid = {29367878}, issn = {2055-5008}, abstract = {Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia. There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.}, }
@article {pmid29366516, year = {2017}, author = {Sandoval-Motta, S and Aldana, M and Frank, A}, title = {Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome.}, journal = {Archives of medical research}, volume = {48}, number = {8}, pages = {780-789}, doi = {10.1016/j.arcmed.2018.01.002}, pmid = {29366516}, issn = {1873-5487}, mesh = {Animals ; *Evolution, Molecular ; *Heredity ; Humans ; *Microbiota ; *Selection, Genetic ; }, abstract = {The importance of microorganisms in human biology is undeniable. The amount of research that supports that microbes have a fundamental role in animal and plant physiology is substantial and increasing every year. Even though we are only beginning to comprehend the broadness and complexity of microbial communities, evolutionary theories need to be recast in the light of such discoveries to fully understand and incorporate the role of microbes in our evolution. Fundamental evolutionary concepts such as diversity, heredity, selection, speciation, etc., which constitute the modern synthesis, are now being challenged, or at least expanded, by the emerging notion of the holobiont, which defines the genetic and metabolic networks of the host and its microbes as a single evolutionary unit. Several concepts originally developed to study ecosystems, can be used to understand the physiology and evolution of such complex systems that constitute "individuals." In this review, we discuss these ecological concepts and also provide examples that range from squids, insects and koalas to other mammals and humans, suggesting that microorganisms have a fundamental role not only in physiology but also in evolution. Current evolutionary theories need to take into account the dynamics and interconnectedness of the host-microbiome network, as animals and plants not only owe their symbiogenetic origin to microbes, but also share a long evolutionary history together.}, }
@article {pmid29334418, year = {2018}, author = {van de Water, JAJM and Chaib De Mares, M and Dixon, GB and Raina, JB and Willis, BL and Bourne, DG and van Oppen, MJH}, title = {Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {1065-1080}, doi = {10.1111/mec.14489}, pmid = {29334418}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/drug effects/genetics/*microbiology ; Anti-Infective Agents/*pharmacology ; *Coral Reefs ; Gene Expression Regulation/drug effects ; Seawater ; Stress, Physiological/*drug effects/genetics ; *Temperature ; Transcriptome/genetics ; }, abstract = {Global increases in coral disease prevalence have been linked to ocean warming through changes in coral-associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase-activating system and multiple immune system-related genes. Elevated seawater temperatures did not induce shifts in the coral-associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocytosis, as well as molecular chaperones. These observations show that M. aequituberculata is capable of maintaining a stable bacterial community under elevated seawater temperatures and thereby contributes to preventing disease development.}, }
@article {pmid29324042, year = {2018}, author = {Bartholomay, LC and Michel, K}, title = {Mosquito Immunobiology: The Intersection of Vector Health and Vector Competence.}, journal = {Annual review of entomology}, volume = {63}, number = {}, pages = {145-167}, doi = {10.1146/annurev-ento-010715-023530}, pmid = {29324042}, issn = {1545-4487}, support = {R21 AI117204/AI/NIAID NIH HHS/United States ; R01 AI095842/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Culicidae/*immunology/microbiology ; Host-Pathogen Interactions/*immunology ; Microbiota ; }, abstract = {As holometabolous insects that occupy distinct aquatic and terrestrial environments in larval and adult stages and utilize hematophagy for nutrient acquisition, mosquitoes are subjected to a wide variety of symbiotic interactions. Indeed, mosquitoes play host to endosymbiotic, entomopathogenic, and mosquito-borne organisms, including protozoa, viruses, bacteria, fungi, fungal-like organisms, and metazoans, all of which trigger and shape innate infection-response capacity. Depending on the infection or interaction, the mosquito may employ, for example, cellular and humoral immune effectors for septic infections in the hemocoel, humoral infection responses in the midgut lumen, and RNA interference and programmed cell death for intracellular pathogens. These responses often function in concert, regardless of the infection type, and provide a robust front to combat infection. Mosquito-borne pathogens and entomopathogens overcome these immune responses, employing avoidance or suppression strategies. Burgeoning methodologies are capitalizing on this concerted deployment of immune responses to control mosquito-borne disease.}, }
@article {pmid29312241, year = {2017}, author = {Florez, JZ and Camus, C and Hengst, MB and Buschmann, AH}, title = {A Functional Perspective Analysis of Macroalgae and Epiphytic Bacterial Community Interaction.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2561}, pmid = {29312241}, issn = {1664-302X}, abstract = {Macroalgae are photosynthetic, multicellular, sessile eukaryotic organisms that offer diverse habitats for the colonization of epiphytic bacteria, therefore establishing biological interactions of diverse complexity. This review focusses on the interactions between macroalgae and their Epiphytic Bacterial Community (EBC); the main aims are to ascertain whether (1) the epiphytic bacterial groups differ at the phylum and genus levels of the macroalgae; (2) the methodologies used so far to study these microorganisms are related in any way to eventual variations of the EBCs on macroalgae; and (3) the EBC of macroalgae has a functional means rather a simple taxonomic grouping. Results showed firstly the taxonomic grouping of macroalgae does not explain the composition and structure of the EBCs. Secondly, the methodology used is important for describing EBCs; and thirdly, multiple bacteria can have the same function and thus to describe the functionality of EBCs it is important to recognize host-specific and generalist bacteria. We recommend the incorporation of a complementary approach between the taxonomic composition and the functional composition analyzes of EBCs, as well as the use of methodological tools that allow analysis of interactions between the EBCs and their hosts, based on the "holobiont" concept.}, }
@article {pmid29312170, year = {2017}, author = {KleinJan, H and Jeanthon, C and Boyen, C and Dittami, SM}, title = {Exploring the Cultivable Ectocarpus Microbiome.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2456}, pmid = {29312170}, issn = {1664-302X}, abstract = {Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal-bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.}, }
@article {pmid29308251, year = {2017}, author = {Sangsawang, L and Casareto, BE and Ohba, H and Vu, HM and Meekaew, A and Suzuki, T and Yeemin, T and Suzuki, Y}, title = {[13]C and [15]N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea.}, journal = {Royal Society open science}, volume = {4}, number = {12}, pages = {171201}, pmid = {29308251}, issn = {2054-5703}, abstract = {Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the 'coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N2 fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with [13]C and [15]N tracers to measure primary production and N2 fixation in coral tissues and endoliths. Assimilation of the [13]C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N2 fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.}, }
@article {pmid29292130, year = {2018}, author = {López, JL and Alvarez, F and Príncipe, A and Salas, ME and Lozano, MJ and Draghi, WO and Jofré, E and Lagares, A}, title = {Isolation, taxonomic analysis, and phenotypic characterization of bacterial endophytes present in alfalfa (Medicago sativa) seeds.}, journal = {Journal of biotechnology}, volume = {267}, number = {}, pages = {55-62}, doi = {10.1016/j.jbiotec.2017.12.020}, pmid = {29292130}, issn = {1873-4863}, mesh = {Actinobacteria/genetics/isolation &amp; purification ; Bacteroidetes/genetics/isolation &amp; purification ; Endophytes/classification/*genetics ; Firmicutes/genetics/isolation &amp; purification ; Medicago sativa/genetics/*microbiology ; Microbiota/*genetics ; *Phylogeny ; Proteobacteria/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Seedlings/microbiology ; Seeds/microbiology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {A growing body of evidence has reinforced the central role of microbiomes in the life of sound multicellular eukaryotes, thus more properly described as true holobionts. Though soil was considered a main source of plant microbiomes, seeds have been shown to be endophytically colonized by microorganisms thus representing natural carriers of a selected microbial inoculum to the young seedlings. In this work we have investigated the type of culturable endophytic bacteria that are carried within surface-sterilized alfalfa seeds. MALDI-TOF analysis revealed the presence of bacteria that belonged to 40 separate genera, distributed within four taxa (Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes). Nonsymbiotic members of the Rhizobiaceae family were also found. The evaluation of nine different in-vitro biochemical activities demonstrated isolates with complex combinations of traits that, upon a Principal-Component-Analysis, could be classified into four phenotypic groups. That isolates from nearly half of the genera identified had been able to colonize alfalfa plants grown under axenic conditions was remarkable. Further analyses should be addressed to investigating the colonization mechanisms of the alfalfa seeds, the evolutionary significance of the alfalfa-seed endophytes, and also how after germination the seed microbiome competes with spermospheric and rhizospheric soil bacteria to colonize newly emerging seedlings.}, }
@article {pmid29271225, year = {2018}, author = {Sebastián Domingo, JJ and Sánchez Sánchez, C}, title = {From the intestinal flora to the microbiome.}, journal = {Revista espanola de enfermedades digestivas}, volume = {110}, number = {1}, pages = {51-56}, doi = {10.17235/reed.2017.4947/2017}, pmid = {29271225}, issn = {1130-0108}, mesh = {Gastroenterology/*history ; Gastrointestinal Diseases/microbiology ; *Gastrointestinal Microbiome ; History, 17th Century ; History, 19th Century ; Humans ; Intestines/*microbiology ; }, abstract = {In this article, the history of the microbiota is reviewed and the related concepts of the microbiota, microbiome, metagenome, pathobiont, dysbiosis, holobiont, phylotype and enterotype are defined. The most precise and current knowledge about the microbiota is presented and the metabolic, nutritional and immunomodulatory functions are reviewed. Some gastrointestinal diseases whose pathogenesis is associated with the intestinal microbiota, including inflammatory bowel disease, irritable bowel syndrome and celiac disease, among others, are briefly discussed. Finally, some prominent and promising data with regard to the fecal microbiota transplantation in certain digestive illness are discussed.}, }
@article {pmid29266341, year = {2018}, author = {Elgart, M and Soen, Y}, title = {Microbiome-Germline Interactions and Their Transgenerational Implications.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {4}, pages = {e1700018}, doi = {10.1002/bies.201700018}, pmid = {29266341}, issn = {1521-1878}, mesh = {Bacteria/genetics ; Epigenesis, Genetic/*genetics ; Gastrointestinal Microbiome/genetics ; Germ Cells/*physiology ; Microbiota/genetics/*physiology ; Symbiosis/genetics/physiology ; }, abstract = {It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the host soma and germline could potentially give rise to emergent phenotypes, which may be partially inherited by three distinguishable modes of transgenerational influence of gut bacteria: 1) "soma-to-soma" 2) "soma-to-germline" and 3) "soma-germline-soma". Here, we discuss these possibilities in light of evidence supporting bacterial-mediated modes of transgenerational inheritance.}, }
@article {pmid29255647, year = {2017}, author = {Yorifuji, M and Harii, S and Nakamura, R and Fudo, M}, title = {Shift of symbiont communities in Acropora tenuis juveniles under heat stress.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4055}, pmid = {29255647}, issn = {2167-8359}, abstract = {Ocean warming is a major threat to coral reefs, leading to an increasing frequency and amplitude of coral bleaching events, where the coral and its algal symbiont associations breakdown. Long-term change and resilience of a symbiont community in coral juveniles is thought to be one of the most important aspects for determining thermal tolerance of the coral holobionts; however, despite its importance, they are not well documented in both under elevated temperature and even under natural condition. Here we investigated changes in symbiont communities in juveniles of the coral Acropora tenuis under controlled heat stress conditions (30 °C, 31/32 °C) and natural variations in seawater temperatures (19-30 °C) for up to four months. Compared with the ambient temperature conditions, coral survival rates were higher when exposed to 30 °C, but survival rates decreased when exposed to 31/32 °C. Symbiodinium types A3, C1, and D1-4 were detected in the juveniles under all thermal conditions; however, in higher water temperatures (31/32 °C), both the prevalence of D1-4 Symbiodinium and the number of juveniles harboring only this type of symbiont increased after two to four months later. In contrast, colonies at lower temperatures (30 °C and ambient) harbored multiple clades of symbionts over the same experimental period. These results highlight the flexibility of the coral-Symbiodinium symbiosis for juvenile A. tenuis under variable thermal conditions. In particular, the benefit of the preferential association with type D1-4 can be considered as a response when under heat-stress conditions, and that could help corals to cope with ocean warming.}, }
@article {pmid29245010, year = {2017}, author = {Kundu, P and Blacher, E and Elinav, E and Pettersson, S}, title = {Our Gut Microbiome: The Evolving Inner Self.}, journal = {Cell}, volume = {171}, number = {7}, pages = {1481-1493}, doi = {10.1016/j.cell.2017.11.024}, pmid = {29245010}, issn = {1097-4172}, mesh = {Aging ; Animals ; Bacteria/classification/*growth &amp; development/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Organ Specificity ; Puberty ; Symbiosis ; }, abstract = {The "holobiont" concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality.}, }
@article {pmid29244764, year = {2017}, author = {Ugarelli, K and Chakrabarti, S and Laas, P and Stingl, U}, title = {The Seagrass Holobiont and Its Microbiome.}, journal = {Microorganisms}, volume = {5}, number = {4}, pages = {}, pmid = {29244764}, issn = {2076-2607}, abstract = {Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H2S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome.}, }
@article {pmid29222444, year = {2018}, author = {Lesser, MP and Morrow, KM and Pankey, SM and Noonan, SHC}, title = {Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {813-824}, pmid = {29222444}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics ; *Coral Reefs ; Dinoflagellida/*metabolism ; Heterotrophic Processes ; Metagenome ; Nitrogen/*metabolism ; Nitrogen Fixation/*physiology/radiation effects ; Photosynthesis/*physiology/radiation effects ; Photosystem II Protein Complex/metabolism ; Sequence Analysis, DNA ; }, abstract = {Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆Fv/Fm') and calcification varied based on irradiance as expected. Rates of N2 fixation were, however, invariant across treatments while the amount of fixed N contributing to Symbiodinium spp. N demand is irradiance dependent. Additionally, both the Symbiodinium and diazotrophic communities are significantly different based on depth, and novel Cluster V nifH gene phylotypes, which are not known to fix nitrogen, were recovered. A functional analysis using PICRUSt also showed that shallow corals were enriched in genes involved in nitrogen metabolism, and N2 fixation specifically. Corals have evolved a number of strategies to derive nitrogen from organic (e.g., heterotrophic feeding) and inorganic sources (e.g., N2 fixation) to maintain critical pathways such as protein synthesis to succeed ecologically in nitrogen-limited habitats.}, }
@article {pmid29211049, year = {2017}, author = {Shapiro, JA}, title = {Living Organisms Author Their Read-Write Genomes in Evolution.}, journal = {Biology}, volume = {6}, number = {4}, pages = {}, pmid = {29211049}, issn = {2079-7737}, abstract = {Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.}, }
@article {pmid29194919, year = {2018}, author = {Lavy, A and Keren, R and Yu, K and Thomas, BC and Alvarez-Cohen, L and Banfield, JF and Ilan, M}, title = {A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {800-814}, pmid = {29194919}, issn = {1462-2920}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/classification/genetics/metabolism ; Genome, Bacterial/genetics ; Indian Ocean ; Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Sulfur/*metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.}, }
@article {pmid29192903, year = {2018}, author = {Ziegler, M and Eguíluz, VM and Duarte, CM and Voolstra, CR}, title = {Rare symbionts may contribute to the resilience of coral-algal assemblages.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {161-172}, pmid = {29192903}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; Coral Reefs ; Dinoflagellida/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; *Symbiosis ; }, abstract = {The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles' heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral-Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host-Symbiodinium communities assemble in non-random 'clusters' of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the 'rare bacterial biosphere') has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host-symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.}, }
@article {pmid33525769, year = {2017}, author = {Ogilvie, LA and Jones, BV}, title = {The human gut virome: form and function.}, journal = {Emerging topics in life sciences}, volume = {1}, number = {4}, pages = {351-362}, doi = {10.1042/ETLS20170039}, pmid = {33525769}, issn = {2397-8554}, abstract = {Advances in next-generation sequencing technologies and the application of metagenomic approaches have fuelled an exponential increase in our understanding of the human gut microbiome. These approaches are now also illuminating features of the diverse and abundant collection of viruses (termed the virome) subsisting with the microbial ecosystems residing within the human holobiont. Here, we focus on the current and emerging knowledge of the human gut virome, in particular on viruses infecting bacteria (bacteriophage or phage), which are a dominant component of this viral community. We summarise current insights regarding the form and function of this 'human gut phageome' and highlight promising avenues for future research. In doing so, we discuss the potential for phage to drive ecological functioning and evolutionary change within this important microbial ecosystem, their contribution to modulation of host-microbiome interactions and stability of the community as a whole, as well as the potential role of the phageome in human health and disease. We also consider the emerging concepts of a 'core healthy gut phageome' and the putative existence of 'viral enterotypes' and 'viral dysbiosis'.}, }
@article {pmid29175233, year = {2018}, author = {Miller, WB}, title = {Biological information systems: Evolution as cognition-based information management.}, journal = {Progress in biophysics and molecular biology}, volume = {134}, number = {}, pages = {1-26}, doi = {10.1016/j.pbiomolbio.2017.11.005}, pmid = {29175233}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Cells/cytology/metabolism ; Cognition ; Humans ; }, abstract = {An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.}, }
@article {pmid29170664, year = {2017}, author = {Grasis, JA}, title = {The Intra-Dependence of Viruses and the Holobiont.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {1501}, pmid = {29170664}, issn = {1664-3224}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, abstract = {Animals live in symbiosis with the microorganisms surrounding them. This symbiosis is necessary for animal health, as a symbiotic breakdown can lead to a disease state. The functional symbiosis between the host, and associated prokaryotes, eukaryotes, and viruses in the context of an environment is the holobiont. Deciphering these holobiont associations has proven to be both difficult and controversial. In particular, holobiont association with viruses has been of debate even though these interactions have been occurring since cellular life began. The controversy stems from the idea that all viruses are parasitic, yet their associations can also be beneficial. To determine viral involvement within the holobiont, it is necessary to identify and elucidate the function of viral populations in symbiosis with the host. Viral metagenome analyses identify the communities of eukaryotic and prokaryotic viruses that functionally associate within a holobiont. Similarly, analyses of the host in response to viral presence determine how these interactions are maintained. Combined analyses reveal how viruses interact within the holobiont and how viral symbiotic cooperation occurs. To understand how the holobiont serves as a functional unit, one must consider viruses as an integral part of disease, development, and evolution.}, }
@article {pmid29167578, year = {2017}, author = {Jarett, JK and MacManes, MD and Morrow, KM and Pankey, MS and Lesser, MP}, title = {Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16039}, pmid = {29167578}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics ; Dinoflagellida/genetics ; Genomics/*methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Montastraea cavernosa is a common coral in the Caribbean basin found in several color morphs. To investigate the causes for brown and orange morphs we undertook a genomics approach on corals collected at the same time and depth in the Bahamas. The coral holobiont includes the host, symbiotic dinoflagellates (Symbiodinium spp.), and a diverse microbiome. While the coral host showed significant genetic differentiation between color morphs both the composition of the Symbiodinium spp. communities and the prokaryotic communities did not. Both targeted and global gene expression differences in the transcriptome of the host show no difference in fluorescent proteins while the metatranscriptome of the microbiome shows that pigments such as phycoerythrin and orange carotenoid protein of cyanobacterial origin are significantly greater in orange morphs, which is also consistent with the significantly greater number of cyanobacteria quantified by 16S rRNA reads and flow cytometry. The microbiome of orange color morphs expressed significantly more nitrogenase (nifH) transcripts consistent with their known ability to fix nitrogen. Both coral and Symbiodinium spp. transcriptomes from orange morphs had significantly increased expression of genes related to immune response and apoptosis, which may potentially be involved in maintaining and regulating the unique symbiont population in orange morphs.}, }
@article {pmid29158985, year = {2017}, author = {Weynberg, KD and Laffy, PW and Wood-Charlson, EM and Turaev, D and Rattei, T and Webster, NS and van Oppen, MJH}, title = {Coral-associated viral communities show high levels of diversity and host auxiliary functions.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4054}, pmid = {29158985}, issn = {2167-8359}, abstract = {Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.}, }
@article {pmid29136422, year = {2017}, author = {Baquero, F}, title = {Transmission as a basic process in microbial biology. Lwoff Award Prize Lecture.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {6}, pages = {816-827}, doi = {10.1093/femsre/fux042}, pmid = {29136422}, issn = {1574-6976}, mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena ; *Microbiology ; *Selection, Genetic ; }, abstract = {Transmission is a basic process in biology and evolution, as it communicates different biological entities within and across hierarchical levels (from genes to holobionts) both in time and space. Vertical descent, replication, is transmission of information across generations (in the time dimension), and horizontal descent is transmission of information across compartments (in the space dimension). Transmission is essentially a communication process that can be studied by analogy of the classic information theory, based on 'emitters', 'messages' and 'receivers'. The analogy can be easily extended to the triad 'emigration', 'migration' and 'immigration'. A number of causes (forces) determine the emission, and another set of causes (energies) assures the reception. The message in fact is essentially constituted by 'meaningful' biological entities. A DNA sequence, a cell and a population have a semiotic dimension, are 'signs' that are eventually recognized (decoded) and integrated by receiver biological entities. In cis-acting or unenclosed transmission, the emitters and receivers correspond to separated entities of the same hierarchical level; in trans-acting or embedded transmission, the information flows between different, but frequently nested, hierarchical levels. The result (as in introgressive events) is constantly producing innovation and feeding natural selection, influencing also the evolution of transmission processes. This review is based on the concepts presented at the André Lwoff Award Lecture in the FEMS Microbiology Congress in Maastricht in 2015.}, }
@article {pmid29108677, year = {2017}, author = {Ellison, MA and Ferrier, MD and Carney, SL}, title = {Salinity stress results in differential Hsp70 expression in the Exaiptasia pallida and Symbiodinium symbiosis.}, journal = {Marine environmental research}, volume = {132}, number = {}, pages = {63-67}, doi = {10.1016/j.marenvres.2017.10.006}, pmid = {29108677}, issn = {1879-0291}, mesh = {Animals ; Dinoflagellida/*physiology ; HSP70 Heat-Shock Proteins/*metabolism ; Salinity ; Sea Anemones/*physiology ; Stress, Physiological/*physiology ; Symbiosis ; }, abstract = {Abiotic factors affect cnidarian-algal symbiosis and, if severe enough, can result in bleaching. Increased temperature and light are well characterized causes of bleaching, but other factors like salinity can also stress the holobiont. In cnidarian-dinoflagellate systems, the expression of host genes, including heat shock protein 70 (Hsp70), changes due to thermal and light stress. In this experiment, we characterized to what extent salinity stress affects Hsp70 expression in the holobiont by simultaneously measuring host and symbiont Hsp70 expression in response to up to 8 h of hypo- and hypersaline conditions in the sea anemone Exaiptasia pallida and its intracellular symbiont Symbiodinium minutum. We show that E. pallida Hsp70 expression increases (6-11-fold) at high salinities whereas Symbiodinium Hsp70 expression shows little change (1.4-2.6-fold). These data suggest that cnidarian Hsp70 response is similar across multiple abiotic stressors further validating the Hsp70 gene as a biomarker for abiotic stress.}, }
@article {pmid29098358, year = {2018}, author = {Baumann, JH and Davies, SW and Aichelman, HE and Castillo, KD}, title = {Coral Symbiodinium Community Composition Across the Belize Mesoamerican Barrier Reef System is Influenced by Host Species and Thermal Variability.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {903-915}, pmid = {29098358}, issn = {1432-184X}, support = {15802-1//Rufford Foundation/ ; OCE 1459522//Division of Ocean Sciences/ ; }, mesh = {Animals ; Anthozoa/genetics/*parasitology ; Belize ; DNA/analysis ; Dinoflagellida/*classification/genetics/*physiology ; Environmental Monitoring ; Genetic Variation ; *Host Specificity ; Hot Temperature ; Oceans and Seas ; Phylogeny ; Symbiosis/physiology ; Temperature ; Thermotolerance ; }, abstract = {Reef-building corals maintain a symbiotic relationship with dinoflagellate algae of the genus Symbiodinium, and this symbiosis is vital for the survival of the coral holobiont. Symbiodinium community composition within the coral host has been shown to influence a coral's ability to resist and recover from stress. A multitude of stressors including ocean warming, ocean acidification, and eutrophication have been linked to global scale decline in coral health and cover in recent decades. Three distinct thermal regimes (highTP, modTP, and lowTP) following an inshore-offshore gradient of declining average temperatures and thermal variation were identified on the Belize Mesoamerican Barrier Reef System (MBRS). Quantitative metabarcoding of the ITS-2 locus was employed to investigate differences and similarities in Symbiodinium genetic diversity of the Caribbean corals Siderastrea siderea, S. radians, and Pseudodiploria strigosa between the three thermal regimes. A total of ten Symbiodinium lineages were identified across the three coral host species. S. siderea was associated with distinct Symbiodinium communities; however, Symbiodinium communities of its congener, S. radians and P. strigosa, were more similar to one another. Thermal regime played a role in defining Symbiodinium communities in S. siderea but not S. radians or P. strigosa. Against expectations, Symbiodinium trenchii, a symbiont known to confer thermal tolerance, was dominant only in S. siderea at one sampled offshore site and was rare inshore, suggesting that coral thermal tolerance in more thermally variable inshore habitats is achieved through alternative mechanisms. Overall, thermal parameters alone were likely not the only primary drivers of Symbiodinium community composition, suggesting that environmental variables unrelated to temperature (i.e., light availability or nutrients) may play key roles in structuring coral-algal communities in Belize and that the relative importance of these environmental variables may vary by coral host species.}, }
@article {pmid29078340, year = {2017}, author = {Hartmann, AC and Petras, D and Quinn, RA and Protsyuk, I and Archer, FI and Ransome, E and Williams, GJ and Bailey, BA and Vermeij, MJA and Alexandrov, T and Dorrestein, PC and Rohwer, FL}, title = {Meta-mass shift chemical profiling of metabolomes from coral reefs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {44}, pages = {11685-11690}, pmid = {29078340}, issn = {1091-6490}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*metabolism ; Coral Reefs ; Metabolome ; Metabolomics/*methods ; Transcriptome ; }, abstract = {Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.g., H2, CH2, COCH2). MeMSChem profiling was used to analyze a publicly available metabolomic dataset of coral, algal, and fungal mat holobionts (i.e., the host and its associated microbes and viruses) sampled from some of Earth's most remote and pristine coral reefs. Each type of holobiont had distinct mass shift profiles, even when the analysis was restricted to molecules found in all samples. This result suggests that holobionts modify the same molecules in different ways and offers insights into the generation of molecular diversity. Three genera of stony corals had distinct patterns of molecular relatedness despite their high degree of taxonomic relatedness. MeMSChem profiles also partially differentiated between individuals, suggesting that every coral reef holobiont is a potential source of novel chemical diversity.}, }
@article {pmid29038057, year = {2017}, author = {Ahila, NK and Prakash, S and Manikandan, B and Ravindran, J and Prabhu, NM and Kannapiran, E}, title = {Bio-prospecting of coral (Porites lutea) mucus associated bacteria, Palk Bay reefs, Southeast coast of India.}, journal = {Microbial pathogenesis}, volume = {113}, number = {}, pages = {113-123}, doi = {10.1016/j.micpath.2017.09.056}, pmid = {29038057}, issn = {1096-1208}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Bacillus/genetics/isolation &amp; purification/*metabolism ; Coral Reefs ; Enterobacter cloacae/genetics/isolation &amp; purification ; India ; Microbiota ; Mucus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Vibrio/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Coral mucus is one of the key localization in the coral holobiont, as this serves as an energy rich substrate for a wide range of abundant, diverse and multifunctional microbiota. However, very little is known about the functional role of bacterial communities in their associations with corals. In the present study, a total of 48 isolates were obtained from Porites lutea wherein the genus of Bacillus sp. and Vibrio sp. were predominant. Bio-prospecting the coral mucus revealed the existence of (10.42%) antagonistic bacteria against the tested bacterial pathogens. Molecular taxonomy (16S rRNA) proved the identity of these antagonistic bacteria belong to Enterobacter cloacae (CM1), Bacillus subtilis (CM2), Bacillus sp. (CM11) and Bacillus marisflavi (CM12). The secondary screening emphasized that the ethyl acetate extract of B. subtilis showed strong antagonistic effect, followed by the chloroform extract of E. cloacae and ethyl acetate extract of B. marisflavi. The antagonistic activity was statistically confirmed by Principal Component Analysis and Hierarchical Cluster Analysis. The privileged coral mucus associated bacterial (CMAB) solvent extracts inhibited the bacterial pathogens at 100 μg/ml (MIC) and ceased the growth at 200 μg/ml (MBC). The hemolytic and brine shrimp lethality assays disclosed the non-toxic nature of solvent extracts of CMAB. Altogether, the present investigation brought out the diversity of bacteria associated with the mucus of P. lutea. In addition, bio-prospecting corroborated the CMAB as the potential source of pharmacologically important bioactive compounds against a wide range of bacterial pathogens.}, }
@article {pmid29027742, year = {2018}, author = {Mera, H and Bourne, DG}, title = {Disentangling causation: complex roles of coral-associated microorganisms in disease.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {431-449}, doi = {10.1111/1462-2920.13958}, pmid = {29027742}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Coral Reefs ; Microbiota ; }, abstract = {Rapidly changing climate regimes combined with other anthropogenic pressures are implicated in increased disease epizootics among reef building corals, resulting in changing habitat structure. These accumulated stressors directly contribute to disease outbreaks by compromising the coral host immune system, modulating virulence of microbial pathogens and/or disrupting the balance within the microbiome of the holobiont. Disentangling coral disease causation has been challenging, and while progress has been made for certain diseases in terms of the roles the associated microorganisms play, it is evident that like in other marine or terrestrial systems, compromised host health cannot always be attributed to a single causative agent. Here, we summarize the current state in knowledge of microbial induced coral diseases, and discuss challenges and strategies to further disentangle disease causation. With the major environmental pressures coral reefs face over the next century, understanding interactions between host, environmental and microbial causative agent(s) that lead to disease, is still a priority to enable development of effective strategies for building resilience into coral populations.}, }
@article {pmid28967236, year = {2018}, author = {Sapp, M and Ploch, S and Fiore-Donno, AM and Bonkowski, M and Rose, LE}, title = {Protists are an integral part of the Arabidopsis thaliana microbiome.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {30-43}, doi = {10.1111/1462-2920.13941}, pmid = {28967236}, issn = {1462-2920}, mesh = {Arabidopsis/*parasitology ; Cercozoa/*classification/genetics/*isolation &amp; purification ; DNA, Intergenic/genetics ; Microbiota/physiology ; Oomycetes/*classification/genetics/*isolation &amp; purification ; Plant Leaves/*parasitology ; Plant Roots/*parasitology ; RNA, Ribosomal, 18S/genetics ; Rhizosphere ; Soil/parasitology ; }, abstract = {Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization. Cercozoa were identified using 18S rRNA gene metabarcoding, whereas the Internal Transcribed Spacer 1 was used to determine oomycetes. Subsequent analyses revealed strong spatial structuring of protist communities between compartments, although oomycetes appeared more specialized than Cercozoa. With regards to oomycetes, only members of the Peronosporales and taxa belonging to the genus Globisporangium were identified as shared members of the A. thaliana microbiome. This also applied to cercozoan taxa belonging to the Glissomonadida and Cercomonadida. We identified a strong influence by edaphic factors on the rhizosphere, but not for the phyllosphere. Distinct differences of Cercozoa found preferably in wood or fresh plant material imply specific niche adaptations. Our results highlight the importance of micro-eukaryotes for the plant holobiont.}, }
@article {pmid28915923, year = {2017}, author = {Sharp, KH and Pratte, ZA and Kerwin, AH and Rotjan, RD and Stewart, FJ}, title = {Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {120}, pmid = {28915923}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Dinoflagellida/*physiology ; *Microbiota ; Seasons ; *Symbiosis ; }, abstract = {BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition.<br><br>RESULTS: Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest,&#xa0;indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density.<br><br>CONCLUSIONS: Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore help to identify basic principles of coral microbiome assembly, as well as functional relationships among holobiont members.}, }
@article {pmid28894639, year = {2017}, author = {Naim, MA and Smidt, H and Sipkema, D}, title = {Fungi found in Mediterranean and North Sea sponges: how specific are they?.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3722}, pmid = {28894639}, issn = {2167-8359}, abstract = {Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.}, }
@article {pmid28893194, year = {2017}, author = {Frazier, M and Helmkampf, M and Bellinger, MR and Geib, SM and Takabayashi, M}, title = {De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {710}, pmid = {28893194}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/*genetics/*growth &amp; development ; *Gene Expression Profiling ; Morphogenesis/genetics ; }, abstract = {BACKGROUND: Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected"). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease.<br><br>RESULTS: The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system.<br><br>CONCLUSION: This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.}, }
@article {pmid28892512, year = {2017}, author = {Mezzasalma, V and Sandionigi, A and Bruni, I and Bruno, A and Lovicu, G and Casiraghi, M and Labra, M}, title = {Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184615}, pmid = {28892512}, issn = {1932-6203}, mesh = {Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; *Environment ; Fungi/classification/genetics ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; Vitis/*microbiology ; *Wine ; }, abstract = {Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits' microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.}, }
@article {pmid28887506, year = {2017}, author = {Evans, JS and Erwin, PM and Shenkar, N and López-Legentil, S}, title = {Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11033}, pmid = {28887506}, issn = {2045-2322}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; North Carolina ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Urochordata/*microbiology ; }, abstract = {Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 47 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.}, }
@article {pmid28875073, year = {2017}, author = {Godoy-Vitorino, F and Ruiz-Diaz, CP and Rivera-Seda, A and Ramírez-Lugo, JS and Toledo-Hernández, C}, title = {The microbial biosphere of the coral Acropora cervicornis in Northeastern Puerto Rico.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3717}, pmid = {28875073}, issn = {2167-8359}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Coral reefs are the most biodiverse ecosystems in the marine realm, and they not only contribute a plethora of ecosystem services to other marine organisms, but they also are beneficial to humankind via, for instance, their role as nurseries for commercially important fish species. Corals are considered holobionts (host + symbionts) since they are composed not only of coral polyps, but also algae, other microbial eukaryotes and prokaryotes. In recent years, Caribbean reef corals, including the once-common scleractinian coral Acropora cervicornis, have suffered unprecedented mortality due to climate change-related stressors. Unfortunately, our basic knowledge of the molecular ecophysiology of reef corals, particularly with respect to their complex bacterial microbiota, is currently too poor to project how climate change will affect this species. For instance, we do not know how light influences microbial communities of A. cervicornis, arguably the most endangered of all Caribbean coral species. To this end, we characterized the microbiota of A. cervicornis inhabiting water depths with different light regimes.<br><br>METHODS: Six A. cervicornis fragments from different individuals were collected at two different depths (three at 1.5 m and three at 11 m) from a reef 3.2 km off the northeastern coast of Puerto Rico. We characterized the microbial communities by sequencing the 16S rRNA gene region V4 with the Illumina platform.<br><br>RESULTS: A total of 173,137 good-quality sequences were binned into 803 OTUs with a 97% similarity. We uncovered eight bacterial phyla at both depths with a dominance of 725 Rickettsiales OTUs (Proteobacteria). A fewer number (38) of low dominance OTUs varied by depth and taxa enriched in shallow water corals included Proteobacteria (e.g. Rhodobacteraceae and Serratia) and Firmicutes (Streptococcus). Those enriched in deeper water corals featured different Proteobacterial taxa (Campylobacterales and Bradyrhizobium) and Firmicutes (Lactobacillus).<br><br>DISCUSSION: Our results confirm that the microbiota of A. cervicornis inhabiting the northeastern region of Puerto Rico is dominated by a Rickettsiales-like bacterium and that there are significant changes in less dominant taxa at different water depths. These changes in less dominant taxa may potentially impact the coral's physiology, particularly with respect to its ability to respond to future increases in temperature and CO2.}, }
@article {pmid28871544, year = {2017}, author = {Arnholdt-Schmitt, B and Patil, VK}, title = {Calorespirometry: A Novel Tool in Functional Hologenomics to Select "Green" Holobionts for Biomass Production.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1670}, number = {}, pages = {193-201}, doi = {10.1007/978-1-4939-7292-0_16}, pmid = {28871544}, issn = {1940-6029}, mesh = {*Biomass ; Cell Respiration ; Chlorella vulgaris/*genetics/*growth &amp; development/metabolism ; Genomics/*methods ; Microalgae/growth &amp; development/metabolism ; Temperature ; }, abstract = {Endophytes can diversify temperature response and biomass production in plants and microalgae. Natural and inoculated endophytes that modify growth performance are increasingly considered in research and practical initiatives for sustainable agriculture. However, efficient, novel tools are required that are able to support identification of differential effects of native endophyte populations and for pre-selection of inocula.This protocol gives instructions for applying calorespirometry as a rapid means for identifying differential effects of endophytes on temperature response and predicted biomass productivity in microalgae and plant holobionts. The protocol can help discriminating hologenomes, genes, and molecular neutral or functional markers for microalgae strain and plant improvement. Here, we focus on the microalga Chlorella vulgaris and associated microorganisms as an example for highlighting the methodology for its integration in research and application.}, }
@article {pmid28871543, year = {2017}, author = {Arnholdt-Schmitt, B}, title = {Respiration Traits as Novel Markers for Plant Robustness Under the Threat of Climate Change: A Protocol for Validation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1670}, number = {}, pages = {183-191}, doi = {10.1007/978-1-4939-7292-0_15}, pmid = {28871543}, issn = {1940-6029}, mesh = {Biochemistry/*methods ; Biomarkers/*metabolism ; Cell Respiration ; *Climate Change ; Daucus carota/cytology/*metabolism ; Meristem/metabolism ; Plant Roots/metabolism ; Plant Shoots/metabolism ; Reproducibility of Results ; }, abstract = {Respiration traits allow calculating temperature-dependent carbon use efficiency and prediction of growth rates. This protocol aims (1) to enable validation of respiration traits as non-DNA biomarkers for breeding on robust plants in support of sustainable and healthy plant production; (2) to provide an efficient, novel way to identify and predict functionality of DNA-based markers (genes, polymorphisms, edited genes, transgenes, genomes, and hologenomes), and (3) to directly help farmers select robust material appropriate for a specified region. The protocol is based on applying isothermal calorespirometry and consists of four steps: plant tissue preparation, calorespirometry measurements, data processing, and final validation through massive field-based data.The methodology can serve selection and improvement for a wide range of crops. Several of them are currently being tested in the author's lab. Among them are important cereals, such as wheat, barley, and rye, and diverse vegetables. However, it is critical that the protocol for measuring respiration traits be well adjusted to the plant species by considering deep knowledge on the specific physiology and functional cell biology behind the final target trait for production. Here, Daucus carota L. is chosen as an advanced example to demonstrate critical species-specific steps for protocol development. Carrot is an important global vegetable that is grown worldwide and in all climate regions (moderate, subtropical, and tropical). Recently, this species is also used in my lab as a model for studies on alternative oxidase (AOX) gene diversity and evolutionary dynamics in interaction with endophytes.}, }
@article {pmid28867132, year = {2017}, author = {Núñez-Pons, L and Bertocci, I and Baghdasarian, G}, title = {Symbiont dynamics during thermal acclimation using cnidarian-dinoflagellate model holobionts.}, journal = {Marine environmental research}, volume = {130}, number = {}, pages = {303-314}, doi = {10.1016/j.marenvres.2017.08.005}, pmid = {28867132}, issn = {1879-0291}, mesh = {*Acclimatization ; Animals ; Anthozoa ; *Cnidaria ; *Dinoflagellida ; Oceans and Seas ; Symbiosis ; }, abstract = {Warming oceans menace reef ecosystems by disrupting symbiosis between cnidarians and Symbiodinium zooxanthellae, thus triggering bleach episodes. Temperature fluctuations promote adjustments in physiological variables and symbiont composition, which can cause stress responses, but can also yield adaptation if fitter host-symbiont homeostasis are achieved. To understand such processes manipulative studies are required, but many reef-building cnidarians pose limitations to experimental prospects. We exposed Exaiptasia anemones to Gradual Thermal Stress (GTS) and Heat Shock (HS) exposures and monitored chlorophyll and symbiont dynamics to test the phenotypic plasticity of these photosynthetic holobionts. GTS enhanced chlorophyll concentrations and decreased Symbiodinium proliferation. A recovery period after GTS returned chlorophyll to lower concentrations and symbiont divisions to higher rates. HS triggered a stress response characterized by intense symbiont declines through degradation and expulsion, algal compensatory proliferation, and chlorophyll accumulation. Anemones pre-exposed to GTS displayed more acute signs of symbiont paucity after HS, demonstrating that recurrent stress does not always induce bleaching-resistance. Our study is the first documenting Symbiodinium C and D, along with the predominant Clade B1 in Exaiptasia anemones. C subclades found in outdoor specimens faded under laboratory exposures. Clade D emerged after HS treatments, and especially after GTS pre-exposure. This highlights the thermotolerance of D subclades found in E. pallida and shows that bleaching-recovery can involve shifts of background symbiont phylotypes. This study enlightens the capability of Exaiptasia anemones to acclimate to gradually increased temperatures, and explores into how thermal history influences in subsequent stress tolerance in symbiotic cnidarians.}, }
@article {pmid28861262, year = {2017}, author = {Rädecker, N and Pogoreutz, C and Ziegler, M and Ashok, A and Barreto, MM and Chaidez, V and Grupstra, CGB and Ng, YM and Perna, G and Aranda, M and Voolstra, CR}, title = {Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa.}, journal = {Ecology and evolution}, volume = {7}, number = {16}, pages = {6614-6621}, pmid = {28861262}, issn = {2045-7758}, abstract = {The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.}, }
@article {pmid28859111, year = {2017}, author = {Woo, S and Yang, SH and Chen, HJ and Tseng, YF and Hwang, SJ and De Palmas, S and Denis, V and Imahara, Y and Iwase, F and Yum, S and Tang, SL}, title = {Geographical variations in bacterial communities associated with soft coral Scleronephthya gracillimum.}, journal = {PloS one}, volume = {12}, number = {8}, pages = {e0183663}, pmid = {28859111}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*genetics/growth &amp; development/*microbiology ; Bacteria/classification/genetics ; Environmental Monitoring ; Geography ; High-Throughput Nucleotide Sequencing ; Japan ; Mycoplasma/*genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Seawater/microbiology ; Symbiosis/*genetics ; Taiwan ; }, abstract = {Environmental impacts can alter relationships between a coral and its symbiotic microbial community. Furthermore, changes in the microbial community associated with increased seawater temperatures can cause opportunistic infections, coral disease and death. Interactions between soft corals and their associated microbes are not well understood. The species Scleronephthya gracillimum is distributed in tropical to temperate zones in coral assemblages along the Kuroshio Current region. In this study we collected S. gracillimum from various sites at different latitudes, and compared composition of their bacterial communities using Next Generation Sequencing. Coral samples from six geographically distinct areas (two sites each in Taiwan, Japan, and Korea) had considerable variation in their associated bacterial communities and diversity. Endozoicimonaceae was the dominant group in corals from Korea and Japan, whereas Mycoplasma was dominant in corals from Taiwan corals. Interestingly, the latter corals had lower relative abundance of Endozoicimonaceae, but greater diversity. These biogeographic differences in bacterial composition may have been due to varying environmental conditions among study locations, or because of host responses to prevailing environmental conditions. This study provided a baseline for future studies of soft coral microbiomes, and assessment of functions of host metabolites and soft coral holobionts.}, }
@article {pmid28857164, year = {2017}, author = {Brodie, J and Ball, SG and Bouget, FY and Chan, CX and De Clerck, O and Cock, JM and Gachon, C and Grossman, AR and Mock, T and Raven, JA and Saha, M and Smith, AG and Vardi, A and Yoon, HS and Bhattacharya, D}, title = {Biotic interactions as drivers of algal origin and evolution.}, journal = {The New phytologist}, volume = {216}, number = {3}, pages = {670-681}, doi = {10.1111/nph.14760}, pmid = {28857164}, issn = {1469-8137}, support = {BB/I013164/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anthozoa/*physiology ; *Biological Evolution ; Chromatophores ; Dinoflagellida/physiology ; Eutrophication ; Host-Pathogen Interactions ; Phaeophyceae/*physiology ; Photosynthesis ; Phycodnaviridae/pathogenicity ; Phylogeny ; Plastids ; Symbiosis ; }, abstract = {Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.}, }
@article {pmid28839925, year = {2017}, author = {Hurst, GDD}, title = {Extended genomes: symbiosis and evolution.}, journal = {Interface focus}, volume = {7}, number = {5}, pages = {20170001}, pmid = {28839925}, issn = {2042-8898}, abstract = {Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont-that an individual's biology is best understood as a composite of the 'host organism' and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this review, I critically examine whether it is useful to consider holobionts as a unit of selection. I argue that microbial heredity-the direct passage of microbes from parent to offspring-is a key factor determining the degree to which the holobiont can usefully be considered a level of selection. Where direct vertical transmission (VT) is common, microbes form part of extended genomes whose dynamics can be modelled with simple population genetics, but that nevertheless have subtle quantitative distinctions from the classic mutation/selection model for nuclear genes. Without direct VT, the correlation between microbial fitness and host individual fitness erodes, and microbe fitness becomes associated with host survival only (rather than reproduction). Furthermore, turnover of microbes within a host may lessen associations between microbial fitness with host survival, and in polymicrobial communities, microbial fitness may derive largely from the ability to outcompete other microbes, to avoid host immune clearance and to minimize mortality through phage infection. These competing selection pressures make holobiont fitness a very minor consideration in determining symbiont evolution. Nevertheless, the importance of non-heritable microbes in organismal function is undoubted-and as such the evolutionary and ecological processes giving rise to variation and evolution of the microbes within and between host individuals represent a key research area in biology.}, }
@article {pmid28835914, year = {2017}, author = {Ochsenkühn, MA and Röthig, T and D'Angelo, C and Wiedenmann, J and Voolstra, CR}, title = {The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1602047}, pmid = {28835914}, issn = {2375-2548}, support = {311179/ERC_/European Research Council/International ; }, mesh = {Adaptation, Physiological/*drug effects ; Animals ; Anthozoa/*physiology ; Carbohydrates/analysis ; Chromatography, Gas ; Coral Reefs ; Dinoflagellida/*physiology ; Glycerol/*analogs &amp; derivatives/pharmacology ; Metabolomics/methods ; *Osmolar Concentration ; *Salinity ; *Symbiosis ; }, abstract = {The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.}, }
@article {pmid28826642, year = {2018}, author = {Moissl-Eichinger, C and Pausan, M and Taffner, J and Berg, G and Bang, C and Schmitz, RA}, title = {Archaea Are Interactive Components of Complex Microbiomes.}, journal = {Trends in microbiology}, volume = {26}, number = {1}, pages = {70-85}, doi = {10.1016/j.tim.2017.07.004}, pmid = {28826642}, issn = {1878-4380}, mesh = {Animals ; Archaea/classification/*physiology ; Biodiversity ; Biofilms ; Ecology ; Ecosystem ; Eukaryota ; Euryarchaeota ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Halobacteriales ; Health ; Humans ; Microbial Consortia ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Mouth/microbiology ; Phylogeny ; Plants/microbiology ; Ruminants/microbiology ; Soil Microbiology ; Symbiosis ; Viruses ; }, abstract = {Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.}, }
@article {pmid28824625, year = {2017}, author = {Rader, BA}, title = {Alkaline Phosphatase, an Unconventional Immune Protein.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {897}, pmid = {28824625}, issn = {1664-3224}, support = {R15 GM119100/GM/NIGMS NIH HHS/United States ; }, abstract = {Recent years have seen an increase in the number of studies focusing on alkaline phosphatases (APs), revealing an expanding complexity of function of these enzymes. Of the four human AP (hAP) proteins, most is known about tissue non-specific AP (TNAP) and intestinal AP (IAP). This review highlights current understanding of TNAP and IAP in relation to human health and disease. TNAP plays a role in multiple processes, including bone mineralization, vitamin B6 metabolism, and neurogenesis, is the genetic cause of hypophosphatasia, influences inflammation through regulation of purinergic signaling, and has been implicated in Alzheimer's disease. IAP regulates fatty acid absorption and has been implicated in the regulation of diet-induced obesity and metabolic syndrome. IAP and TNAP can dephosphorylate bacterial-derived lipopolysaccharide, and IAP has been identified as a potential regulator of the composition of the intestinal microbiome, an evolutionarily conserved function. Endogenous and recombinant bovine APs and recombinant hAPs are currently being explored for their potential as pharmacological agents to treat AP-associated diseases and mitigate multiple sources of inflammation. Continued research on these versatile proteins will undoubtedly provide insight into human pathophysiology, biochemistry, and the human holobiont.}, }
@article {pmid28818037, year = {2017}, author = {Brüwer, JD and Agrawal, S and Liew, YJ and Aranda, M and Voolstra, CR}, title = {Association of coral algal symbionts with a diverse viral community responsive to heat shock.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {174}, pmid = {28818037}, issn = {1471-2180}, mesh = {Animals ; Anthozoa/*physiology/*virology ; Climate Change ; Cold Temperature ; Coral Reefs ; Darkness ; Dinoflagellida/physiology/virology ; Ecosystem ; Gene Expression Regulation, Viral ; Genes, Viral ; Hot Temperature ; Phylogeny ; Sequence Analysis, RNA ; *Symbiosis ; Viral Proteins/genetics/metabolism ; *Virus Physiological Phenomena ; Viruses/*classification/genetics ; }, abstract = {BACKGROUND: Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin.<br><br>RESULTS: Here, we re-analyzed an RNA-Seq dataset from a cultured coral symbiont (Symbiodinium microadriaticum, Clade A1) across four experimental treatments (control, cold shock, heat shock, dark shock) to characterize associated viral diversity, abundance, and gene expression. Our approach comprised the filtering and removal of host sequence reads, subsequent phylogenetic assignment of sequence reads of putative viral origin, and the assembly and analysis of differentially expressed viral genes. About 15.46% (123 million) of all sequence reads were non-host-related, of which <1% could be classified as archaea, bacteria, or virus. Of these, 18.78% were annotated as virus and comprised a diverse community consistent across experimental treatments. Further, non-host related sequence reads assembled into 56,064 contigs, including 4856 contigs of putative viral origin that featured 43 differentially expressed genes during heat shock. The differentially expressed genes included viral kinases, ubiquitin, and ankyrin repeat proteins (amongst others), which are suggested to help the virus proliferate and inhibit the algal host's antiviral response.<br><br>CONCLUSION: Our results suggest that a diverse viral community is associated with coral algal endosymbionts of the genus Symbiodinium, which prompts further research on their ecological role in coral health and resilience.}, }
@article {pmid28811517, year = {2017}, author = {Quigley, KM and Willis, BL and Bay, LK}, title = {Heritability of the Symbiodinium community in vertically- and horizontally-transmitting broadcast spawning corals.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {8219}, pmid = {28811517}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*parasitology ; *Biodiversity ; Dinoflagellida/classification/*physiology ; *Ecosystem ; Genetic Variation ; Genome, Protozoan ; *Host-Parasite Interactions ; Phylogeny ; *Symbiosis ; }, abstract = {The dinoflagellate-coral partnership influences the coral holobiont's tolerance to thermal stress and bleaching. However, the comparative roles of host genetic versus environmental factors in determining the composition of this symbiosis are largely unknown. Here we quantify the heritability of the initial Symbiodinium communities for two broadcast-spawning corals with different symbiont transmission modes: Acropora tenuis has environmental acquisition, whereas Montipora digitata has maternal transmission. Using high throughput sequencing of the ITS-2 region to characterize communities in parents, juveniles and eggs, we describe previously undocumented Symbiodinium diversity and dynamics in both corals. After one month of uptake in the field, Symbiodinium communities associated with A. tenuis juveniles were dominated by A3, C1, D1, A-type CCMP828, and D1a in proportional abundances conserved between experiments in two years. M. digitata eggs were predominantly characterized by C15, D1, and A3. In contrast to current paradigms, host genetic influences accounted for a surprising 29% of phenotypic variation in Symbiodinium communities in the horizontally-transmitting A. tenuis, but only 62% in the vertically-transmitting M. digitata. Our results reveal hitherto unknown flexibility in the acquisition of Symbiodinium communities and substantial heritability in both species, providing material for selection to produce partnerships that are locally adapted to changing environmental conditions.}, }
@article {pmid28799900, year = {2017}, author = {Vorholt, JA and Vogel, C and Carlström, CI and Müller, DB}, title = {Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research.}, journal = {Cell host &amp; microbe}, volume = {22}, number = {2}, pages = {142-155}, doi = {10.1016/j.chom.2017.07.004}, pmid = {28799900}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Bacterial Physiological Phenomena ; Ecosystem ; Host-Pathogen Interactions ; Metagenome ; Microbial Consortia/physiology ; Microbial Interactions ; *Microbiota/genetics/physiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plant microbiome research highlights the importance of indigenous microbial communities for host phenotypes such as growth and health. It aims to discover the molecular basis by which host-microbe and microbe-microbe interactions shape and maintain microbial communities and to understand the role of individual microorganisms, as well as their collective ecosystem function. Here, we discuss reductionist approaches to disentangle the inherent complexity of interactions in situ. Experimentally tractable, synthetic communities enable testing of hypotheses by targeted manipulation in gnotobiotic systems. Modifications of microbial, host, and environmental parameters allow for the quantitative assessment of host and microbe characteristics with dynamic and spatial resolution. We summarize first insights from this emerging field and discuss current challenges and limitations. Using multifaceted approaches to detect interactions and functions will provide new insights into the fundamental biology of plant-microbe interactions and help to harness the power of the microbiome.}, }
@article {pmid28787582, year = {2017}, author = {Roossinck, MJ and Bazán, ER}, title = {Symbiosis: Viruses as Intimate Partners.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {123-139}, doi = {10.1146/annurev-virology-110615-042323}, pmid = {28787582}, issn = {2327-0578}, mesh = {Animals ; Bacteria/genetics ; DNA, Viral/*genetics ; Evolution, Molecular ; Genome ; *Host-Pathogen Interactions ; Humans ; Phylogeny ; *Symbiosis ; *Virus Physiological Phenomena ; }, abstract = {Viruses must establish an intimate relationship with their hosts and vectors in order to infect, replicate, and disseminate; hence, viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology. Although antagonistic relationships are thought to lead to coevolution, this is not always clear in virus-host interactions, and impacts on evolution may be complex. Commensalism implies a hitchhiking role for viruses-selfish elements just along for the ride. Mutualistic relationships have been described in detail in the past decade, and they reveal how important viruses are in considering host ecology. Ultimately, symbiosis can lead to symbiogenesis, or speciation through fusion, and the presence of large amounts of viral sequence in the genomes of everything from bacteria to humans, including some important functional genes, illustrates the significance of viral symbiogenesis in the evolution of all life on Earth.}, }
@article {pmid28785524, year = {2017}, author = {Conlan, JA and Rocker, MM and Francis, DS}, title = {A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3645}, pmid = {28785524}, issn = {2167-8359}, abstract = {Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral's condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1) tissue isolation by air-spraying and (2) crushing the coral in toto. Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes (Acropora millepora, Montipora crassotuberculata, Porites cylindrica, and Pocillopora damicornis). Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55-69% and 56-64%, respectively). As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.}, }
@article {pmid28766142, year = {2017}, author = {Leite, L and Jude-Lemeilleur, F and Raymond, N and Henriques, I and Garabetian, F and Alves, A}, title = {Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {27}, pages = {21721-21732}, pmid = {28766142}, issn = {1614-7499}, support = {UID/AMB/50017/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00835/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/00492/2013//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/86879/2012//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; TC-08_12//Programa de A&#xe7;&#xf5;es Universit&#xe1;rias Integradas &#x2028;Luso-Francesas (PAULIF)/ ; }, mesh = {Actinomycetales ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Bivalvia/chemistry/*microbiology ; DNA, Ribosomal ; France ; Gills/microbiology ; Hemolymph/microbiology ; *Microbiota ; Molecular Typing ; Phylogeny ; Portugal ; }, abstract = {According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.}, }
@article {pmid28732267, year = {2017}, author = {Sánchez-Cañizares, C and Jorrín, B and Poole, PS and Tkacz, A}, title = {Understanding the holobiont: the interdependence of plants and their microbiome.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {188-196}, doi = {10.1016/j.mib.2017.07.001}, pmid = {28732267}, issn = {1879-0364}, mesh = {*Ecosystem ; *Microbiota ; Plants/*microbiology ; }, abstract = {The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control, the microbiome is still able to adapt and thrive. The molecular knowledge behind these interactions and microbial '-omic' technologies are developing to the point of enabling holobiont engineering. For a long time microorganisms were in the background of plant biology but new multidisciplinary approaches have led to an appreciation of the importance of the holobiont, where plants and microbes are interdependent.}, }
@article {pmid28729652, year = {2017}, author = {Johnston, EC and Forsman, ZH and Flot, JF and Schmidt-Roach, S and Pinzón, JH and Knapp, ISS and Toonen, RJ}, title = {A genomic glance through the fog of plasticity and diversification in Pocillopora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5991}, pmid = {28729652}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; *Biodiversity ; Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Open Reading Frames/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Time Factors ; }, abstract = {Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.}, }
@article {pmid28724687, year = {2017}, author = {Morimoto, J and Simpson, SJ and Ponton, F}, title = {Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster.}, journal = {Biology letters}, volume = {13}, number = {7}, pages = {}, pmid = {28724687}, issn = {1744-957X}, mesh = {Acetobacter ; Animals ; Drosophila melanogaster ; Female ; *Gastrointestinal Microbiome ; Male ; Reproduction ; Sexual Behavior, Animal ; }, abstract = {There is increasing evidence of the far-reaching effects of gut bacteria on physiological and behavioural traits, yet the fitness-related consequences of changes in the gut bacteria composition of sexually interacting individuals remain unknown. To address this question, we manipulated the gut microbiota of fruit flies, Drosophila melanogaster, by monoinfecting flies with either Acetobacter pomorum (AP) or Lactobacillus plantarum (LP). Re-inoculated individuals were paired in all treatment combinations. LP-infected males had longer mating duration and induced higher short-term offspring production in females compared with AP-infected males. Furthermore, females of either re-inoculation state mated with AP-infected males were more likely to have zero offspring after mating, suggesting a negative effect of AP on male fertility. Finally, we found that the effects of male and female gut bacteria interacted to modulate their daughters', but not sons' body mass, revealing a new trans-generational effect of parental gut microbiota. In conclusion, this study shows direct and trans-generational effects of the gut microbiota on mating and reproduction.}, }
@article {pmid28717593, year = {2017}, author = {Gerth, M and Hurst, GDD}, title = {Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3529}, pmid = {28717593}, issn = {2167-8359}, abstract = {High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these 'contaminations' provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee (Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo. We conclude that 'contamination' in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses.}, }
@article {pmid28710460, year = {2017}, author = {Pineda, MC and Strehlow, B and Sternel, M and Duckworth, A and Haan, JD and Jones, R and Webster, NS}, title = {Effects of sediment smothering on the sponge holobiont with implications for dredging management.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5156}, pmid = {28710460}, issn = {2045-2322}, abstract = {One of the ways dredging can affect benthic habitats is through high levels of sediment deposition, which has the potential to smother sessile organisms such as sponges. In order to provide pressure-response values to sedimentation and tease apart the different cause-effect pathways of high turbidity, 5 sponge species, including heterotrophic and phototrophic nutritional modes, were exposed for up to 30 d to multiple sediment deposition events, each of which resulted in an initial covering of 80-100% of the surface of the sponges in a layer ~0.5 mm thick. The response of the sponges was examined using a suite of different response variables including growth, respiration, lipid content, community composition of the microbial symbionts, and maximum quantum yield and chlorophyll content of the phototrophic symbionts. Different species showed different mechanisms of sediment rejection and different patterns of sediment clearance. All species survived the treatments, were able to tolerate high levels of partial covering of their surfaces, and for most species the treatment did not alter the health of the sponge holobiont. Results from this study will guide interpretation of experiments examining the combined effects of all three dredging-related pressures, and aid the development of water quality thresholds for impact prediction purposes.}, }
@article {pmid28702013, year = {2017}, author = {Pogoreutz, C and Rädecker, N and Cárdenas, A and Gärdes, A and Wild, C and Voolstra, CR}, title = {Nitrogen Fixation Aligns with nifH Abundance and Expression in Two Coral Trophic Functional Groups.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1187}, pmid = {28702013}, issn = {1664-302X}, abstract = {Microbial nitrogen fixation (diazotrophy) is a functional trait widely associated with tropical reef-building (scleractinian) corals. While the integral role of nitrogen fixation in coral nutrient dynamics is recognized, its ecological significance across different coral functional groups remains yet to be evaluated. Here we set out to compare molecular and physiological patterns of diazotrophy (i.e., nifH gene abundance and expression as well as nitrogen fixation rates) in two coral families with contrasting trophic strategies: highly heterotrophic, free-living members of the family Fungiidae (Pleuractis granulosa, Ctenactis echinata), and mostly autotrophic coral holobionts with low heterotrophic capacity (Pocilloporidae: Pocillopora verrucosa, Stylophora pistillata). The Fungiidae exhibited low diazotroph abundance (based on nifH gene copy numbers) and activity (based on nifH gene expression and the absence of detectable nitrogen fixation rates). In contrast, the mostly autotrophic Pocilloporidae exhibited nifH gene copy numbers and gene expression two orders of magnitude higher than in the Fungiidae, which coincided with detectable nitrogen fixation activity. Based on these data, we suggest that nitrogen fixation compensates for the low heterotrophic nitrogen uptake in autotrophic corals. Consequently, the ecological importance of diazotrophy in coral holobionts may be determined by the trophic functional group of the host.}, }
@article {pmid28694508, year = {2017}, author = {Pineda, MC and Strehlow, B and Sternel, M and Duckworth, A and Jones, R and Webster, NS}, title = {Effects of suspended sediments on the sponge holobiont with implications for dredging management.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4925}, pmid = {28694508}, issn = {2045-2322}, mesh = {Analysis of Variance ; Animals ; Biomarkers ; *Geologic Sediments ; Microbiota ; Porifera/microbiology/*physiology ; }, abstract = {Dredging can cause high suspended sediment concentrations (SSC) in the water column, posing a hazard to filter feeding organisms like sponges as sediment may clog their aquiferous systems and reduce feeding. In order to provide pressure-response values for sponges to SSC and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were experimentally exposed to a range of dredging-relevant SSC of up to 100 mg L[-1], with light compensation across treatments to ensure that SSC was the primary physical parameter. This study shows that some sponge species exposed to high SSC (≥23 mg L[-1]) for extended periods (28 d) have lower survival, increased necrosis and depletion of energy reserves. In contrast, SSC of ≤10 mg L[-1] caused few, if any, negative effects and is thus suggested as a prudent sub-lethal threshold for sponges. Microbial communities did not change significantly among SSC treatments, although a nutritional shift from mixotrophy towards increased phototrophy was detected for some sponge species exposed to high SSC. Importantly however, it is expected that the combined effect of SSC with low light availability and sediment smothering as occurs during dredging operations will increase the negative effects on sponges.}, }
@article {pmid28682223, year = {2017}, author = {Burcelin, R}, title = {[Gut microbiota and immune crosstalk in metabolic disease].}, journal = {Biologie aujourd'hui}, volume = {211}, number = {1}, pages = {1-18}, doi = {10.1051/jbio/2017008}, pmid = {28682223}, issn = {2105-0686}, mesh = {Animals ; Dysbiosis/complications/immunology/microbiology/prevention &amp; control ; Gastrointestinal Microbiome/immunology/*physiology ; Gastrointestinal Tract/immunology/metabolism ; Humans ; Immune System/*physiology ; Inflammation/etiology/microbiology ; Metabolic Diseases/*immunology/metabolism/*microbiology ; Signal Transduction/immunology ; }, abstract = {The aim of the review is to discuss about the role played by the defence crosstalk between the gut microbiota and the intestinal immune system, in the development of metabolic disease focusing on obesity and diabetes. Starting from physiological and pathological stand points and based on the latest published data, this review is addressing how the concept of the hologenome theory of evolution can drive the fate of metabolic disease. The notion of "metabolic infection" to explain the "metabolic inflammation" is discussed. This imply comments about the process of bacterial translocation and impaired intestinal immune defense against commensals. Eventually this review sets the soil for personalized medicine. The monthly increase in the number of publications on the gut microbiota to intestinal immune defense and the control of metabolism demonstrate the importance of this field of investigation. The notion of commensal as "self or non-self" has to be reevaluated in the light of the current data. Furthermore, data demonstrate the major role played by short chain fatty acids, secondary bile acids, LPS, peptidoglycans, indole derivatives, and other bacteria-related molecules on the shaping of cells involved in the intestinal protection against commensals is now becoming a central player in the incidence of metabolic diseases. The literature demonstrates that the onset of metabolic diseases and some specific co-morbidities can be explained by a gut microbiota to intestinal immune system crosstalk. Therefore, one should now consider this avenue of investigation as a putative source of biomarkers and therapeutic targets to personalize the treatment of metabolic disease and its co-morbidities. Gut microbiota is considered as a major regulator of metabolic disease. This reconciles the notion of metabolic inflammation and the epidemic development of the disease. In addition to evidence showing that a specific gut microbiota characterizes patients with obesity, type 2 diabetes, and hepatic steatosis, the mechanisms causal to the disease could be related to the translocation of microbiota from the gut to the tissues, which induces inflammation. The mechanisms regulating such a process are based on the crosstalk between the gut microbiota and the host immune system. The hologenome theory of evolution supports this concept and implies that therapeutic strategies aiming to control glycemia should take into account both the gut microbiota and the host immune system. This review discusses the latest evidence regarding the bidirectional impact of the gut microbiota on host immune system crosstalk for the control of metabolic disease, hyperglycemia, and obesity. To avoid redundancies with the literature, we will focus our attention on the intestinal immune system, identifying evidence for the generation of novel therapeutic strategies, which could be based on the control of the translocation of gut bacteria to tissues. Such novel strategies should hamper the role played by gut microbiota dysbiosis on the development of metabolic inflammation. Recent evidence in rodents allows us to conclude that an impaired intestinal immune system characterizes and could be causal in the development of metabolic disease. The fine understanding of the molecular mechanisms should allow for the development of a first line of treatment for metabolic disease and its co-morbidities.}, }
@article {pmid28681143, year = {2018}, author = {van de Water, JAJM and Voolstra, CR and Rottier, C and Cocito, S and Peirano, A and Allemand, D and Ferrier-Pagès, C}, title = {Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {274-288}, pmid = {28681143}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; High-Throughput Nucleotide Sequencing ; Mediterranean Sea ; *Microbiota ; Phylogeny ; Seasons ; Seawater ; Symbiosis ; }, abstract = {Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.}, }
@article {pmid28679724, year = {2017}, author = {Smith, EG and D'Angelo, C and Sharon, Y and Tchernov, D and Wiedenmann, J}, title = {Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1858}, pages = {}, pmid = {28679724}, issn = {1471-2954}, support = {311179/ERC_/European Research Council/International ; }, mesh = {*Acclimatization ; Animals ; Anthozoa/physiology/*radiation effects ; Coral Reefs ; Dinoflagellida/physiology/*radiation effects ; Fluorescence ; *Light ; *Pigmentation ; Symbiosis ; }, abstract = {The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate that host pigments, specifically photoconvertible red fluorescent proteins (pcRFPs), can promote coral adaptation/acclimatization to deeper-water light environments by transforming the prevalent blue light into orange-red light, which can penetrate deeper within zooxanthellae-containing tissues; this facilitates a more homogeneous distribution of photons across symbiont communities. The ecological importance of pcRFPs in deeper reefs is supported by the increasing proportion of red fluorescent corals with depth (measured down to 45 m) and increased survival of colour morphs with strong expression of pcRFPs in long-term light manipulation experiments. In addition to screening by host pigments from high light intensities in shallow water, the spectral transformation observed in deeper-water corals highlights the importance of GFP-like protein expression as an ecological mechanism to support the functioning of the coral-Symbiodinium association across steep environmental gradients.}, }
@article {pmid28659968, year = {2017}, author = {Sandoval-Motta, S and Aldana, M and Martínez-Romero, E and Frank, A}, title = {The Human Microbiome and the Missing Heritability Problem.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {80}, pmid = {28659968}, issn = {1664-8021}, abstract = {The "missing heritability" problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this "missing heritability" have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies.}, }
@article {pmid28659905, year = {2017}, author = {Yang, SH and Tseng, CH and Huang, CR and Chen, CP and Tandon, K and Lee, STM and Chiang, PW and Shiu, JH and Chen, CA and Tang, SL}, title = {Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1094}, pmid = {28659905}, issn = {1664-302X}, abstract = {The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas) were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.}, }
@article {pmid28654220, year = {2017}, author = {Campisano, A and Albanese, D and Yousaf, S and Pancher, M and Donati, C and Pertot, I}, title = {Temperature drives the assembly of endophytic communities' seasonal succession.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3353-3364}, doi = {10.1111/1462-2920.13843}, pmid = {28654220}, issn = {1462-2920}, mesh = {Bradyrhizobium/classification/growth &amp; development/isolation &amp; purification ; Burkholderia/classification/growth &amp; development/isolation &amp; purification ; Endophytes/*classification/*growth &amp; development/isolation &amp; purification ; Mesorhizobium/classification/growth &amp; development/isolation &amp; purification ; *Microbiota ; Plant Roots/*microbiology ; Propionibacterium/classification/growth &amp; development/isolation &amp; purification ; Ralstonia/classification/growth &amp; development/isolation &amp; purification ; Seasons ; Temperature ; Vitis/*microbiology ; }, abstract = {Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. The variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field were studied. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures. The findings revealed the succession of endophytic communities over the year. Endophytic communities of roots and stems differ in terms of composition and dynamic response to temperature. Noticeably, compositional differences during the seasons affected bacterial taxa more in stems than in roots, suggesting that roots offer a more stable and less easily perturbed environment. Correlation abundance networks showed that the presence of several taxa (including Bradyrhizobium, Burkholderia, Dyella, Mesorhizobium, Propionibacterium and Ralstonia) is linked in both the field and the greenhouse.}, }
@article {pmid28646902, year = {2017}, author = {Pitlik, SD and Koren, O}, title = {How holobionts get sick-toward a unifying scheme of disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {64}, pmid = {28646902}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Animals ; Bacteria/pathogenicity ; Biological Evolution ; *Disease ; Genome ; Host-Pathogen Interactions ; Humans ; *Microbiota ; Plants ; Symbiosis ; }, abstract = {All humans, animals, and plants are holobionts. Holobionts comprise the host and a myriad of interacting microorganisms-the microbiota. The hologenome encompasses the genome of the host plus the composite of all microbial genomes (the microbiome). In health, there is a fine-tuned and resilient equilibrium within the members of the microbiota and between them and the host. This relative stability is maintained by a high level of microbial diversity, a delicate bio-geographic distribution of microorganisms, and a sophisticated and intricate molecular crosstalk among the multiple components of the holobiont. Pathobionts are temporarily benign microbes with the potential, under modified ecosystem conditions, to become key players in disease. Pathobionts may be endogenous, living for prolonged periods of time inside or on the host, or exogenous, invading the host during opportunistic situations. In both cases, the end result is the transformation of the beneficial microbiome into a health-perturbing pathobiome. We hypothesize that probably all diseases of holobionts, acute or chronic, infectious or non-infectious, and regional or systemic, are characterized by a perturbation of the healthy microbiome into a diseased pathobiome.}, }
@article {pmid28631353, year = {2017}, author = {Zhou, G and Cai, L and Yuan, T and Tian, R and Tong, H and Zhang, W and Jiang, L and Guo, M and Liu, S and Qian, PY and Huang, H}, title = {Microbiome dynamics in early life stages of the scleractinian coral Acropora gemmifera in response to elevated pCO2.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3342-3352}, doi = {10.1111/1462-2920.13840}, pmid = {28631353}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/embryology/*microbiology ; Archaea/*classification/genetics ; Carbon Dioxide/metabolism ; Coral Reefs ; Cyanobacteria/*classification/genetics ; DNA, Intergenic/genetics ; Dinoflagellida/*classification/genetics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Reef-building corals are complex holobionts, harbouring diverse microorganisms that play essential roles in maintaining coral health. However, microbiome development in early life stages of corals remains poorly understood. Here, microbiomes of Acropora gemmifera were analysed during spawning and early developmental stages, and also under different seawater partial pressure of CO2 (pCO2) conditions, using amplicon sequencing of 16S rRNA gene for bacteria and archaea and of ITS2 for Symbiodinium. No remarkable microbiome shift was observed in adults before and after spawning. Moreover, microbiomes in eggs were highly similar to those in spawned adults, possibly suggesting a vertical transmission from parents to offspring. However, significant stage-specific changes were found in coral microbiome during development, indicating that host development played a dominant role in shaping coral microbiome. Specifically, Cyanobacteria were particularly abundant in 6-day-old juveniles, but decreased largely in 31-day-old juveniles with a possible subclade shift in Symbiodinium dominance from C2r to D17. Larval microbiome showed changes in elevated pCO2 , while juvenile microbiomes remained rather stable in response to higher pCO2 . This study provides novel insights into the microbiome development during the critical life stages of coral.}, }
@article {pmid28625867, year = {2017}, author = {Postler, TS and Ghosh, S}, title = {Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System.}, journal = {Cell metabolism}, volume = {26}, number = {1}, pages = {110-130}, pmid = {28625867}, issn = {1932-7420}, support = {R01 DK102180/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Immune System/*metabolism/microbiology ; Inflammation/*metabolism/microbiology ; Inflammatory Bowel Diseases/metabolism/microbiology ; Metabolic Diseases/*metabolism/microbiology ; *Metabolome ; }, abstract = {The human gastrointestinal tract is populated by a diverse, highly mutualistic microbial flora, which is known as the microbiome. Disruptions to the microbiome have been shown to be associated with severe pathologies of the host, including metabolic disease, cancer, and inflammatory bowel disease. Mood and behavior are also susceptible to alterations in the gut microbiota. A particularly striking example of the symbiotic effects of the microbiome is the immune system, whose cells depend critically on a diverse array of microbial metabolites for normal development and behavior. This includes metabolites that are produced by bacteria from dietary components, metabolites that are produced by the host and biochemically modified by gut bacteria, and metabolites that are synthesized de novo by gut microbes. In this review, we highlight the role of the intestinal microbiome in human metabolic and inflammatory diseases and focus in particular on the molecular mechanisms that govern the gut-immune axis.}, }
@article {pmid28624904, year = {2017}, author = {Coelho-Souza, SA and Jenkins, SR and Casarin, A and Baeta-Neves, MH and Salgado, LT and Guimaraes, JRD and Coutinho, R}, title = {The Effect of Light on Bacterial Activity in a Seaweed Holobiont.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {868-876}, pmid = {28624904}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Autotrophic Processes ; *Bacterial Physiological Phenomena/drug effects ; *Biofilms/drug effects/growth &amp; development/radiation effects ; Brazil ; Circadian Rhythm ; *Light ; Sargassum/microbiology ; Seasons ; }, abstract = {Holobionts are characterized by the relationship between host and their associated organisms such as the biofilm associated with macroalgae. Considering that light is essential to macroalgae survival, the aim of this study was to verify the effect of light on the heterotrophic activity in biofilms of the brown macroalgae Sargassum furcatum during its growth cycle. Measurements of heterotrophic activity were done under natural light levels at different times during a daily cycle and under an artificial extinction of natural light during the afternoon. We also measured Sargassum primary production under these light levels in the afternoon. Both measurements were done with and without photosynthesis inhibitor and antibiotics. Biofilm composition was mainly represented by bacteria but diatoms, cyanobacteria, and other organisms were also common. When a peak of diatom genera was recorded, the heterotrophic activity of the biofilm was higher. Heterotrophic activity was usually highest during the afternoon and the presence of a photosynthesis inhibitor caused an average reduction of 17% but there was no relationship with Sargassum primary production. These results indicate that autotrophic production in the biofilm was reduced by the inhibitor with consequences on bacterial activity. Heterotrophic activity was mainly bacterial and the antibiotics chloramphenicol and penicillin were more effective than streptomycin. We suggest primary producers in the biofilm are more important to increase bacterial activity than the macroalgae itself because of coherence of the peaks of heterotrophic and autotrophic activity in biofilm during the afternoon and the effects of autotrophic inhibitors on heterotrophic activity.}, }
@article {pmid28607345, year = {2017}, author = {Chen, HK and Wang, LH and Chen, WU and Mayfield, AB and Levy, O and Lin, CS and Chen, CS}, title = {Coral lipid bodies as the relay center interconnecting diel-dependent lipidomic changes in different cellular compartments.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {3244}, pmid = {28607345}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/cytology/*microbiology/*physiology ; Circadian Rhythm ; Dinoflagellida/physiology ; Lipid Droplets ; Lipid Metabolism/*physiology ; Symbiosis/physiology ; }, abstract = {Lipid bodies (LBs) in the coral gastrodermal tissues are key organelles in the regulation of endosymbiosis and exhibit a diel rhythmicity. Using the scleractinian Euphyllia glabrescens collected across the diel cycle, we observed temporally dynamic lipid profiles in three cellular compartments: host coral gastrodermal cells, LBs, and in hospite Symbiodinium. Particularly, the lipidome varied over time, demonstrating the temporally variable nature of the coral-Symbiodinium endosymbiosis. The lipidome-scale data highlight the dynamic, light-driven metabolism of such associations and reveal that LBs are not only lipid storage organelles but also act as a relay center in metabolic trafficking. Furthermore, lipogenesis in LBs is significantly regulated by coral hosts and the lipid metabolites within holobionts featured predominantly triacylglycerols, sterol esters, and free fatty acids. Given these findings through a time-varied lipidome status, the present study provided valuable insights likely to be crucial to understand the cellular biology of the coral-Symbiodinium endosymbiosis.}, }
@article {pmid28601483, year = {2017}, author = {Tripp, EA and Zhang, N and Schneider, H and Huang, Y and Mueller, GM and Hu, Z and Häggblom, M and Bhattacharya, D}, title = {Reshaping Darwin's Tree: Impact of the Symbiome.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {8}, pages = {552-555}, doi = {10.1016/j.tree.2017.05.002}, pmid = {28601483}, issn = {1872-8383}, mesh = {*Biodiversity ; Humans ; *Phylogeny ; }, abstract = {Much of the undescribed biodiversity on Earth is microbial, often in mutualistic or pathogenic associations. Physically associated and coevolving life forms comprise a symbiome. We propose that systematics research can accelerate progress in science by introducing a new framework for phylogenetic analysis of symbiomes, here termed SYMPHY (symbiome phylogenetics).}, }
@article {pmid28572677, year = {2017}, author = {Wright, RM and Kenkel, CD and Dunn, CE and Shilling, EN and Bay, LK and Matz, MV}, title = {Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2609}, pmid = {28572677}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/immunology ; Disease Resistance ; Gene Expression Profiling ; Genetic Markers/genetics ; *Genotype ; Hydrobiology ; Species Specificity ; Stress, Physiological/*genetics/immunology ; Transcriptome ; Vibrio/*physiology ; Vibrio Infections/*immunology ; }, abstract = {Disease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eight Acropora millepora colonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4-6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i.e., did not launch a large stress response). Our results suggest that lesions appeared due to changes in the coral pathobiome (multiple bacterial species associated with disease) and general health deterioration after the biotic disturbance, rather than the direct activity of any specific pathogen. If diseases in nature arise because of weaknesses in holobiont physiology, instead of the virulence of any single etiological agent, environmental stressors compromising coral condition might play a larger role in disease outbreaks than is currently thought. To facilitate the diagnosis of compromised individuals, we developed and independently cross-validated a biomarker assay to predict mortality based on genes whose expression in asymptomatic individuals coincides with mortality rates.}, }
@article {pmid28553264, year = {2017}, author = {Carrier, TJ and Reitzel, AM}, title = {The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {802}, pmid = {28553264}, issn = {1664-302X}, abstract = {Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the "hologenome" across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may associate with a larger microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the "host-associated microbial repertoire," which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three "signatures" of the concept.}, }
@article {pmid28549621, year = {2017}, author = {Lemanceau, P and Blouin, M and Muller, D and Moënne-Loccoz, Y}, title = {Let the Core Microbiota Be Functional.}, journal = {Trends in plant science}, volume = {22}, number = {7}, pages = {583-595}, doi = {10.1016/j.tplants.2017.04.008}, pmid = {28549621}, issn = {1878-4372}, mesh = {Plants/*microbiology ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.}, }
@article {pmid28546553, year = {2017}, author = {Smith, EG and Vaughan, GO and Ketchum, RN and McParland, D and Burt, JA}, title = {Symbiont community stability through severe coral bleaching in a thermally extreme lagoon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2428}, pmid = {28546553}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; DNA, Intergenic ; Dinoflagellida/*physiology ; Environment ; *Symbiosis ; Temperature ; }, abstract = {Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals' responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C, Min = 16.8 °C) lagoon located in the southern Persian/Arabian Gulf using next generation sequencing of ITS2 amplicons. Despite experiencing extreme temperatures, severe bleaching and many factors that would be expected to promote the presence of, or transition to clade D dominance, the symbiont communities of the lagoon remain dominated by the C3 variant, Symbiodinium thermophilum. The stability of this symbiosis across multiple genera with different means of symbiont transmission highlights the importance of Symbiodinium thermophilum for corals living at the acclimatory limits of modern day corals. Corals in this extreme environment did not undergo adaptive bleaching, suggesting they are living at the edge of their acclimatory potential and that this valuable source of thermally tolerant genotypes may be lost in the near future under climate change.}, }
@article {pmid28540040, year = {2017}, author = {Pinzon, EH and Sierra, DA and Suarez, MO and Orduz, S and Florez, AM}, title = {DNA secondary structure formation by DNA shuffling of the conserved domains of the Cry protein of Bacillus thuringiensis.}, journal = {BMC biophysics}, volume = {10}, number = {}, pages = {4}, pmid = {28540040}, issn = {2046-1682}, abstract = {BACKGROUND: The Cry toxins, or δ-endotoxins, are a diverse group of proteins produced by Bacillus thuringiensis. While DNA secondary structures are biologically relevant, it is unknown if such structures are formed in regions encoding conserved domains of Cry toxins under shuffling conditions. We analyzed 5 holotypes that encode Cry toxins and that grouped into 4 clusters according to their phylogenetic closeness. The mean number of DNA secondary structures that formed and the mean Gibbs free energy [Formula: see text] were determined by an in silico analysis using different experimental DNA shuffling scenarios. In terms of spontaneity, shuffling efficiency was directly proportional to the formation of secondary structures but inversely proportional to ∆G.<br><br>RESULTS: The results showed a shared thermodynamic pattern for each cluster and relationships among sequences that are phylogenetically close at the protein level. The regions of the cry11Aa, Ba and Bb genes that encode domain I showed more spontaneity and thus a greater tendency to form secondary structures (<&#x2206;G). In the region of domain III; this tendency was lower (>&#x2206;G) in the cry11Ba and Bb genes. Proteins that are phylogenetically closer to Cry11Ba and Cry11Bb, such as Cry2Aa and Cry18Aa, maintained the same thermodynamic pattern. More distant proteins, such as Cry1Aa, Cry1Ab, Cry30Aa and Cry30Ca, featured different thermodynamic patterns in their DNA.<br><br>CONCLUSION: These results suggest the presence of thermodynamic variations associated to the formation of secondary structures and an evolutionary relationship with regions that encode highly conserved domains in Cry proteins. The findings of this study may have a role in the in silico design of cry gene assembly by DNA shuffling techniques.}, }
@article {pmid28534879, year = {2017}, author = {Frischkorn, KR and Rouco, M and Van Mooy, BAS and Dyhrman, ST}, title = {Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2090-2101}, pmid = {28534879}, issn = {1751-7370}, mesh = {Nitrogen/metabolism ; Nitrogen Fixation ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Trichodesmium/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting 'new' nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont. Here we demonstrate the presence of a core Trichodesmium microbiome that is modulated to suit different ocean regions, and contributes over 10 times the metabolic potential of Trichodesmium to the holobiont. Given the ubiquitous nature of epibionts on colonies, the substantial functional diversity within the microbiome is likely an integral facet of Trichodesmium physiological ecology across the oligotrophic oceans where this biogeochemically significant diazotroph thrives.}, }
@article {pmid28533520, year = {2017}, author = {Strand, R and Whalan, S and Webster, NS and Kutti, T and Fang, JKH and Luter, HM and Bannister, RJ}, title = {The response of a boreal deep-sea sponge holobiont to acute thermal stress.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1660}, pmid = {28533520}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Animals ; *Aquatic Organisms ; Energy Metabolism ; Intracellular Membranes/metabolism ; Lysosomes/metabolism ; Microbiota ; Nutritional Physiological Phenomena ; Oxygen Consumption ; Porifera/microbiology/*physiology ; *Seawater ; *Stress, Physiological ; *Temperature ; }, abstract = {Effects of elevated seawater temperatures on deep-water benthos has been poorly studied, despite reports of increased seawater temperature (up to 4 °C over 24 hrs) coinciding with mass mortality events of the sponge Geodia barretti at Tisler Reef, Norway. While the mechanisms driving these mortality events are unclear, manipulative laboratory experiments were conducted to quantify the effects of elevated temperature (up to 5 °C, above ambient levels) on the ecophysiology (respiration rate, nutrient uptake, cellular integrity and sponge microbiome) of G. barretti. No visible signs of stress (tissue necrosis or discolouration) were evident across experimental treatments; however, significant interactive effects of time and treatment on respiration, nutrient production and cellular stress were detected. Respiration rates and nitrogen effluxes doubled in responses to elevated temperatures (11 °C &amp; 12 °C) compared to control temperatures (7 °C). Cellular stress, as measured through lysosomal destabilisation, was 2-5 times higher at elevated temperatures than for control temperatures. However, the microbiome of G. barretti remained stable throughout the experiment, irrespective of temperature treatment. Mortality was not evident and respiration rates returned to pre-experimental levels during recovery. These results suggest other environmental processes, either alone or in combination with elevated temperature, contributed to the mortality of G. barretti at Tisler reef.}, }
@article {pmid28509908, year = {2017}, author = {Webster, NS and Reusch, TBH}, title = {Microbial contributions to the persistence of coral reefs.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2167-2174}, pmid = {28509908}, issn = {1751-7370}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology/physiology ; *Coral Reefs ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Microbiota/genetics ; }, abstract = {On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, the microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute to the physiology, development, immunity and behaviour of their hosts, and can respond very rapidly to changing environmental conditions, providing a powerful mechanism for acclimatisation and also possibly rapid evolution of coral reef holobionts. Environmentally acquired fluctuations in the microbiome can have significant functional consequences for the holobiont phenotype upon which selection can act. Environmentally induced changes in microbial abundance may be analogous to host gene duplication, symbiont switching / shuffling as a result of environmental change can either remove or introduce raw genetic material into the holobiont; and horizontal gene transfer can facilitate rapid evolution within microbial strains. Vertical transmission of symbionts is a key feature of many reef holobionts and this would enable environmentally acquired microbial traits to be faithfully passed to future generations, ultimately facilitating microbiome-mediated transgenerational acclimatisation (MMTA) and potentially even adaptation of reef species in a rapidly changing climate. In this commentary, we highlight the capacity and mechanisms for MMTA in reef species, propose a modified Price equation as a framework for assessing MMTA and recommend future areas of research to better understand how microorganisms contribute to the transgenerational acclimatisation of reef organisms, which is essential if we are to reliably predict the consequences of global change for reef ecosystems.}, }
@article {pmid28491055, year = {2017}, author = {Xia, X and Gurr, GM and Vasseur, L and Zheng, D and Zhong, H and Qin, B and Lin, J and Wang, Y and Song, F and Li, Y and Lin, H and You, M}, title = {Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {663}, pmid = {28491055}, issn = {1664-302X}, abstract = {Herbivore specialists adapt to feed on a specific group of host plants by evolving various mechanisms to respond to plant defenses. Insects also possess complex gut microbiotas but their potential role in adaptation is poorly understood. Our previous study of the genome of diamondback moth, Plutella xylostella, revealed an intrinsic capacity to detoxify plant defense compounds, which is an important factor in its success as a pest. Here we expand on that work with a complete taxonomic and functional profile of the P. xylostella gut microbiota obtained by metagenomic sequencing. Gene enrichment in the metagenome, accompanied by functional identification, revealed an important role of specific gut bacteria in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids. Microbes participating in these pathways mainly belonged to three highly abundant bacteria: Enterobacter cloacae, Enterobacter asburiae, and Carnobacterium maltaromaticum. Results show that while the gut microbial community may be complex, a small number of functionally active species can be disproportionally important. The presence of specific enzymes in the microbiota community, such as supporting amino acid synthesis, digestion and detoxification functions, demonstrates the beneficial interactions between P. xylostella and its gut microbiota. These interactions can be potential targets for manipulation to provide novel pest management approaches.}, }
@article {pmid28486655, year = {2017}, author = {Silveira, CB and Cavalcanti, GS and Walter, JM and Silva-Lima, AW and Dinsdale, EA and Bourne, DG and Thompson, CC and Thompson, FL}, title = {Microbial processes driving coral reef organic carbon flow.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {4}, pages = {575-595}, doi = {10.1093/femsre/fux018}, pmid = {28486655}, issn = {1574-6976}, mesh = {Biodiversity ; Carbon/*metabolism ; *Coral Reefs ; Ecosystem ; Microbiota/*physiology ; Mucus/microbiology ; *Water Microbiology ; }, abstract = {Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.}, }
@article {pmid28484479, year = {2017}, author = {Smith, DL and Gravel, V and Yergeau, E}, title = {Editorial: Signaling in the Phytomicrobiome.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {611}, pmid = {28484479}, issn = {1664-462X}, }
@article {pmid28473829, year = {2017}, author = {Romano, M}, title = {Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {721}, pmid = {28473829}, issn = {1664-302X}, abstract = {According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.}, }
@article {pmid28464532, year = {2017}, author = {Sogin, EM and Putnam, HM and Nelson, CE and Anderson, P and Gates, RD}, title = {Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.}, journal = {Environmental microbiology reports}, volume = {9}, number = {3}, pages = {310-315}, doi = {10.1111/1758-2229.12541}, pmid = {28464532}, issn = {1758-2229}, mesh = {Alveolata/*growth &amp; development/metabolism ; Animals ; Anthozoa/*microbiology/*parasitology ; Archaea/classification/*growth &amp; development/metabolism ; Biodiversity ; Coral Reefs ; Gammaproteobacteria/*growth &amp; development/metabolism ; Metabolome/physiology ; Symbiosis/*physiology ; Vibrionaceae/*growth &amp; development/metabolism ; }, abstract = {Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.}, }
@article {pmid28447372, year = {2017}, author = {Chakravarti, LJ and Beltran, VH and van Oppen, MJH}, title = {Rapid thermal adaptation in photosymbionts of reef-building corals.}, journal = {Global change biology}, volume = {23}, number = {11}, pages = {4675-4688}, doi = {10.1111/gcb.13702}, pmid = {28447372}, issn = {1365-2486}, mesh = {*Acclimatization/physiology ; Animals ; Anthozoa/*physiology ; Climate ; Coral Reefs ; Dinoflagellida/*physiology ; Genotype ; Photosynthesis ; *Symbiosis ; Temperature ; }, abstract = {Climate warming is occurring at a rate not experienced by life on Earth for 10 s of millions of years, and it is unknown whether the coral-dinoflagellate (Symbiodinium spp.) symbiosis can evolve fast enough to ensure coral reef persistence. Coral thermal tolerance is partly dependent on the Symbiodinium hosted. Therefore, directed laboratory evolution in Symbiodinium has been proposed as a strategy to enhance coral holobiont thermal tolerance. Using a reciprocal transplant design, we show that the upper temperature tolerance and temperature tolerance range of Symbiodinium C1 increased after ~80 asexual generations (2.5 years) of laboratory thermal selection. Relative to wild-type cells, selected cells showed superior photophysiological performance and growth rate at 31°C in vitro, and performed no worse at 27°C; they also had lower levels of extracellular reactive oxygen species (exROS). In contrast, wild-type cells were unable to photosynthesise or grow at 31°C and produced up to 17 times more exROS. In symbiosis, the increased thermal tolerance acquired ex hospite was less apparent. In recruits of two of three species tested, those harbouring selected cells showed no difference in growth between the 27 and 31°C treatments, and a trend of positive growth at both temperatures. Recruits that were inoculated with wild-type cells, however, showed a significant difference in growth rates between the 27 and 31°C treatments, with a negative growth trend at 31°C. There were no significant differences in the rate and severity of bleaching in coral recruits harbouring wild-type or selected cells. Our findings highlight the need for additional Symbiodinium genotypes to be tested with this assisted evolution approach. Deciphering the genetic basis of enhanced thermal tolerance in Symbiodinium and the cause behind its limited transference to the coral holobiont in this genotype of Symbiodinium C1 are important next steps for developing methods that aim to increase coral bleaching tolerance.}, }
@article {pmid28446691, year = {2017}, author = {Enríquez, S and Méndez, ER and Hoegh-Guldberg, O and Iglesias-Prieto, R}, title = {Key functional role of the optical properties of coral skeletons in coral ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1853}, pages = {}, pmid = {28446691}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; Ecology ; *Light ; Optical Phenomena ; Symbiosis ; }, abstract = {Multiple scattering of light on coral skeleton enhances light absorption efficiency of coral symbionts and plays a key role in the regulation of their internal diffuse light field. To understand the dependence of this enhancement on skeleton meso- and macrostructure, we analysed the scattering abilities of naked coral skeletons for 74 Indo-Pacific species. Sensitive morphotypes to thermal and light stress, flat-extraplanate and branching corals, showed the most efficient structures, while massive-robust species were less efficient. The lowest light-enhancing scattering abilities were found for the most primitive colonial growth form: phaceloid. Accordingly, the development of highly efficient light-collecting structures versus the selection of less efficient but more robust holobionts to cope with light stress may constitute a trade-off in the evolution of modern symbiotic scleractinian corals, characterizing two successful adaptive solutions. The coincidence of the most important structural modifications with epitheca decline supports the importance of the enhancement of light transmission across coral skeleton in modern scleractinian diversification, and the central role of these symbioses in the design and optimization of coral skeleton. Furthermore, the same ability that lies at the heart of the success of symbiotic corals as coral-reef-builders can also explain the 'Achilles's heel' of these symbioses in a warming ocean.}, }
@article {pmid28437665, year = {2017}, author = {Carvalhais, LC and Schenk, PM and Dennis, PG}, title = {Jasmonic acid signalling and the plant holobiont.}, journal = {Current opinion in microbiology}, volume = {37}, number = {}, pages = {42-47}, doi = {10.1016/j.mib.2017.03.009}, pmid = {28437665}, issn = {1879-0364}, mesh = {Cyclopentanes/*metabolism ; *Microbiota ; Oxylipins/*metabolism ; Plant Growth Regulators/*metabolism ; Plants/*metabolism/*microbiology ; *Signal Transduction ; }, abstract = {The plant holobiont - which is the plant and its associated microbiome - is increasingly viewed as an evolving entity. Some interacting microbes that compose the microbiome assist plants in combating pathogens and herbivorous insects. However, knowledge of the factors that influence the microbiome in the context of defence signalling pathways is still in its infancy. Recent research reported that changes in jasmonic acid (JA) and salicylic acid signalling affects the root microbiome of Arabidopsis thaliana. This review aims to present the hypothesis that the JA pathway represents a novel mechanism for microbiome engineering for improved holobiont fitness in agricultural systems.}, }
@article {pmid28431245, year = {2017}, author = {Scott, TA and Quintaneiro, LM and Norvaisas, P and Lui, PP and Wilson, MP and Leung, KY and Herrera-Dominguez, L and Sudiwala, S and Pessia, A and Clayton, PT and Bryson, K and Velagapudi, V and Mills, PB and Typas, A and Greene, NDE and Cabreiro, F}, title = {Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans.}, journal = {Cell}, volume = {169}, number = {3}, pages = {442-456.e18}, pmid = {28431245}, issn = {1097-4172}, support = {/WT_/Wellcome Trust/United Kingdom ; 102532/Z/12/Z/WT_/Wellcome Trust/United Kingdom ; MR/N003713/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antineoplastic Agents/*metabolism ; Autophagy ; Caenorhabditis elegans ; Cell Death ; Colorectal Neoplasms/drug therapy ; Diet ; Escherichia coli/enzymology/genetics/*metabolism ; Fluorouracil/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Models, Animal ; Pentosyltransferases/genetics ; }, abstract = {Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism. Also, disturbances in bacterial deoxynucleotide pools amplify 5-FU-induced autophagy and cell death in host cells, an effect regulated by the nucleoside diphosphate kinase ndk-1. Our data suggest a two-way bacterial mediation of fluoropyrimidine effects on host metabolism, which contributes to drug efficacy. These findings highlight the potential therapeutic power of manipulating intestinal microbiota to ensure host metabolic health and treat disease.}, }
@article {pmid28430944, year = {2017}, author = {Berg, G and Köberl, M and Rybakova, D and Müller, H and Grosch, R and Smalla, K}, title = {Plant microbial diversity is suggested as the key to future biocontrol and health trends.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix050}, pmid = {28430944}, issn = {1574-6941}, support = {J 3638/FWF_/Austrian Science Fund FWF/Austria ; T 847/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Biodiversity ; Biological Control Agents ; Ecosystem ; Microbiota/*physiology ; Plant Development ; Plant Diseases/*microbiology ; Plants/*microbiology ; Symbiosis/*physiology ; Volatile Organic Compounds/metabolism ; }, abstract = {The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species. The beneficial interplay of the host and its microbiome is responsible for maintaining the health of the holobiont, while diseases are often correlated with microbial dysbioses. Microbial diversity was identified as a key factor in preventing diseases and can be implemented as a biomarker in plant protection strategies. Targeted and predictive biocontrol approaches are possible by developing microbiome-based solutions. Moreover, combined breeding and biocontrol strategies maintaining diversity and ecosystem health are required. The analysis of plant microbiome data has brought about a paradigm shift in our understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.}, }
@article {pmid28429531, year = {2017}, author = {Pogoreutz, C and Rädecker, N and Cárdenas, A and Gärdes, A and Voolstra, CR and Wild, C}, title = {Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching.}, journal = {Global change biology}, volume = {23}, number = {9}, pages = {3838-3848}, doi = {10.1111/gcb.13695}, pmid = {28429531}, issn = {1365-2486}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Dinoflagellida ; *Nitrogen Fixation ; Symbiosis ; }, abstract = {The disruption of the coral-algae symbiosis (coral bleaching) due to rising sea surface temperatures has become an unprecedented global threat to coral reefs. Despite decades of research, our ability to manage mass bleaching events remains hampered by an incomplete mechanistic understanding of the processes involved. In this study, we induced a coral bleaching phenotype in the absence of heat and light stress by adding sugars. The sugar addition resulted in coral symbiotic breakdown accompanied by a fourfold increase of coral-associated microbial nitrogen fixation. Concomitantly, increased N:P ratios by the coral host and algal symbionts suggest excess availability of nitrogen and a disruption of the nitrogen limitation within the coral holobiont. As nitrogen fixation is similarly stimulated in ocean warming scenarios, here we propose a refined coral bleaching model integrating the cascading effects of stimulated microbial nitrogen fixation. This model highlights the putative role of nitrogen-fixing microbes in coral holobiont functioning and breakdown.}, }
@article {pmid28425179, year = {2017}, author = {Gajigan, AP and Diaz, LA and Conaco, C}, title = {Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28425179}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/*radiation effects ; Biota/*radiation effects ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont.}, }
@article {pmid28410570, year = {2017}, author = {Valadez-Cano, C and Olivares-Hernández, R and Resendis-Antonio, O and DeLuna, A and Delaye, L}, title = {Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {99}, pmid = {28410570}, issn = {1471-2148}, mesh = {Biological Evolution ; Cercozoa/*cytology/genetics/*physiology ; Computer Simulation ; Cyanobacteria/genetics/*physiology ; Hexoses/metabolism ; Selection, Genetic ; Symbiosis ; Synechococcus/cytology/metabolism ; }, abstract = {BACKGROUND: Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore.<br><br>RESULTS: We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by improvements in the gluconeogenic pathway the metabolism of the endosymbiont uses more efficiently the carbon source for reduced-carbon production. In addition, our in silico simulations of the evolutionary process leading to the reduced metabolic network of the chromatophore showed that the predicted rate of released reduced-carbon is obtained in less than 5% of the times under a process guided by random gene deletion and genetic drift. We interpret previous findings as evidence that natural selection at holobiont level shaped the rate at which reduced-carbon is exported to the host. Finally, our model also predicts that the ABC phosphate transporter (pstSACB) which is conserved in the genome of the chromatophore of P. chromatophora strain CCAC 0185 is a necessary component to release reduced-carbon molecules to the host.<br><br>CONCLUSION: Our evolutionary analysis suggests that in the case of Paulinella chromatophora natural selection at the holobiont level played a prominent role in shaping the metabolic specialization of the chromatophore. We propose that natural selection acted as a "metabolic engineer" by favoring metabolic restructurings that led to an increased release of reduced-carbon to the host.}, }
@article {pmid28404738, year = {2017}, author = {Galla, S and Chakraborty, S and Mell, B and Vijay-Kumar, M and Joe, B}, title = {Microbiotal-Host Interactions and Hypertension.}, journal = {Physiology (Bethesda, Md.)}, volume = {32}, number = {3}, pages = {224-233}, pmid = {28404738}, issn = {1548-9221}, support = {R01 HL020176/HL/NHLBI NIH HHS/United States ; R37 HL020176/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Hypertension/*genetics/*microbiology ; *Metagenome ; Mice ; *Microbiota ; }, abstract = {Hypertension, or elevated blood pressure (BP), has been extensively researched over decades and clearly demonstrated to be caused due to a combination of host genetic and environmental factors. Although much research remains to be conducted to pin-point the precise genetic elements on the host genome that control BP, new lines of evidence are emerging to indicate that, besides the host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP. Unlike the rigid host genome, the microbiome or the "second genome" can be altered by diet or microbiotal transplantation in the host. This possibility is attractive from the perspective of exploiting the microbiotal composition for clinical management of inherited hypertension. Thus, focusing on the limited current literature supporting a role for the microbiome in BP regulation, this review highlights the need to further explore the role of the co-existence of host and the microbiota as an organized biological unit called the "holobiont" in the context of BP regulation.}, }
@article {pmid28366817, year = {2017}, author = {Forsman, ZH and Knapp, ISS and Tisthammer, K and Eaton, DAR and Belcaid, M and Toonen, RJ}, title = {Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa.}, journal = {Molecular phylogenetics and evolution}, volume = {111}, number = {}, pages = {132-148}, doi = {10.1016/j.ympev.2017.03.023}, pmid = {28366817}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*genetics ; Gene Flow/*genetics ; Genome, Mitochondrial ; Genomics/*methods ; Geography ; Hawaii ; *Hybridization, Genetic ; Likelihood Functions ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sequence Alignment ; Species Specificity ; }, abstract = {Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawai'i, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability.}, }
@article {pmid28326066, year = {2017}, author = {Peixoto, RS and Rosado, PM and Leite, DC and Rosado, AS and Bourne, DG}, title = {Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {341}, pmid = {28326066}, issn = {1664-302X}, abstract = {The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental "probiotics" to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.}, }
@article {pmid28319100, year = {2017}, author = {Agarwal, V and Blanton, JM and Podell, S and Taton, A and Schorn, MA and Busch, J and Lin, Z and Schmidt, EW and Jensen, PR and Paul, VJ and Biggs, JS and Golden, JW and Allen, EE and Moore, BS}, title = {Metagenomic discovery of polybrominated diphenyl ether biosynthesis by marine sponges.}, journal = {Nature chemical biology}, volume = {13}, number = {5}, pages = {537-543}, pmid = {28319100}, issn = {1552-4469}, support = {R00 ES026620/ES/NIEHS NIH HHS/United States ; S10 OD010640/OD/NIH HHS/United States ; R01 GM107557/GM/NIGMS NIH HHS/United States ; P01 ES021921/ES/NIEHS NIH HHS/United States ; R01 CA172310/CA/NCI NIH HHS/United States ; K99 ES026620/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Biological Products/chemistry/*metabolism ; Bone Morphogenetic Proteins/*genetics/*metabolism ; Halogenated Diphenyl Ethers/chemistry/*metabolism ; *Metagenomics ; Molecular Structure ; Porifera/*metabolism ; }, abstract = {Naturally produced polybrominated diphenyl ethers (PBDEs) pervade the marine environment and structurally resemble toxic man-made brominated flame retardants. PBDEs bioaccumulate in marine animals and are likely transferred to the human food chain. However, the biogenic basis for PBDE production in one of their most prolific sources, marine sponges of the order Dysideidae, remains unidentified. Here, we report the discovery of PBDE biosynthetic gene clusters within sponge-microbiome-associated cyanobacterial endosymbionts through the use of an unbiased metagenome-mining approach. Using expression of PBDE biosynthetic genes in heterologous cyanobacterial hosts, we correlate the structural diversity of naturally produced PBDEs to modifications within PBDE biosynthetic gene clusters in multiple sponge holobionts. Our results establish the genetic and molecular foundation for the production of PBDEs in one of the most abundant natural sources of these molecules, further setting the stage for a metagenomic-based inventory of other PBDE sources in the marine environment.}, }
@article {pmid28302492, year = {2017}, author = {O'Malley, MA}, title = {From endosymbiosis to holobionts: Evaluating a conceptual legacy.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {34-41}, doi = {10.1016/j.jtbi.2017.03.008}, pmid = {28302492}, issn = {1095-8541}, mesh = {*Biological Evolution ; *Microbiota ; Research ; *Symbiosis ; Terminology as Topic ; }, abstract = {In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research.}, }
@article {pmid28296889, year = {2017}, author = {Cowart, DA and Durand, L and Cambon-Bonavita, MA and Arnaud-Haond, S}, title = {Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0172543}, pmid = {28296889}, issn = {1932-6203}, mesh = {Animals ; Crustacea/*microbiology ; Gastrointestinal Tract/*microbiology ; *Geography ; }, abstract = {Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.}, }
@article {pmid28295957, year = {2017}, author = {Partida-Martínez, LP}, title = {The fungal holobiont: Evidence from early diverging fungi.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2919-2923}, doi = {10.1111/1462-2920.13731}, pmid = {28295957}, issn = {1462-2920}, mesh = {*Fungi ; *Phylogeny ; }, }
@article {pmid28290203, year = {2017}, author = {Eymann, C and Lassek, C and Wegner, U and Bernhardt, J and Fritsch, OA and Fuchs, S and Otto, A and Albrecht, D and Schiefelbein, U and Cernava, T and Aschenbrenner, I and Berg, G and Grube, M and Riedel, K}, title = {Symbiotic Interplay of Fungi, Algae, and Bacteria within the Lung Lichen Lobaria pulmonaria L. Hoffm. as Assessed by State-of-the-Art Metaproteomics.}, journal = {Journal of proteome research}, volume = {16}, number = {6}, pages = {2160-2173}, doi = {10.1021/acs.jproteome.6b00974}, pmid = {28290203}, issn = {1535-3907}, mesh = {*Ascomycota ; Biodiversity ; *Chlorophyta ; *Cyanobacteria ; *Lichens ; Metabolomics ; Microbial Interactions ; Proteomics ; Pulmonaria ; *Symbiosis ; }, abstract = {Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed the structure and functionality of the entire lung lichen Lobaria pulmonaria L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to the green algae and the ascomycetous fungus, a lichenicolous fungus as well as a complex prokaryotic community (different from the cyanobacteria) was found, the latter dominated by methanotrophic Rhizobiales. Various partner-specific proteins could be assigned to the different lichen symbionts, for example, fungal proteins involved in vesicle transport, algal proteins functioning in photosynthesis, cyanobacterial nitrogenase and GOGAT involved in nitrogen fixation, and bacterial enzymes responsible for methanol/C1-compound metabolism as well as CO-detoxification. Structural and functional information on proteins expressed by the lichen community complemented and extended our recent symbiosis model depicting the functional multiplayer network of single holobiont partners.1 Our new metaproteome analysis strongly supports the hypothesis (i) that interactions within the self-supporting association are multifaceted and (ii) that the strategy of functional diversification within the single lichen partners may support the longevity of L. pulmonaria under certain ecological conditions.}, }
@article {pmid28273475, year = {2017}, author = {Leulier, F and MacNeil, LT and Lee, WJ and Rawls, JF and Cani, PD and Schwarzer, M and Zhao, L and Simpson, SJ}, title = {Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health.}, journal = {Cell metabolism}, volume = {25}, number = {3}, pages = {522-534}, pmid = {28273475}, issn = {1932-7420}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; R01 DK081426/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/*physiology ; *Health ; Humans ; Models, Animal ; *Nutritional Physiological Phenomena ; Phenotype ; Systems Biology ; }, abstract = {Nutrition is paramount in shaping all aspects of animal biology. In addition, the influence of the intestinal microbiota on physiology is now widely recognized. Given that diet also shapes the intestinal microbiota, this raises the question of how the nutritional environment and microbial assemblages together influence animal physiology. This research field constitutes a new frontier in the field of organismal biology that needs to be addressed. Here we review recent studies using animal models and humans and propose an integrative framework within which to define the study of the diet-physiology-microbiota systems and ultimately link it to human health. Nutritional Geometry sits centrally in the proposed framework and offers means to define diet compositions that are optimal for individuals and populations.}, }
@article {pmid28249568, year = {2017}, author = {Chen, C and Uematsu, K and Linse, K and Sigwart, JD}, title = {By more ways than one: Rapid convergence at hydrothermal vents shown by 3D anatomical reconstruction of Gigantopelta (Mollusca: Neomphalina).}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {62}, pmid = {28249568}, issn = {1471-2148}, mesh = {Acclimatization ; Animals ; Bacteria/isolation &amp; purification/ultrastructure ; Ecosystem ; Gastropoda/*anatomy &amp; histology/*classification/genetics/microbiology ; Gills/microbiology ; *Hydrothermal Vents ; Indian Ocean ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Extreme environments prompt the evolution of characteristic adaptations. Yet questions remain about whether radiations in extreme environments originate from a single lineage that masters a key adaptive pathway, or if the same features can arise in parallel through convergence. Species endemic to deep-sea hydrothermal vents must accommodate high temperature and low pH. The most successful vent species share a constrained pathway to successful energy exploitation: hosting symbionts. The vent-endemic gastropod genus Gigantopelta, from the Southern and Indian Oceans, shares unusual features with a co-occurring peltospirid, the 'scaly-foot gastropod' Chrysomallon squamiferum. Both are unusually large for the clade and share other adaptive features such as a prominent enlarged trophosome-like oesophageal gland, not found in any other vent molluscs.<br><br>RESULTS: Transmission electron microscopy confirmed endosymbiont bacteria in the oesophageal gland of Gigantopelta, as also seen in Chrysomallon. They are the only known members of their phylum in vent ecosystems hosting internal endosymbionts; other vent molluscs host endosymbionts in or on their gills, or in the mantle cavity. A five-gene phylogenetic reconstruction demonstrated that Gigantopelta and Chrysomallon are not phylogenetically sister-taxa, despite their superficial similarity. Both genera have specialist adaptations to accommodate internalised endosymbionts, but with anatomical differences that indicate separate evolutionary origins. Hosting endosymbionts in an internal organ within the host means that all resources required by the bacteria must be supplied by the animal, rather than directly by the vent fluid. Unlike Chrysomallon, which has an enlarged oesophageal gland throughout post-settlement life, the oesophageal gland in Gigantopelta is proportionally much smaller in juveniles and the animals likely undergo a trophic shift during ontogeny. The circulatory system is hypertrophied in both but the overall size is smaller in Gigantopelta. In contrast with Chrysomallon, Gigantopelta possesses true ganglia and is gonochoristic.<br><br>CONCLUSIONS: Key anatomical differences between Gigantopelta and Chrysomallon demonstrate these two genera acquired a similar way of life through independent and convergent adaptive pathways. What appear to be the holobiont's adaptations to an extreme environment, are driven by optimising bacteria's access to vent nutrients. By comparing Gigantopelta and Chrysomallon, we show that metazoans are capable of rapidly and repeatedly evolving equivalent anatomical adaptations and close-knit relationships with chemoautotrophic bacteria, achieving the same end-product through parallel evolutionary trajectories.}, }
@article {pmid28245221, year = {2017}, author = {Richardson, LA}, title = {Evolving as a holobiont.}, journal = {PLoS biology}, volume = {15}, number = {2}, pages = {e2002168}, pmid = {28245221}, issn = {1545-7885}, mesh = {Animals ; Biological Evolution ; Evolution, Molecular ; Humans ; Microbiota/*physiology ; Phylogeny ; Symbiosis/physiology ; }, }
@article {pmid28240318, year = {2017}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Water flow buffers shifts in bacterial community structure in heat-stressed Acropora muricata.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43600}, pmid = {28240318}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/*classification/genetics ; *Biodiversity ; Environment ; *Hot Temperature ; Metagenome ; Metagenomics/methods ; Seasons ; Seawater ; *Stress, Physiological ; *Symbiosis ; Temperature ; Vibrio/classification/genetics ; }, abstract = {Deterioration of coral health and associated change in the coral holobiont's bacterial community are often a result of different environmental stressors acting synergistically. There is evidence that water flow is important for a coral's resistance to elevated seawater temperature, but there is no information on how water flow affects the coral-associated bacterial community under these conditions. In a laboratory cross-design experiment, Acropora muricata nubbins were subjected to interactive effects of seawater temperature (27 °C to 31 °C) and water flow (0.20 m s[-1] and 0.03 m s[-1]). In an in situ experiment, water flow manipulation was conducted with three colonies of A. muricata during the winter and summer, by partially enclosing each colony in a clear plastic mesh box. 16S rRNA amplicon pyrosequencing showed an increase in the relative abundance of Flavobacteriales and Rhodobacterales in the laboratory experiment, and Vibrio spp. in the in situ experiment when corals were exposed to elevated temperature and slow water flow. In contrast, corals that were exposed to faster water flow under laboratory and in situ conditions had a stable bacterial community. These findings indicate that water flow plays an important role in the maintenance of specific coral-bacteria associations during times of elevated thermal stress.}, }
@article {pmid28233813, year = {2017}, author = {Weigel, BL and Erwin, PM}, title = {Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43247}, pmid = {28233813}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Microbiota ; *Nitrogen Cycle ; Porifera/*metabolism/*microbiology ; Symbiosis ; }, abstract = {Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.}, }
@article {pmid28223979, year = {2017}, author = {Leite, DC and Leão, P and Garrido, AG and Lins, U and Santos, HF and Pires, DO and Castro, CB and van Elsas, JD and Zilberberg, C and Rosado, AS and Peixoto, RS}, title = {Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {176}, pmid = {28223979}, issn = {1664-302X}, abstract = {The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.}, }
@article {pmid28181581, year = {2017}, author = {Lin, Z and Chen, M and Dong, X and Zheng, X and Huang, H and Xu, X and Chen, J}, title = {Transcriptome profiling of Galaxea fascicularis and its endosymbiont Symbiodinium reveals chronic eutrophication tolerance pathways and metabolic mutualism between partners.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {42100}, pmid = {28181581}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/genetics/*growth &amp; development/*parasitology ; Aquatic Organisms/genetics/growth &amp; development/parasitology ; China ; Dinoflagellida/genetics/*growth &amp; development ; *Eutrophication ; *Gene Expression Profiling ; *Metabolic Networks and Pathways ; Stress, Physiological ; *Symbiosis ; }, abstract = {In the South China Sea, coastal eutrophication in the Beibu Gulf has seriously threatened reef habitats by subjecting corals to chronic physiological stress. To determine how coral holobionts may tolerate such conditions, we examined the transcriptomes of healthy colonies of the galaxy coral Galaxea fascicularis and its endosymbiont Symbiodinium from two reef sites experiencing pristine or eutrophied nutrient regimes. We identified 236 and 205 genes that were differentially expressed in eutrophied hosts and symbionts, respectively. Both gene sets included pathways related to stress responses and metabolic interactions. An analysis of genes originating from each partner revealed striking metabolic integration with respect to vitamins, cofactors, amino acids, fatty acids, and secondary metabolite biosynthesis. The expression levels of these genes supported the existence of a continuum of mutualism in this coral-algal symbiosis. Additionally, large sets of transcription factors, cell signal transduction molecules, biomineralization components, and galaxin-related proteins were expanded in G. fascicularis relative to other coral species.}, }
@article {pmid28155809, year = {2017}, author = {Rivera-Pérez, JI and González, AA and Toranzos, GA}, title = {From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity.}, journal = {Microbiology spectrum}, volume = {5}, number = {1}, pages = {}, pmid = {28155809}, issn = {2165-0497}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Helicobacter pylori/*pathogenicity ; *Host-Pathogen Interactions ; Humans ; JC Virus/*pathogenicity ; Legionella/*pathogenicity ; }, abstract = {As the "human microbiome era" continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of "accidental pathogens," meaning previously nonpathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift toward pathogenicity. For instance, symbionts such as Helicobacter pylori and JC polyomavirus have been shown to have accompanied humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of accidental pathogens in the form of emerging pathogens.}, }
@article {pmid28152002, year = {2017}, author = {Goulet, TL and Shirur, KP and Ramsby, BD and Iglesias-Prieto, R}, title = {The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171032}, pmid = {28152002}, issn = {1932-6203}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/chemistry/*physiology ; Caribbean Region ; Chlorophyll/analysis/metabolism ; Chlorophyll A ; Dinoflagellida/genetics/*physiology ; Enzymes/metabolism ; Genotype ; Mexico ; Seawater ; Symbiosis/physiology ; Temperature ; }, abstract = {Global climate change not only leads to elevated seawater temperatures but also to episodic anomalously high or low temperatures lasting for several hours to days. Scleractinian corals are detrimentally affected by thermal fluctuations, which often lead to an uncoupling of their mutualism with Symbiodinium spp. (coral bleaching) and potentially coral death. Consequently, on many Caribbean reefs scleractinian coral cover has plummeted. Conversely, gorgonian corals persist, with their abundance even increasing. How gorgonians react to thermal anomalies has been investigated utilizing limited parameters of either the gorgonian, Symbiodinium or the combined symbiosis (holobiont). We employed a holistic approach to examine the effect of an experimental five-day elevated temperature episode on parameters of the host, symbiont, and the holobiont in Eunicea tourneforti, E. flexuosa and Pseudoplexaura porosa. These gorgonian corals reacted and coped with 32°C seawater temperatures. Neither Symbiodinium genotypes nor densities differed between the ambient 29.5°C and 32°C. Chlorophyll a and c2 per Symbiodinium cell, however, were lower at 32°C leading to a reduction in chlorophyll content in the branches and an associated reduction in estimated absorbance and increase in the chlorophyll a specific absorption coefficient. The adjustments in the photochemical parameters led to changes in photochemical efficiencies, although these too showed that the gorgonians were coping. For example, the maximum excitation pressure, Qm, was significantly lower at 32°C than at 29.5°C. In addition, although per dry weight the amount of protein and lipids were lower at 32°C, the overall energy content in the tissues did not differ between the temperatures. Antioxidant activity either remained the same or increased following exposure to 32°C further reiterating a response that dealt with the stressor. Taken together, the capability of Caribbean gorgonian corals to modify symbiont, host and consequently holobiont parameters may partially explain their persistence on reefs faced with climate change.}, }
@article {pmid28133884, year = {2017}, author = {Arnaud-Haond, S and Aires, T and Candeias, R and Teixeira, SJL and Duarte, CM and Valero, M and Serrão, EA}, title = {Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia.}, journal = {Molecular ecology}, volume = {26}, number = {8}, pages = {2379-2391}, doi = {10.1111/mec.14030}, pmid = {28133884}, issn = {1365-294X}, mesh = {Bacteria/classification ; Caulerpa/*genetics/*microbiology ; DNA, Bacterial/genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; *Introduced Species ; Mediterranean Sea ; *Microbiota ; Microsatellite Repeats ; RNA, Ribosomal, 16S/genetics ; South Australia ; *Symbiosis ; }, abstract = {Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and β diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.}, }
@article {pmid28119709, year = {2016}, author = {Rotini, A and Mejia, AY and Costa, R and Migliore, L and Winters, G}, title = {Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {2015}, pmid = {28119709}, issn = {1664-462X}, abstract = {Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species' capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.}, }
@article {pmid28115399, year = {2017}, author = {Esteves, AI and Cullen, A and Thomas, T}, title = {Competitive interactions between sponge-associated bacteria.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, doi = {10.1093/femsec/fix008}, pmid = {28115399}, issn = {1574-6941}, mesh = {Animals ; Bacillus/genetics ; Bacteria/genetics/*metabolism ; Biotechnology ; Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics/physiology ; }, abstract = {The diversity of the microbial communities associated with marine sponges has been extensively studied, but their functioning and interactions within the sponge holobiont are only recently being appreciated. Sponge-associated microorganisms are known for the production of a range of inhibitory metabolites with biotechnological application, but the ecological role that these compounds remains elusive. In this work, we explore the competitive interactions between cultivated sponge-associated bacteria to inspect whether bacteria that produce antimicrobial activities are able to inhibit potentially pathogenic bacteria. We isolated a Bacillus sp. bacterium with sponge-degrading activity, which likely has a negative impact on the host. This bacterium, along with other sponge isolates from the same genus, was found to be inhibited by a subpopulation of closely related sponge-derived Pseudovibrio spp. In some Pseudovibrio strains, these inhibitory activities were correlated with the genetic capacity to produce polyketides, such as erythronolide. Our observations suggest that antagonistic activities likely influence the composition of the sponge microbiome, including the abundance of bacteria that can be harmful to the host.}, }
@article {pmid28103686, year = {2017}, author = {Alcolombri, U and Lei, L and Meltzer, D and Vardi, A and Tawfik, DS}, title = {Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor.}, journal = {ACS chemical biology}, volume = {12}, number = {1}, pages = {41-46}, doi = {10.1021/acschembio.6b00844}, pmid = {28103686}, issn = {1554-8937}, mesh = {Animals ; Anthozoa/drug effects/enzymology/*metabolism ; Bacteria/drug effects/enzymology/metabolism ; Carbon-Sulfur Lyases/antagonists &amp; inhibitors/metabolism ; Enzyme Inhibitors/metabolism ; Haptophyta/drug effects/enzymology/*metabolism ; Oceans and Seas ; Sulfides/*metabolism ; }, abstract = {Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.}, }
@article {pmid28097070, year = {2017}, author = {Fiore, CL and Freeman, CJ and Kujawinski, EB}, title = {Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2870}, pmid = {28097070}, issn = {2167-8359}, abstract = {Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.}, }
@article {pmid28088765, year = {2017}, author = {Karlin, EF and Smouse, PE}, title = {Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.}, journal = {Annals of botany}, volume = {120}, number = {2}, pages = {221-231}, pmid = {28088765}, issn = {1095-8290}, mesh = {Alleles ; Argentina ; Australia ; *Biological Evolution ; Chile ; Genetic Variation ; Genome, Plant ; *Hybridization, Genetic ; Microsatellite Repeats ; New Zealand ; Sphagnopsida/*genetics ; Tasmania ; *Triploidy ; }, abstract = {BACKGROUND AND AIMS: Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations.<br><br>METHODS: Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures.<br><br>KEY RESULTS: The majority (76&#xa0;%) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83&#xa0;% of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5&#xa0;% of the total information.<br><br>CONCLUSIONS: Sphagnum &#xd7; falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.}, }
@article {pmid28066403, year = {2016}, author = {Pita, L and Fraune, S and Hentschel, U}, title = {Emerging Sponge Models of Animal-Microbe Symbioses.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2102}, pmid = {28066403}, issn = {1664-302X}, abstract = {Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host-microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.}, }
@article {pmid28050778, year = {2017}, author = {Miller, WB and Torday, JS}, title = {A systematic approach to cancer: evolution beyond selection.}, journal = {Clinical and translational medicine}, volume = {6}, number = {1}, pages = {2}, pmid = {28050778}, issn = {2001-1326}, abstract = {Cancer is typically scrutinized as a pathological process characterized by chromosomal aberrations and clonal expansion subject to stochastic Darwinian selection within adaptive cellular ecosystems. Cognition based evolution is suggested as an alternative approach to cancer development and progression in which neoplastic cells of differing karyotypes and cellular lineages are assessed as self-referential agencies with purposive participation within tissue microenvironments. As distinct self-aware entities, neoplastic cells occupy unique participant/observer status within tissue ecologies. In consequence, neoplastic proliferation by clonal lineages is enhanced by the advantaged utilization of ecological resources through flexible re-connection with progenitor evolutionary stages.}, }
@article {pmid28003808, year = {2016}, author = {Gopal, M and Gupta, A}, title = {Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1971}, pmid = {28003808}, issn = {1664-302X}, abstract = {"No plant is an island too…" Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.}, }
@article {pmid27995440, year = {2017}, author = {Catania, F and Krohs, U and Chittò, M and Ferro, D and Ferro, K and Lepennetier, G and Görtz, HD and Schreiber, RS and Kurtz, J and Gadau, J}, title = {The hologenome concept: we need to incorporate function.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {136}, number = {3-4}, pages = {89-98}, pmid = {27995440}, issn = {1611-7530}, mesh = {*Adaptation, Biological ; Animals ; Anthozoa ; *Biological Evolution ; Biology/*methods ; Drosophila ; Ecology/*methods ; Fungi ; Humans ; Paramecium ; Phenotype ; Plants ; Rickettsia ; Symbiosis ; }, abstract = {Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called 'typical' organisms no longer organisms in their own right? Is the study of the holobiont-host plus its symbiotic microorganisms-no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host's environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.}, }
@article {pmid27980125, year = {2017}, author = {Hawkins, TD and Warner, ME}, title = {Warm preconditioning protects against acute heat-induced respiratory dysfunction and delays bleaching in a symbiotic sea anemone.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 6}, pages = {969-983}, doi = {10.1242/jeb.150391}, pmid = {27980125}, issn = {1477-9145}, mesh = {*Acclimatization ; Animals ; Dinoflagellida/enzymology/*physiology ; Heat-Shock Response ; Hot Temperature ; Mitochondria/enzymology/metabolism ; Oxygen Consumption ; Photosynthesis ; Sea Anemones/enzymology/*physiology ; *Symbiosis ; }, abstract = {Preconditioning to non-stressful warming can protect some symbiotic cnidarians against the high temperature-induced collapse of their mutualistic endosymbiosis with photosynthetic dinoflagellates (Symbiodinium spp.), a process known as bleaching. Here, we sought to determine whether such preconditioning is underpinned by differential regulation of aerobic respiration. We quantified in vivo metabolism and mitochondrial respiratory enzyme activity in the naturally symbiotic sea anemone Exaiptasia pallida preconditioned to 30°C for >7 weeks as well as anemones kept at 26°C. Preconditioning resulted in increased Symbiodinium photosynthetic activity and holobiont (host+symbiont) respiration rates. Biomass-normalised activities of host respiratory enzymes [citrate synthase and the mitochondrial electron transport chain (mETC) complexes I and IV] were higher in preconditioned animals, suggesting that increased holobiont respiration may have been due to host mitochondrial biogenesis and/or enlargement. Subsequent acute heating of preconditioned and 'thermally naive' animals to 33°C induced dramatic increases in host mETC complex I and Symbiodinium mETC complex II activities only in thermally naive E. pallida These changes were not reflected in the activities of other respiratory enzymes. Furthermore, bleaching in preconditioned E. pallida (defined as the significant loss of symbionts) was delayed by several days relative to the thermally naive group. These findings suggest that changes to mitochondrial biogenesis and/or function in symbiotic cnidarians during warm preconditioning might play a protective role during periods of exposure to stressful heating.}, }
@article {pmid27958345, year = {2016}, author = {Pineda, MC and Strehlow, B and Duckworth, A and Doyle, J and Jones, R and Webster, NS}, title = {Effects of light attenuation on the sponge holobiont- implications for dredging management.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39038}, pmid = {27958345}, issn = {2045-2322}, mesh = {Animals ; Biota/*physiology ; *Light ; Porifera/*physiology ; Symbiosis/*physiology ; }, abstract = {Dredging and natural sediment resuspension events can cause high levels of turbidity, reducing the amount of light available for photosynthetic benthic biota. To determine how marine sponges respond to light attenuation, five species were experimentally exposed to a range of light treatments. Tolerance thresholds and capacity for recovery varied markedly amongst species. Whilst light attenuation had no effect on the heterotrophic species Stylissa flabelliformis and Ianthella basta, the phototrophic species Cliona orientalis and Carteriospongia foliascens discoloured (bleached) over a 28 day exposure period to very low light (<0.8 mol photons m[-2] d[-1]). In darkness, both species discoloured within a few days, concomitant with reduced fluorescence yields, chlorophyll concentrations and shifts in their associated microbiomes. The phototrophic species Cymbastela coralliophila was less impacted by light reduction. C. orientalis and C. coralliophila exhibited full recovery under normal light conditions, whilst C. foliascens did not recover and showed high levels of mortality. The light treatments used in the study are directly relevant to conditions that can occur in situ during dredging projects, indicating that light attenuation poses a risk to photosynthetic marine sponges. Examining benthic light levels over temporal scales would enable dredging proponents to be aware of conditions that could impact on sponge physiology.}, }
@article {pmid27924868, year = {2016}, author = {Diaz, JM and Hansel, CM and Apprill, A and Brighi, C and Zhang, T and Weber, L and McNally, S and Xun, L}, title = {Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13801}, pmid = {27924868}, issn = {2041-1723}, mesh = {Animals ; Anthozoa/*metabolism/microbiology ; Circadian Rhythm ; Dinoflagellida/*metabolism ; Larva/physiology ; Microbiota ; *Pigmentation ; Species Specificity ; Superoxides/*metabolism ; *Symbiosis ; }, abstract = {The reactive oxygen species superoxide (O2[·-]) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ∼120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology.}, }
@article {pmid27920768, year = {2016}, author = {Zhang, Y and Yang, Q and Ling, J and Van Nostrand, JD and Shi, Z and Zhou, J and Dong, J}, title = {The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1870}, pmid = {27920768}, issn = {1664-302X}, abstract = {The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.}, }
@article {pmid27919551, year = {2017}, author = {Hernandez-Agreda, A and Gates, RD and Ainsworth, TD}, title = {Defining the Core Microbiome in Corals' Microbial Soup.}, journal = {Trends in microbiology}, volume = {25}, number = {2}, pages = {125-140}, doi = {10.1016/j.tim.2016.11.003}, pmid = {27919551}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*microbiology/*parasitology ; Bacteria/*isolation &amp; purification ; *Coral Reefs ; Dinoflagellida/*isolation &amp; purification ; Dysbiosis/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis/physiology ; }, abstract = {Corals are considered one of the most complex microbial biospheres studied to date, hosting thousands of bacterial phylotypes in species-specific associations. There are, however, substantial knowledge gaps and challenges in understanding the functional significance of bacterial communities and bacterial symbioses of corals. The ubiquitous nature of some bacterial interactions has only recently been investigated and an accurate differentiation between the healthy (symbiotic) and unhealthy (dysbiotic) microbial state has not yet been determined. Here we review the complexity of the coral holobiont, coral microbiome diversity, and recently proposed bacterial symbioses of corals. We provide insight into coupling the core microbiome framework with community ecology principals, and draw on the theoretical insights from other complex systems, to build a framework to aid in deciphering ecologically significant microbes within a corals' microbial soup.}, }
@article {pmid27908589, year = {2017}, author = {Shapira, M}, title = {Adaptation from Within or from Without: A Reply to Rodrigo et al.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {2}, pages = {85}, doi = {10.1016/j.tree.2016.11.003}, pmid = {27908589}, issn = {1872-8383}, mesh = {*Adaptation, Physiological ; Humans ; *Symbiosis ; }, }
@article {pmid27907979, year = {2017}, author = {Webster, NS}, title = {Conceptual and methodological advances for holobiont research.}, journal = {Environmental microbiology reports}, volume = {9}, number = {1}, pages = {30-32}, doi = {10.1111/1758-2229.12500}, pmid = {27907979}, issn = {1758-2229}, mesh = {Animals ; Aquatic Organisms/*microbiology/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Seawater/*microbiology ; *Symbiosis ; }, }
@article {pmid27877161, year = {2016}, author = {Horn, H and Slaby, BM and Jahn, MT and Bayer, K and Moitinho-Silva, L and Förster, F and Abdelmohsen, UR and Hentschel, U}, title = {An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1751}, pmid = {27877161}, issn = {1664-302X}, abstract = {Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. This study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.}, }
@article {pmid27858116, year = {2017}, author = {Lee, HU and McPherson, ZE and Tan, B and Korecka, A and Pettersson, S}, title = {Host-microbiome interactions: the aryl hydrocarbon receptor and the central nervous system.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {95}, number = {1}, pages = {29-39}, pmid = {27858116}, issn = {1432-1440}, mesh = {Animals ; Central Nervous System/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Host-Pathogen Interactions ; Humans ; Ligands ; *Microbiota ; Neurodegenerative Diseases/etiology/metabolism/pathology ; Neurogenesis ; Receptors, Aryl Hydrocarbon/*metabolism ; *Signal Transduction ; }, abstract = {The microbiome located within a given host and its organs forms a holobiont, an intimate functional entity with evolutionarily designed interactions to support nutritional intake and reproduction. Thus, all organs in a holobiont respond to changes within the microbiome. The development and function of the central nervous system and its homeostatic mechanisms are no exception and are also subject to regulation by the gut microbiome. In order for the holobiont to function effectively, the microbiome and host must communicate. The aryl hydrocarbon receptor is an evolutionarily conserved receptor recognizing environmental compounds, including a number of ligands produced directly and indirectly by the microbiome. This review focuses on the microbiome-gut-brain axis in regard to the aryl hydrocarbon receptor signaling pathway and its impact on underlying mechanisms in neurodegeneration.}, }
@article {pmid27857087, year = {2016}, author = {Kilian, M and Chapple, IL and Hannig, M and Marsh, PD and Meuric, V and Pedersen, AM and Tonetti, MS and Wade, WG and Zaura, E}, title = {The oral microbiome - an update for oral healthcare professionals.}, journal = {British dental journal}, volume = {221}, number = {10}, pages = {657-666}, pmid = {27857087}, issn = {1476-5373}, mesh = {*Dental Caries ; Humans ; *Microbiota ; Mouth/*microbiology ; *Oral Health ; Periodontitis ; }, abstract = {For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.}, }
@article {pmid27833995, year = {2017}, author = {Thomas, P and Sekhar, AC}, title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {885-899}, pmid = {27833995}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation &amp; purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular "Cytobacts" and "Peribacts" with possible roles in plant holobiome and hologenome.}, }
@article {pmid27822559, year = {2016}, author = {Apprill, A and Weber, LG and Santoro, AE}, title = {Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes.}, journal = {mSystems}, volume = {1}, number = {5}, pages = {}, pmid = {27822559}, issn = {2379-5077}, abstract = {The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively. Across all coral species, we found that 46 tissue- and 22 mucus-specific microbial members consistently associated with the different habitats. Sequences classifying as "Candidatus Amoebophilus," Bacteroidetes-affiliated intracellular symbionts of amoebae, emerged as previously unrecognized tissue associates of three coral species. This study demonstrates how coral habitat differentiation enables highly resolved examination of ecological interactions between corals and their associated microorganisms and identifies previously unrecognized tissue and mucus associates of Caribbean corals for future targeted study. IMPORTANCE This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to "Candidatus Amoebophilus," recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats.}, }
@article {pmid27822520, year = {2016}, author = {Theis, KR and Dheilly, NM and Klassen, JL and Brucker, RM and Baines, JF and Bosch, TC and Cryan, JF and Gilbert, SF and Goodnight, CJ and Lloyd, EA and Sapp, J and Vandenkoornhuyse, P and Zilber-Rosenberg, I and Rosenberg, E and Bordenstein, SR}, title = {Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.}, journal = {mSystems}, volume = {1}, number = {2}, pages = {}, pmid = {27822520}, issn = {2379-5077}, abstract = {Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.}, }
@article {pmid27819340, year = {2016}, author = {Kumar, S and Jang, IH and Kim, CW and Kang, DW and Lee, WJ and Jo, H}, title = {Functional screening of mammalian mechanosensitive genes using Drosophila RNAi library- Smarcd3/Bap60 is a mechanosensitive pro-inflammatory gene.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {36461}, pmid = {27819340}, issn = {2045-2322}, support = {P01 HL095070/HL/NHLBI NIH HHS/United States ; P20 HL113451/HL/NHLBI NIH HHS/United States ; R01 HL119798/HL/NHLBI NIH HHS/United States ; R01 HL124879/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Aorta/cytology ; Cells, Cultured ; Chromosomal Proteins, Non-Histone/antagonists &amp; inhibitors/genetics/*metabolism ; Drosophila/metabolism ; Drosophila Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Endothelial Cells/cytology/metabolism ; Gene Library ; Human Umbilical Vein Endothelial Cells ; Humans ; Inflammation/etiology ; Interleukin-8/metabolism ; Mice ; Mice, Inbred C57BL ; Muscle Proteins/antagonists &amp; inhibitors/genetics/*metabolism ; Promoter Regions, Genetic ; RNA Interference ; Shear Strength ; Transcription Factors/antagonists &amp; inhibitors/genetics/*metabolism ; Vascular Cell Adhesion Molecule-1/metabolism ; }, abstract = {Disturbed blood flow (d-flow) induces atherosclerosis by altering the expression of mechanosensitive genes in the arterial endothelium. Previously, we identified >580 mechanosensitive genes in the mouse arterial endothelium, but their role in endothelial inflammation is incompletely understood. From this set, we obtained 84 Drosophila RNAi lines that silences the target gene under the control of upstream activation sequence (UAS) promoter. These lines were crossed with C564-GAL4 flies expressing GFP under the control of drosomycin promoter, an NF-κB target gene and a marker of pathogen-induced inflammation. Silencing of psmd12 or ERN1 decreased infection-induced drosomycin expression, while Bap60 silencing significantly increased the drosomycin expression. Interestingly, knockdown of Bap60 in adult flies using temperature-inducible Bap60 RNAi (C564[ts]-GAL4-Bap60-RNAi) enhanced drosomycin expression upon Gram-positive bacterial challenge but the basal drosomycin expression remained unchanged compared to the control. In the mammalian system, smarcd3 (mammalian ortholog of Bap60) expression was reduced in the human- and mouse aortic endothelial cells exposed to oscillatory shear in vitro as well as in the d-flow regions of mouse arterial endothelium in vivo. Moreover, siRNA-mediated knockdown of smarcd3 induced endothelial inflammation. In summary, we developed an in vivo Drosophila RNAi screening method to identify flow-sensitive genes that regulate endothelial inflammation.}, }
@article {pmid27819120, year = {2016}, author = {Li, Z and Wang, Y and Li, J and Liu, F and He, L and He, Y and Wang, S}, title = {Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {6}, pages = {659-671}, pmid = {27819120}, issn = {1436-2236}, mesh = {Animals ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Carbon/metabolism ; Fungi/classification/*genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbiota/genetics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Stramenopiles/classification/*genetics/metabolism ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.}, }
@article {pmid27818648, year = {2016}, author = {Kopac, SM and Klassen, JL}, title = {Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1647}, pmid = {27818648}, issn = {1664-302X}, abstract = {Virtually all multicellular organisms host a community of symbionts composed of mutualistic, commensal, and pathogenic microbes, i.e., their microbiome. The mechanism of selection on host-microbe assemblages remains contentious, particularly regarding whether selection acts differently on hosts and their microbial symbionts. Here, we attempt to reconcile these viewpoints using a model that describes how hosts and their microbial symbionts alter each other's niche and thereby fitness. We describe how host-microbe interactions might change the shape of the host niche and/or reproductive rates within it, which are directly related to host fitness. A host may also alter the niche of a symbiotic microbe, although this depends on the extent to which that microbe is dependent on the host for reproduction. Finally, we provide a mathematical model to test whether interactions between hosts and microbes are necessary to describe the niche of either partner. Our synthesis highlights the phenotypic effects of host-microbe interactions while respecting the unique lifestyles of each partner, and thereby provides a unified framework to describe how selection might act on a host that is associated with its microbiome.}, }
@article {pmid27809267, year = {2016}, author = {Xu, L and Shi, Z and Wang, B and Lu, M and Sun, J}, title = {Pine Defensive Monoterpene α-Pinene Influences the Feeding Behavior of Dendroctonus valens and Its Gut Bacterial Community Structure.}, journal = {International journal of molecular sciences}, volume = {17}, number = {11}, pages = {}, pmid = {27809267}, issn = {1422-0067}, mesh = {Animals ; Bacteria/classification/genetics ; Bicyclic Monoterpenes ; Coleoptera/*drug effects/microbiology/physiology ; DNA, Bacterial/chemistry/genetics ; Dose-Response Relationship, Drug ; Feeding Behavior/*drug effects ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Genetic Variation ; Host-Pathogen Interactions/drug effects ; Monoterpenes/*pharmacology ; Phloem/chemistry ; Pinus/*chemistry ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The exposure to plant defense chemicals has negative effects on insect feeding activity and modifies insect gut microbial community composition. Dendroctonus valens is a very destructive forest pest in China, and harbors a large diversity and abundance of gut microorganisms. Host pine defensive chemicals can protect the pines from attack by the holobiont. In this study, boring length of D. valens feeding on 0 mg/g α-pinene and 9 mg/g α-pinene concentration in phloem media for 6 and 48 h were recorded, and their gut bacterial communities were analyzed in parallel. Nine milligram per gram α-pinene concentration significantly inhibited boring length of D. valens and altered its gut microbial community structure after 6 h. The inhibition of boring length from 9 mg/g α-pinene in diets ceased after 48 h. No significant differences of the bacterial communities were observed between the beetles in 0 and 9 mg/g α-pinene concentration in phloem media after 48 h. Our results showed that the inhibition of the feeding behavior of D. valens and the disturbance to its gut bacterial communities in 9 mg/g α-pinene concentration in phloem media after 6 h were eliminated after 48 h. The resilience of gut bacterial community of D. valens may help the beetle catabolize pine defense chemical.}, }
@article {pmid27803185, year = {2016}, author = {Schröder, K and Bosch, TC}, title = {The Origin of Mucosal Immunity: Lessons from the Holobiont Hydra.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27803185}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; Hydra/*immunology ; *Immunity, Innate ; *Immunity, Mucosal ; Models, Animal ; Vertebrates/*immunology ; }, abstract = {Historically, mucosal immunity-i.e., the portion of the immune system that protects an organism's various mucous membranes from invasion by potentially pathogenic microbes-has been studied in single-cell epithelia in the gastrointestinal and upper respiratory tracts of vertebrates. Phylogenetically, mucosal surfaces appeared for the first time about 560 million years ago in members of the phylum Cnidaria. There are remarkable similarities and shared functions of mucosal immunity in vertebrates and innate immunity in cnidarians, such as Hydra species. Here, we propose a common origin for both systems and review observations that indicate that the ultimately simple holobiont Hydra provides both a new perspective on the relationship between bacteria and animal cells and a new prism for viewing the emergence and evolution of epithelial tissue-based innate immunity. In addition, recent breakthroughs in our understanding of immune responses in Hydra polyps reared under defined short-term gnotobiotic conditions open up the potential of Hydra as an animal research model for the study of common mucosal disorders.}, }
@article {pmid27799924, year = {2016}, author = {Berg, M and Zhou, XY and Shapira, M}, title = {Host-Specific Functional Significance of Caenorhabditis Gut Commensals.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1622}, pmid = {27799924}, issn = {1664-302X}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, abstract = {The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200-300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized.}, }
@article {pmid27795310, year = {2017}, author = {Morrow, KM and Bromhall, K and Motti, CA and Munn, CB and Bourne, DG}, title = {Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27795310}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/drug effects/*microbiology ; Archaea/drug effects/genetics/growth &amp; development/isolation &amp; purification ; Bacteria/drug effects/genetics/growth &amp; development/pathogenicity ; Coral Reefs ; Ecosystem ; Larva/drug effects ; Metagenomics ; Microbial Consortia/drug effects/genetics ; Microbiota/*drug effects/genetics ; Phaeophyceae/*chemistry/physiology ; Pheromones/biosynthesis/chemistry/*pharmacology ; Population Dynamics ; RNA, Ribosomal, 16S ; Seaweed/chemistry/growth &amp; development/*physiology ; Vibrio/*isolation &amp; purification/pathogenicity/physiology ; }, abstract = {UNLABELLED: Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml[-1]) than calculated natural concentrations (4.4 mg · ml[-1]). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure.<br><br>IMPORTANCE: Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure.}, }
@article {pmid27594308, year = {2016}, author = {Root-Bernstein, R}, title = {Autoimmunity and the microbiome: T-cell receptor mimicry of "self" and microbial antigens mediates self tolerance in holobionts: The concepts of "holoimmunity" (TcR-mediated tolerance for the holobiont) and "holoautoimmunity" (loss of tolerance for the holobiont) are introduced.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {11}, pages = {1068-1083}, pmid = {27594308}, issn = {1521-1878}, mesh = {*Autoimmunity ; Humans ; Immune Tolerance ; Microbiota/*immunology ; Receptors, Antigen, T-Cell/*immunology ; }, abstract = {I propose a T-cell receptor (TcR)-based mechanism by which immunity mediates both "genetic self" and "microbial self" thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross-reactivity with "self," resulting in selection for a TcR repertoire mimicking "genetic self." Second, evolution has selected for a "microbial self" that mimics "genetic self" so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR-microbiome mimicry "holoimmunity" to denote immune tolerance to the "holobiont self." Logically, microbiome-host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross-react with host antigens producing "holoautoimmunity."}, }
@article {pmid27777745, year = {2016}, author = {Aichelman, HE and Townsend, JE and Courtney, TA and Baumann, JH and Davies, SW and Castillo, KD}, title = {Heterotrophy mitigates the response of the temperate coral Oculina arbuscula to temperature stress.}, journal = {Ecology and evolution}, volume = {6}, number = {18}, pages = {6758-6769}, pmid = {27777745}, issn = {2045-7758}, abstract = {Anthropogenic increases in atmospheric carbon dioxide concentration have caused global average sea surface temperature (SST) to increase by approximately 0.11°C per decade between 1971 and 2010 - a trend that is projected to continue through the 21st century. A multitude of research studies have demonstrated that increased SSTs compromise the coral holobiont (cnidarian host and its symbiotic algae) by reducing both host calcification and symbiont density, among other variables. However, we still do not fully understand the role of heterotrophy in the response of the coral holobiont to elevated temperature, particularly for temperate corals. Here, we conducted a pair of independent experiments to investigate the influence of heterotrophy on the response of the temperate scleractinian coral Oculina arbuscula to thermal stress. Colonies of O. arbuscula from Radio Island, North Carolina, were exposed to four feeding treatments (zero, low, moderate, and high concentrations of newly hatched Artemia sp. nauplii) across two independent temperature experiments (average annual SST (20°C) and average summer temperature (28°C) for the interval 2005-2012) to quantify the effects of heterotrophy on coral skeletal growth and symbiont density. Results suggest that heterotrophy mitigated both reduced skeletal growth and decreased symbiont density observed for unfed corals reared at 28°C. This study highlights the importance of heterotrophy in maintaining coral holobiont fitness under thermal stress and has important implications for the interpretation of coral response to climate change.}, }
@article {pmid27726033, year = {2017}, author = {van de Water, JA and Melkonian, R and Voolstra, CR and Junca, H and Beraud, E and Allemand, D and Ferrier-Pagès, C}, title = {Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {466-478}, pmid = {27726033}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Classification ; Coral Reefs ; DNA, Bacterial/genetics ; Gene Library ; Mediterranean Sea ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology ; Species Specificity ; Temperature ; }, abstract = {Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.}, }
@article {pmid27721807, year = {2016}, author = {Dittmer, J and van Opstal, EJ and Shropshire, JD and Bordenstein, SR and Hurst, GD and Brucker, RM}, title = {Disentangling a Holobiont - Recent Advances and Perspectives in Nasonia Wasps.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1478}, pmid = {27721807}, issn = {1664-302X}, abstract = {The parasitoid wasp genus Nasonia (Hymenoptera: Chalcidoidea) is a well-established model organism for insect development, evolutionary genetics, speciation, and symbiosis. The host-microbiota assemblage which constitutes the Nasonia holobiont (a host together with all of its associated microbes) consists of viruses, two heritable bacterial symbionts and a bacterial community dominated in abundance by a few taxa in the gut. In the wild, all four Nasonia species are systematically infected with the obligate intracellular bacterium Wolbachia and can additionally be co-infected with Arsenophonus nasoniae. These two reproductive parasites have different transmission modes and host manipulations (cytoplasmic incompatibility vs. male-killing, respectively). Pioneering studies on Wolbachia in Nasonia demonstrated that closely related Nasonia species harbor multiple and mutually incompatible Wolbachia strains, resulting in strong symbiont-mediated reproductive barriers that evolved early in the speciation process. Moreover, research on host-symbiont interactions and speciation has recently broadened from its historical focus on heritable symbionts to the entire microbial community. In this context, each Nasonia species hosts a distinguishable community of gut bacteria that experiences a temporal succession during host development and members of this bacterial community cause strong hybrid lethality during larval development. In this review, we present the Nasonia species complex as a model system to experimentally investigate questions regarding: (i) the impact of different microbes, including (but not limited to) heritable endosymbionts, on the extended phenotype of the holobiont, (ii) the establishment and regulation of a species-specific microbiota, (iii) the role of the microbiota in speciation, and (iv) the resilience and adaptability of the microbiota in wild populations subjected to different environmental pressures. We discuss the potential for easy microbiota manipulations in Nasonia as a promising experimental approach to address these fundamental aspects.}, }
@article {pmid27716053, year = {2016}, author = {Peterson, BF and Scharf, ME}, title = {Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {772}, pmid = {27716053}, issn = {1471-2164}, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Antibiosis ; Bacteria/*genetics ; Computational Biology/methods ; Fungi/physiology ; Gene Expression Profiling ; Genes, rRNA ; Glutathione Transferase/metabolism ; Isoptera/*immunology/metabolism/*microbiology ; *Metagenome ; *Metagenomics/methods ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; *Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota; however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen.<br><br>RESULTS: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; &#x3b1;/FDR&#x2009;=&#x2009;0.05) including an upregulated bacterial amidohydrolase.<br><br>CONCLUSIONS: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense.}, }
@article {pmid27708547, year = {2016}, author = {Torday, JS and Miller, WB}, title = {Life is determined by its environment.}, journal = {International journal of astrobiology}, volume = {15}, number = {4}, pages = {345-350}, pmid = {27708547}, issn = {1473-5504}, support = {R01 HL055268/HL/NHLBI NIH HHS/United States ; //United States NHLBI/ ; }, abstract = {A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges.}, }
@article {pmid27690269, year = {2016}, author = {McIlroy, SE and Gillette, P and Cunning, R and Klueter, A and Capo, T and Baker, AC and Coffroth, MA}, title = {The effects of Symbiodinium (Pyrrhophyta) identity on growth, survivorship, and thermal tolerance of newly settled coral recruits.}, journal = {Journal of phycology}, volume = {52}, number = {6}, pages = {1114-1124}, doi = {10.1111/jpy.12471}, pmid = {27690269}, issn = {1529-8817}, mesh = {Animals ; Anthozoa/growth &amp; development/*physiology ; Dinoflagellida/*physiology ; Florida ; Species Specificity ; *Symbiosis ; *Thermotolerance ; }, abstract = {For many coral species, the obligate association with phylogenetically diverse algal endosymbiont species is dynamic in time and space. Here, we used controlled laboratory inoculations of newly settled, aposymbiotic corals (Orbicella faveolata) with two cultured species of algal symbiont (Symbiodinium microadriaticum and S. minutum) to examine the role of symbiont identity on growth, survivorship, and thermal tolerance of the coral holobiont. We evaluated these data in the context of Symbiodinium photophysiology for 9 months post-settlement and also during a 5-d period of elevated temperatures Our data show that recruits that were inoculated with S. minutum grew significantly slower than those inoculated with S. microadriaticum (occasionally co-occurring with S. minutum), but that there was no difference in survivorship of O. faveolata polyps infected with Symbiodinium. However, photophysiological metrics (∆Fv/F'm, the efficiency with which available light is used to drive photosynthesis and α, the maximum light utilization coefficient) were higher in those slower growing recruits containing S. minutum. These findings suggest that light use (i.e., photophysiology) and carbon acquisition by the coral host (i.e., host growth) are decoupled, but did not distinguish the source of this difference. Neither Symbiodinium treatment demonstrated a significant negative effect of a 5-d exposure to temperatures as high as 32°C under low light conditions similar to those measured at settlement habitats.}, }
@article {pmid27690185, year = {2016}, author = {Rubio-Portillo, E and Santos, F and Martínez-García, M and de Los Ríos, A and Ascaso, C and Souza-Egipsy, V and Ramos-Esplá, AA and Anton, J}, title = {Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4564-4578}, doi = {10.1111/1462-2920.13548}, pmid = {27690185}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Mediterranean Sea ; Vibrio/isolation &amp; purification/physiology ; }, abstract = {Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future.}, }
@article {pmid27688961, year = {2016}, author = {Wada, N and Pollock, FJ and Willis, BL and Ainsworth, T and Mano, N and Bourne, DG}, title = {In situ visualization of bacterial populations in coral tissues: pitfalls and solutions.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2424}, pmid = {27688961}, issn = {2167-8359}, abstract = {In situ visualization of microbial communities within their natural habitats provides a powerful approach to explore complex interactions between microorganisms and their macroscopic hosts. Specifically, the application of fluorescence in situ hybridization (FISH) to simultaneously identify and visualize diverse microbial taxa associated with coral hosts, including symbiotic algae (Symbiodinium), Bacteria, Archaea, Fungi and protists, could help untangle the structure and function of these diverse taxa within the coral holobiont. However, the application of FISH approaches to coral samples is constrained by non-specific binding of targeted rRNA probes to cellular structures within the coral animal tissues (including nematocysts, spirocysts, granular gland cells within the gastrodermis and cnidoglandular bands of mesenterial filaments). This issue, combined with high auto-fluorescence of both host tissues and endosymbiotic dinoflagellates (Symbiodinium), make FISH approaches for analyses of coral tissues challenging. Here we outline the major pitfalls associated with applying FISH to coral samples and describe approaches to overcome these challenges.}, }
@article {pmid27668211, year = {2016}, author = {Miller, WB}, title = {The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life.}, journal = {Frontiers in pediatrics}, volume = {4}, number = {}, pages = {96}, pmid = {27668211}, issn = {2296-2360}, abstract = {All eukaryotic organisms are holobionts representing complex collaborations between the entire microbiome of each eukaryote and its innate cells. These linked constituencies form complex localized and interlocking ecologies in which the specific microbial constituents and their relative abundance differ substantially according to age and environmental exposures. Rapid advances in microbiology and genetic research techniques have uncovered a significant previous underestimate of the extent of that microbial contribution and its metabolic and developmental impact on holobionts. Therefore, a re-calibration of the neonatal period is suggested as a transitional phase in development that includes the acquisition of consequential collaborative microbial life from extensive environmental influences. These co-dependent, symbiotic relationships formed in the fetal and neonatal stages extend into adulthood and even across generations.}, }
@article {pmid27643794, year = {2016}, author = {Ueda, Y and Frindte, K and Knief, C and Ashrafuzzaman, M and Frei, M}, title = {Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0163178}, pmid = {27643794}, issn = {1932-6203}, mesh = {Bacteria/genetics/*metabolism ; Oryza/*metabolism/microbiology ; Ozone/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to changes of the function of the communities.}, }
@article {pmid27630618, year = {2016}, author = {Francino, MP and Medina, M}, title = {Editorial: Recent Advances in Symbiosis Research: Integrative Approaches.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1331}, doi = {10.3389/fmicb.2016.01331}, pmid = {27630618}, issn = {1664-302X}, }
@article {pmid27617200, year = {2016}, author = {Burcelin, R}, title = {Gut microbiota and immune crosstalk in metabolic disease.}, journal = {Molecular metabolism}, volume = {5}, number = {9}, pages = {771-781}, pmid = {27617200}, issn = {2212-8778}, abstract = {BACKGROUND: Gut microbiota is considered as a major regulator of metabolic disease. This reconciles the notion of metabolic inflammation and the epidemic development of the disease. In addition to evidence showing that a specific gut microbiota characterizes patients with obesity, type 2 diabetes, and hepatic steatosis, the mechanisms causal to the disease could be related to the translocation of microbiota from the gut to the tissues, inducing inflammation. The mechanisms regulating such a process are based on the crosstalk between the gut microbiota and the host immune system. The hologenome theory of evolution supports this concept and implies that therapeutic strategies aiming to control glycemia should take into account both the gut microbiota and the host immune system.<br><br>SCOPE OF REVIEW: This review discusses the latest evidence regarding the bidirectional impact of the gut microbiota on host immune system crosstalk for the control of metabolic disease, hyperglycemia, and obesity. To avoid redundancies with the literature, we will focus our attention on the intestinal immune system, identifying evidence for the generation of novel therapeutic strategies, which could be based on the control of the translocation of gut bacteria to tissues. Such novel strategies should hamper the role played by gut microbiota dysbiosis on the development of metabolic inflammation.<br><br>MAJOR CONCLUSIONS: Recent evidence in rodents allows us to conclude that an impaired intestinal immune system characterizes and could be causal in the development of metabolic disease. The fine understanding of the molecular mechanisms should allow for the development of a first line of treatment for metabolic disease and its co-morbidities. This article is part of a special issue on microbiota.}, }
@article {pmid27602023, year = {2016}, author = {Hahn, MA and Dheilly, NM}, title = {Experimental Models to Study the Role of Microbes in Host-Parasite Interactions.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1300}, pmid = {27602023}, issn = {1664-302X}, abstract = {Until recently, parasitic infections have been primarily studied as interactions between the parasite and the host, leaving out crucial players: microbes. The recent realization that microbes play key roles in the biology of all living organisms is not only challenging our understanding of host-parasite evolution, but it also provides new clues to develop new therapies and remediation strategies. In this paper we provide a review of promising and advanced experimental organismal systems to examine the dynamic of host-parasite-microbe interactions. We address the benefits of developing new experimental models appropriate to this new research area and identify systems that offer the best promises considering the nature of the interactions among hosts, parasites, and microbes. Based on these systems, we identify key criteria for selecting experimental models to elucidate the fundamental principles of these complex webs of interactions. It appears that no model is ideal and that complementary studies should be performed on different systems in order to understand the driving roles of microbes in host and parasite evolution.}, }
@article {pmid27581522, year = {2016}, author = {Rouco, M and Haley, ST and Dyhrman, ST}, title = {Microbial diversity within the Trichodesmium holobiont.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5151-5160}, doi = {10.1111/1462-2920.13513}, pmid = {27581522}, issn = {1462-2920}, mesh = {*Biodiversity ; Nitrogen/metabolism ; Nitrogen Fixation ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Trichodesmium/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Nitrogen-fixing cyanobacteria in the genus Trichodesmium play a critical role in the productivity of the tropical and subtropical oligotrophic oceans. The ecological success of these populations is likely associated with the diverse microbial interactions occurring within the Trichodesmium holobiont, especially between Trichodesmium and heterotrophic bacterial epibionts. Yet, the composition of the Trichodesmium holobiont and the processes governing microbial assemblage are not well documented. Here, we used high-resolution 16S rDNA amplicon sequencing to examine the diversity of Trichodesmium and associated epibionts across different ocean regions and colony morphologies (puffs and rafts). Trichodesmium Clade I (i.e., T. thiebautii-like) dominated the colonies in all ocean basins regardless of morphology, although the Trichodesmium community structure significantly varied between morphologies in some regions. On average, Alphaproteobacteria (i.e., Thalassobius), Gammaproteobacteria (i.e., Pseudoalteromonas), Sphingobacteria (i.e., Microscilla and Vibrio) and Flavobacteria dominated the epibiont communities, but community composition and structure significantly differed between regions. Epibionts from the two colony morphologies were taxonomically and functionally distinct in the North Atlantic and North Pacific. These findings suggest that the colony types might define two distinct niches and that epibiont assemblage might be driven in part by selective processes, where epibionts are selected according to their influence on colony metabolism.}, }
@article {pmid27551278, year = {2016}, author = {Amin, AK and Feng, G and Al-Saari, N and Meirelles, PM and Yamazaki, Y and Mino, S and Thompson, FL and Sawabe, T and Sawabe, T}, title = {The First Temporal and Spatial Assessment of Vibrio Diversity of the Surrounding Seawater of Coral Reefs in Ishigaki, Japan.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1185}, pmid = {27551278}, issn = {1664-302X}, abstract = {Coral reefs perform a major role in regulating marine biodiversity and serve as hotspot for highly dynamic and diverse microbiomes as holobionts. Corals around Ishigaki, however, are at risk due to tremendous stressors including elevation of seawater temperature, eutrophication and so on. However, no information is currently available on how Vibrio diversity fluctuates spatially and temporally due to environmental determinants in Ishigaki coral reef ecosystems. The aim of this study is to elucidate spatiotemporal Vibrio diversity dynamic at both community and population levels and to assess the environmental drivers correlated to Vibrio abundance and diversity. The Vibrio community identified based on pyrH gene phylogeny of 685 isolates from seawater directly connecting to Ishigaki coral holobionts consisted of 22 known and 12 potential novel Vibrionaceae species. The most prominent species were V. hyugaensis, V. owensii and V. harveyi followed by V. maritimus/V. variabillis, V. campbellii, V. coralliilyticus, and Photobacterium rosenbergii. The Vibrio community fluctuations, assessed by PCoA with UniFrac distance and clustering with Euclidiean distance were varied less not only by year but also by site. Interestingly, significant positive correlation was observed between rising seawater temperature and the abundance of V. campbellii (r = 0.62; P < 0.05) whereas the opposite was observed for V. owensii (r = -0.58; P < 0.05) and the C6 group of V. hyugaensis (r = -0.62; P < 0.05). AdaptML-based microhabitat differentiation revealed that V. harveyi, V. campbellii, P. rosenbergii, and V. coralliilyticus populations were less-ecologically distinctive whereas V. astriarenae and V. ishigakensis were ecologically diverse. This knowledge could be important clue for the future actions of coral conservation.}, }
@article {pmid27507098, year = {2016}, author = {Schnorr, SL and Sankaranarayanan, K and Lewis, CM and Warinner, C}, title = {Insights into human evolution from ancient and contemporary microbiome studies.}, journal = {Current opinion in genetics &amp; development}, volume = {41}, number = {}, pages = {14-26}, pmid = {27507098}, issn = {1879-0380}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Ecology ; *Evolution, Molecular ; Humans ; Microbiota/*genetics ; Primates/genetics/*microbiology ; }, abstract = {Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.}, }
@article {pmid27492757, year = {2016}, author = {Garcia, GD and Santos, Ede O and Sousa, GV and Zingali, RB and Thompson, CC and Thompson, FL}, title = {Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensis.}, journal = {Molecular ecology}, volume = {25}, number = {18}, pages = {4632-4644}, doi = {10.1111/mec.13775}, pmid = {27492757}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*genetics/*microbiology ; Bacteria/*classification ; Brazil ; Proteomics ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Infectious diseases such as white plague syndrome (WPS) and black band disease (BBD) have caused massive coral loss worldwide. We performed a metaproteomic study on the Abrolhos coral Mussismilia braziliensis to define the types of proteins expressed in healthy corals compared to WPS- and BBD-affected corals. A total of 6363 MS/MS spectra were identified as 361 different proteins. Healthy corals had a set of proteins that may be considered markers of holobiont homoeostasis, including tubulin, histone, Rab family, ribosomal, peridinin-chlorophyll a-binding protein, F0F1-type ATP synthase, alpha-iG protein, calmodulin and ADP-ribosylation factor. Cnidaria proteins found in healthy M. braziliensis were associated with Cnidaria-Symbiodinium endosymbiosis and included chaperones (hsp70, hsp90 and calreticulin), structural and membrane modelling proteins (actin) and proteins with functions related to intracellular vesicular traffic (Rab7 and ADP-ribosylation factor 1) and signal transduction (14-3-3 protein and calmodulin). WPS resulted in a clear shift in the predominance of proteins, from those related to aerobic nitrogen-fixing bacteria (i.e. Rhizobiales, Sphingomonadales and Actinomycetales) in healthy corals to those produced by facultative/anaerobic sulphate-reducing bacteria (i.e. Enterobacteriales, Alteromonadales, Clostridiales and Bacteroidetes) in WPS corals. BBD corals developed a diverse community dominated by cyanobacteria and sulphur cycle bacteria. Hsp60, hsp90 and adenosylhomocysteinase proteins were produced mainly by cyanobacteria in BBD corals, which is consistent with elevated oxidative stress in hydrogen sulphide- and cyanotoxin-rich environments. This study demonstrates the usefulness of metaproteomics for gaining better comprehension of coral metabolic status in health and disease, especially in reef systems such as the Abrolhos that are suffering from the increase in global and local threatening events.}, }
@article {pmid27486438, year = {2016}, author = {Seston, SL and Beinart, RA and Sarode, N and Shockey, AC and Ranjan, P and Ganesh, S and Girguis, PR and Stewart, FJ}, title = {Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1074}, pmid = {27486438}, issn = {1664-302X}, abstract = {Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.}, }
@article {pmid27485233, year = {2016}, author = {Mansour, TA and Rosenthal, JJ and Brown, CT and Roberson, LM}, title = {Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages.}, journal = {GigaScience}, volume = {5}, number = {1}, pages = {33}, pmid = {27485233}, issn = {2047-217X}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/genetics/*growth &amp; development/parasitology ; Caribbean Region ; Coral Reefs ; Dinoflagellida/*genetics/physiology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Gene Library ; Sequence Analysis, RNA/*methods ; Symbiosis ; }, abstract = {BACKGROUND: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host-symbiont interactions.<br><br>FINDINGS: A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases.<br><br>CONCLUSIONS: This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.}, }
@article {pmid27482741, year = {2016}, author = {Bourne, DG and Morrow, KM and Webster, NS}, title = {Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {317-340}, doi = {10.1146/annurev-micro-102215-095440}, pmid = {27482741}, issn = {1545-3251}, mesh = {Animals ; Anthozoa/genetics/*microbiology/*physiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Coral Reefs ; Ecosystem ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Microbiota ; }, abstract = {Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.}, }
@article {pmid27468993, year = {2017}, author = {Bandyopadhyay, P and Bhuyan, SK and Yadava, PK and Varma, A and Tuteja, N}, title = {Emergence of plant and rhizospheric microbiota as stable interactomes.}, journal = {Protoplasma}, volume = {254}, number = {2}, pages = {617-626}, pmid = {27468993}, issn = {1615-6102}, mesh = {Ecosystem ; *Microbial Interactions ; *Microbiota ; Models, Biological ; Plants/*microbiology ; *Rhizosphere ; }, abstract = {The growing human population and depletion of resources have necessitated development of sustainable agriculture. Beneficial plant-microbe associations have been known for quite some time now. To maintain sustainability, one could show better reliance upon beneficial attributes of the rhizosphere microbiome. To harness the best agronomic traits, understanding the entire process of recruitment, establishment, and maintenance of microbiota as stable interactome within the rhizosphere is important. In this article, we highlight the process of recruitment and establishment of microbiota within rhizosphere. Further, we have discussed the interlinkages and the ability of multiple (microbial and plant) partners to interact with one another forming a stable plant holobiont system. Lastly, we address the possibility of exploring the knowledge gained from the holobiont system to tailor the rhizosphere microbiome for better productivity and maintenance of agroecosystems. The article provide new insights into the broad principles of stable plant-microbe interactions which could be useful for sustaining agriculture and food security.}, }
@article {pmid27446031, year = {2016}, author = {Egan, S and Gardiner, M}, title = {Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {991}, pmid = {27446031}, issn = {1664-302X}, abstract = {With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.}, }
@article {pmid27418200, year = {2016}, author = {Mitter, B and Pfaffenbichler, N and Sessitsch, A}, title = {Plant-microbe partnerships in 2020.}, journal = {Microbial biotechnology}, volume = {9}, number = {5}, pages = {635-640}, pmid = {27418200}, issn = {1751-7915}, mesh = {Agriculture/*methods/trends ; *Ecosystem ; Plants/*microbiology ; }, abstract = {The plant holobiont comprises the plant and its associated microbiota, which interact with each other and determine holobiont functioning and plant performance. We have started to understand the complexity of the involved microorganisms and their interactions, however, we need more research on plant-microbiome interactions to understand holobiont functioning. By 2020 we expect that our knowledge on these interactions will have considerably increased facilitating crop management practices based on the interactions of the plant holobiont.}, }
@article {pmid27415413, year = {2016}, author = {Scheidegger, C}, title = {As thick as three in a bed.}, journal = {Molecular ecology}, volume = {25}, number = {14}, pages = {3261-3263}, doi = {10.1111/mec.13710}, pmid = {27415413}, issn = {1365-294X}, mesh = {Ascomycota ; Chlorophyta/classification ; Lichens/*microbiology ; *Phylogeny ; Symbiosis ; }, abstract = {During the evolution of the lichen symbiosis, shifts from one main type of photobiont to another were infrequent (Miadlikowska et al.) but some remarkable transitions from green algal to diazotrophic cyanobacterial photobionts are known from unrelated fungal clades within the ascomycetes. Cyanobacterial, including tripartite, associations (green algal and cyanobacterial photobionts in one lichen individual) facilitate these holobionts to live as C- and N-autotrophs. Tripartite lichens are among the most productive lichens, which provide N-fertilization to forest ecosystems under oceanic climates (Peltigerales) or deliver low, but ecologically significant N-input into subarctic and alpine soil communities (Lecanorales, Agyriales). In this issue of Molecular Ecology, Schneider et al. (2016) mapped morphometric data against an eight-locus fungal phylogeny across a transition of photobiont interactions from green algal to a tripartite association and used a phylogenetic comparative framework to explore the role of nitrogen-fixing cyanobacteria in size differences in the Trapelia-Placopsis clade (Agyriales). Within the group of tripartite species, the volume of cyanobacteria-containing structures (cephalodia) correlates with thallus thickness in both phylogenetic generalized least squares and phylogenetic generalized linear mixed-effects analyses, and the fruiting body core volume increased ninefold. The authors conclude that cyanobacterial symbiosis appears to have enabled lichens to overcome size constraints in oligotrophic environments such as rock surfaces. The Trapelia-Placopsis clade analyzed by Schneider et al. (2016) is an exciting example of interactions between ecology, phylogeny and lichen biology including development - from thin crustose green algal microlichens to thick placodioid, tripartite macrolichens: as thick as three in a bed (Scott).}, }
@article {pmid27392086, year = {2017}, author = {Neave, MJ and Rachmawati, R and Xun, L and Michell, CT and Bourne, DG and Apprill, A and Voolstra, CR}, title = {Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {186-200}, pmid = {27392086}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/classification/*microbiology ; Coral Reefs ; Gammaproteobacteria/classification/genetics/isolation &amp; purification/*physiology ; Genotype ; In Situ Hybridization, Fluorescence ; *Symbiosis ; }, abstract = {Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.}, }
@article {pmid27375564, year = {2016}, author = {Laffy, PW and Wood-Charlson, EM and Turaev, D and Weynberg, KD and Botté, ES and van Oppen, MJ and Webster, NS and Rattei, T}, title = {HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {822}, pmid = {27375564}, issn = {1664-302X}, abstract = {Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.}, }
@article {pmid27349680, year = {2016}, author = {Wiegertjes, GF and Lee, WJ}, title = {Preface to the special issue: Intestinal immunity.}, journal = {Developmental and comparative immunology}, volume = {64}, number = {}, pages = {1}, doi = {10.1016/j.dci.2016.06.007}, pmid = {27349680}, issn = {1879-0089}, mesh = {Animals ; Fish Diseases/*immunology ; Fish Proteins ; Fishes/*immunology ; Host-Pathogen Interactions ; Humans ; *Immunity, Mucosal ; Immunoglobulins/metabolism ; Infections/*immunology ; Insecta/*immunology ; Intestinal Mucosa/*immunology ; Pest Control ; *Physiology, Comparative ; }, }
@article {pmid27281649, year = {2016}, author = {Chen, X and Lee, KA and Ren, X and Ryu, JC and Kim, G and Ryu, JH and Lee, WJ and Yoon, J}, title = {Synthesis of a highly HOCl-selective fluorescent probe and its use for imaging HOCl in cells and organisms.}, journal = {Nature protocols}, volume = {11}, number = {7}, pages = {1219-1228}, pmid = {27281649}, issn = {1750-2799}, mesh = {Animals ; Cells, Cultured ; Drosophila/chemistry/microbiology ; Fluorescent Dyes/chemical synthesis/*chemistry ; Hypochlorous Acid/*analysis ; Intestines/chemistry/microbiology ; Mice ; Mice, Inbred C57BL ; Microscopy, Confocal/methods ; Neutrophils/chemistry/cytology ; Optical Imaging/*methods ; Rhodamines/chemical synthesis/*chemistry ; }, abstract = {During infection, nicotinamide adenine dinucleotide phosphate-oxidase of innate immune cells generates important microbicidal reactive oxygen species (ROS) such as hypochlorous acid (HOCl) to kill the invading pathogens. However, excess amounts of HOCl induce oxidative damage of functional biomolecules such as DNA and proteins, which may cause chronic inflammatory diseases. Herein, we outline protocols for the preparation of a rhodamine-based HOCl probe, as well as applications thereof, with which to detect HOCl in living cells and organisms. The probe (R19S) can be prepared from a commercially available rhodamine, rhodamine 6G, in two steps. When R19S is treated with HOCl, the sulfur atom is replaced by an oxygen atom, resulting in opening of the lactone ring; thus, nonfluorescent R19S is converted to highly fluorescent rhodamine 19 (R19). R19S exhibits high selectivity for HOCl over other ROS and high sensitivity in a weakly acidic environment. In addition, we describe fluorescence imaging assays of HOCl in mouse neutrophils and Drosophila targeted using this probe. The approximate amount of time required to synthesize the probe is 2-3 d, after which it can be used for up to 5 h in the bioimaging of living cells.}, }
@article {pmid27264698, year = {2016}, author = {Ribes, M and Calvo, E and Movilla, J and Logares, R and Coma, R and Pelejero, C}, title = {Restructuring of the sponge microbiome favors tolerance to ocean acidification.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {536-544}, doi = {10.1111/1758-2229.12430}, pmid = {27264698}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Animals ; Hydrogen-Ion Concentration ; *Microbiota ; Oceans and Seas ; Porifera/drug effects/*microbiology/*physiology ; Seawater/*chemistry ; Survival Analysis ; }, abstract = {Ocean acidification is increasing and affects many marine organisms. However, certain sponge species can withstand low-pH conditions. This may be related to their complex association with microbes. We hypothesized that species with greater microbial diversity may develop functional redundancy that could enable the holobiont to survive even if particular microbes are lost at low-pH conditions. We evaluated the effects of acidification on the growth and associated microbes of three ubiquitous Mediterranean sponges by exposing them to the present pH level and that predicted for the year 2100. We found marked differences among the species in the acquisition of new microbes, being high in Dysidea avara, moderate in Agelas oroides and null in Chondrosia reniformis; however, we did not observe variation in the overall microbiome abundance, richness or diversity. The relative abilities to alter the microbiomes contributes to survivorship in an OA scenario as demonstrated by lowered pH severely affecting the growth of C. reniformis, halving that of A. oroides, and unaffecting D. avara. Our results indicate that functional stability of the sponge holobiont to withstand future OA is species-specific and is linked to the species' ability to use horizontal transmission to modify the associated microbiome to adapt to environmental change.}, }
@article {pmid27263657, year = {2016}, author = {van de Water, JA and Melkonian, R and Junca, H and Voolstra, CR and Reynaud, S and Allemand, D and Ferrier-Pagès, C}, title = {Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {27277}, pmid = {27263657}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Mediterranean Sea ; Microbiota ; Oceanospirillaceae/classification/genetics/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; Spirochaeta/classification/genetics/*isolation &amp; purification ; Symbiosis ; }, abstract = {Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species' bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans.}, }
@article {pmid27234003, year = {2016}, author = {Cardini, U and van Hoytema, N and Bednarz, VN and Rix, L and Foster, RA and Al-Rshaidat, MM and Wild, C}, title = {Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2620-2633}, doi = {10.1111/1462-2920.13385}, pmid = {27234003}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa/metabolism/microbiology/parasitology ; Bacteria/growth &amp; development/*metabolism ; Dinoflagellida/growth &amp; development/*metabolism ; Global Warming ; Heterotrophic Processes ; Hot Temperature ; Microbiota/physiology ; Nitrogen Fixation/*physiology ; Photosynthesis/physiology ; Stress, Physiological/physiology ; Symbiosis/physiology ; }, abstract = {Coral holobionts (i.e., coral-algal-prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral-associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.}, }
@article {pmid27230747, year = {2016}, author = {Maistrenko, OM and Serga, SV and Vaiserman, AM and Kozeretska, IA}, title = {Longevity-modulating effects of symbiosis: insights from Drosophila-Wolbachia interaction.}, journal = {Biogerontology}, volume = {17}, number = {5-6}, pages = {785-803}, doi = {10.1007/s10522-016-9653-9}, pmid = {27230747}, issn = {1573-6768}, mesh = {Aging/*physiology ; Animals ; Bacterial Proteins/metabolism ; Drosophila/*microbiology/*physiology ; Drosophila Proteins/metabolism ; Longevity/*physiology ; Models, Biological ; Symbiosis/*physiology ; Wolbachia/*physiology ; }, abstract = {Microbial communities are known to significantly affect various fitness components and survival of their insect hosts, including Drosophila. The composition of symbiotic microbiota has been shown to change with the host's aging. It is unclear whether these changes are caused by the aging process or, vice versa, they affect the host's aging and longevity. Recent findings indicate that fitness and lifespan of Drosophila are affected by endosymbiotic bacteria Wolbachia. These effects, however, are inconsistent and have been reported both to extend and shorten longevity. The main molecular pathways underlying the lifespan-modulating effects of Wolbachia remain unclear, however insulin/insulin-like growth factor, immune deficiency, ecdysteroid synthesis and signaling and c-Jun N-terminal kinase pathways as well as heat shock protein synthesis and autophagy have been proposed to play a role. Here we revise the current evidence that elucidates the impact of Wolbachia endosymbionts on the aging processes in Drosophila.}, }
@article {pmid27213462, year = {2016}, author = {Miller, WB}, title = {Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, pmid = {27213462}, issn = {2079-7737}, abstract = {As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.}, }
@article {pmid27174263, year = {2016}, author = {Gálvez, EJ and Carrillo-Castro, K and Zárate, L and Güiza, L and Pieper, DH and García-Bonilla, E and Salazar, M and Junca, H}, title = {Draft Genome Sequence of Bacillus licheniformis CG-B52, a Highly Virulent Bacterium of Pacific White Shrimp (Litopenaeus vannamei), Isolated from a Colombian Caribbean Aquaculture Outbreak.}, journal = {Genome announcements}, volume = {4}, number = {3}, pages = {}, pmid = {27174263}, issn = {2169-8287}, abstract = {Bacillus licheniformis strain CG-B52 was isolated as the etiological agent producing a self-limited outbreak of high mortalities in commercial Litopenaeus vannamei culture ponds on the Colombian Caribbean coast in 2005. Here, we report its draft genome and three novel extrachromosomal elements that it harbors.}, }
@article {pmid27160191, year = {2016}, author = {Dirksen, P and Marsh, SA and Braker, I and Heitland, N and Wagner, S and Nakad, R and Mader, S and Petersen, C and Kowallik, V and Rosenstiel, P and Félix, MA and Schulenburg, H}, title = {The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {38}, pmid = {27160191}, issn = {1741-7007}, mesh = {Animals ; Antifungal Agents/metabolism ; Caenorhabditis elegans/growth &amp; development/*microbiology ; Life Cycle Stages ; *Microbiota ; *Models, Biological ; Phenotype ; Proteobacteria/isolation &amp; purification/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics.<br><br>RESULTS: Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo.<br><br>CONCLUSION: This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions.}, }
@article {pmid27148918, year = {2016}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Do microbiotas warm their hosts?.}, journal = {Gut microbes}, volume = {7}, number = {4}, pages = {283-285}, pmid = {27148918}, issn = {1949-0984}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Energy Metabolism ; Gastrointestinal Tract/metabolism/*microbiology ; Hot Temperature ; Humans ; Insecta/microbiology ; *Microbiota ; Plants/microbiology ; }, abstract = {All natural animals and plants are holobionts, consisting of a host and abundant and diverse microbiota. During the last 20 years, numerous studies have shown that microbiotas participate in the ability of their hosts to survive and reproduce in a particular environment in many ways, including contributing to their morphology, development, behavior, physiology, resistance to disease and to their evolution. Here we posit another possible contribution of microbiotas to their hosts, which has been underexplored - the generation of heat. We estimate that microbial metabolism in the human gut, for example, produces 61 kcal/h, which corresponds to approximately 70% of the total heat production of an average person at rest.}, }
@article {pmid27148239, year = {2016}, author = {Aires, T and Serrão, EA and Engelen, AH}, title = {Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {559}, pmid = {27148239}, issn = {1664-302X}, abstract = {As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.}, }
@article {pmid27148067, year = {2016}, author = {Hawkins, TD and Hagemeyer, JC and Hoadley, KD and Marsh, AG and Warner, ME}, title = {Partitioning of Respiration in an Animal-Algal Symbiosis: Implications for Different Aerobic Capacity between Symbiodinium spp.}, journal = {Frontiers in physiology}, volume = {7}, number = {}, pages = {128}, pmid = {27148067}, issn = {1664-042X}, abstract = {Cnidarian-dinoflagellate symbioses are ecologically important and the subject of much investigation. However, our understanding of critical aspects of symbiosis physiology, such as the partitioning of total respiration between the host and symbiont, remains incomplete. Specifically, we know little about how the relationship between host and symbiont respiration varies between different holobionts (host-symbiont combinations). We applied molecular and biochemical techniques to investigate aerobic respiratory capacity in naturally symbiotic Exaiptasia pallida sea anemones, alongside animals infected with either homologous ITS2-type A4 Symbiodinium or a heterologous isolate of Symbiodinium minutum (ITS2-type B1). In naturally symbiotic anemones, host, symbiont, and total holobiont mitochondrial citrate synthase (CS) enzyme activity, but not host mitochondrial copy number, were reliable predictors of holobiont respiration. There was a positive association between symbiont density and host CS specific activity (mg protein(-1)), and a negative correlation between host- and symbiont CS specific activities. Notably, partitioning of total CS activity between host and symbiont in this natural E. pallida population was significantly different to the host/symbiont biomass ratio. In re-infected anemones, we found significant between-holobiont differences in the CS specific activity of the algal symbionts. Furthermore, the relationship between the partitioning of total CS activity and the host/symbiont biomass ratio differed between holobionts. These data have broad implications for our understanding of cnidarian-algal symbiosis. Specifically, the long-held assumption of equivalency between symbiont/host biomass and respiration ratios can result in significant overestimation of symbiont respiration and potentially erroneous conclusions regarding the percentage of carbon translocated to the host. The interspecific variability in symbiont aerobic capacity provides further evidence for distinct physiological differences that should be accounted for when studying diverse host-symbiont combinations.}, }
@article {pmid27122568, year = {2016}, author = {Quinn, RA and Vermeij, MJ and Hartmann, AC and Galtier d'Auriac, I and Benler, S and Haas, A and Quistad, SD and Lim, YW and Little, M and Sandin, S and Smith, JE and Dorrestein, PC and Rohwer, F}, title = {Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1829}, pages = {}, pmid = {27122568}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/genetics/microbiology/*physiology ; Biological Evolution ; *Coral Reefs ; Lipids/*physiology ; Metabolomics ; Models, Biological ; Platelet Activating Factor/analogs &amp; derivatives/genetics/physiology ; Rhodophyta/physiology ; Symbiosis/physiology ; Transcriptome ; }, abstract = {Holobionts are assemblages of microbial symbionts and their macrobial host. As extant representatives of some of the oldest macro-organisms, corals and algae are important for understanding how holobionts develop and interact with one another. Using untargeted metabolomics, we show that non-self interactions altered the coral metabolome more than self-interactions (i.e. different or same genus, respectively). Platelet activating factor (PAF) and Lyso-PAF, central inflammatory modulators in mammals, were major lipid components of the coral holobionts. When corals were damaged during competitive interactions with algae, PAF increased along with expression of the gene encoding Lyso-PAF acetyltransferase; the protein responsible for converting Lyso-PAF to PAF. This shows that self and non-self recognition among some of the oldest extant holobionts involve bioactive lipids identical to those in highly derived taxa like humans. This further strengthens the hypothesis that major players of the immune response evolved during the pre-Cambrian.}, }
@article {pmid27103626, year = {2016}, author = {Webster, NS and Thomas, T}, title = {The Sponge Hologenome.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00135-16}, pmid = {27103626}, issn = {2150-7511}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Genome, Bacterial ; Microbial Consortia ; Porifera/*microbiology/physiology ; Symbiosis ; }, abstract = {A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host's phenotype and evolution. In the process, an era of "holobiont" research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge's phenotype in fact act on the genomic interplay between the different components of the holobiont.}, }
@article {pmid27092120, year = {2016}, author = {Lawler, SN and Kellogg, CA and France, SC and Clostio, RW and Brooke, SD and Ross, SW}, title = {Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {458}, pmid = {27092120}, issn = {1664-302X}, abstract = {Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.}, }
@article {pmid27092109, year = {2016}, author = {Saurav, K and Bar-Shalom, R and Haber, M and Burgsdorf, I and Oliviero, G and Costantino, V and Morgenstern, D and Steindler, L}, title = {In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {416}, pmid = {27092109}, issn = {1664-302X}, abstract = {Owing to the extensive development of drug resistance in pathogens against the available antibiotic arsenal, antimicrobial resistance is now an emerging major threat to public healthcare. Anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. One promising example of this therapeutic concept targets bacterial quorum sensing (QS), because QS controls many virulence factors responsible for bacterial infections. Marine sponges and their associated bacteria are considered a still untapped source for unique chemical leads with a wide range of biological activities. In the present study, we screened extracts of 14 sponge species collected from the Red and Mediterranean Sea for their quorum-quenching (QQ) potential. Half of the species showed QQ activity in at least 2 out of 3 replicates. Six out of the 14 species were selected for bacteria isolation, to test for QQ activity also in isolates, which, once cultured, represent an unlimited source of compounds. We show that ≈20% of the isolates showed QQ activity based on a Chromobacterium violaceum CV026 screen, and that the presence or absence of QQ activity in a sponge extract did not correlate with the abundance of isolates with the same activity from the same sponge species. This can be explained by the unknown source of QQ compounds in sponge-holobionts (host or symbionts), and further by the possible non-symbiotic nature of bacteria isolated from sponges. The potential symbiotic nature of the isolates showing QQ activity was tested according to the distribution and abundance of taxonomically close bacterial Operational Taxonomic Units (OTUs) in a dataset including 97 sponge species and 178 environmental samples (i.e., seawater, freshwater, and marine sediments). Most isolates were found not to be enriched in sponges and may simply have been trapped in the filtration channels of the sponge at the time of collection. Our results highlight potential for QQ-bioactive lead molecules for anti-virulence therapy both from sponges and the bacteria isolated thereof, independently on the symbiotic nature of the latter.}, }
@article {pmid27084955, year = {2016}, author = {Collier, RJ and Casadevall, A}, title = {The Holobiont/Hologenome Concept Series.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00605-16}, doi = {10.1128/mBio.00605-16}, pmid = {27084955}, issn = {2150-7511}, mesh = {Editorial Policies ; *Genome ; Humans ; *Symbiosis ; }, }
@article {pmid27074334, year = {2016}, author = {Swain, TD and Vega-Perkins, JB and Oestreich, WK and Triebold, C and DuBois, E and Henss, J and Baird, A and Siple, M and Backman, V and Marcelino, L}, title = {Coral bleaching response index: a new tool to standardize and compare susceptibility to thermal bleaching.}, journal = {Global change biology}, volume = {22}, number = {7}, pages = {2475-2488}, pmid = {27074334}, issn = {1365-2486}, support = {R01 CA128641/CA/NCI NIH HHS/United States ; R01 EB003682/EB/NIBIB NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*physiology ; Coral Reefs ; Ecology/*methods ; Microalgae/*physiology ; Models, Theoretical ; *Symbiosis ; }, abstract = {As coral bleaching events become more frequent and intense, our ability to predict and mitigate future events depends upon our capacity to interpret patterns within previous episodes. Responses to thermal stress vary among coral species; however the diversity of coral assemblages, environmental conditions, assessment protocols, and severity criteria applied in the global effort to document bleaching patterns creates challenges for the development of a systemic metric of taxon-specific response. Here, we describe and validate a novel framework to standardize bleaching response records and estimate their measurement uncertainties. Taxon-specific bleaching and mortality records (2036) of 374 coral taxa (during 1982-2006) at 316 sites were standardized to average percent tissue area affected and a taxon-specific bleaching response index (taxon-BRI) was calculated by averaging taxon-specific response over all sites where a taxon was present. Differential bleaching among corals was widely variable (mean taxon-BRI = 25.06 ± 18.44%, ±SE). Coral response may differ because holobionts are biologically different (intrinsic factors), they were exposed to different environmental conditions (extrinsic factors), or inconsistencies in reporting (measurement uncertainty). We found that both extrinsic and intrinsic factors have comparable influence within a given site and event (60% and 40% of bleaching response variance of all records explained, respectively). However, when responses of individual taxa are averaged across sites to obtain taxon-BRI, differential response was primarily driven by intrinsic differences among taxa (65% of taxon-BRI variance explained), not conditions across sites (6% explained), nor measurement uncertainty (29% explained). Thus, taxon-BRI is a robust metric of intrinsic susceptibility of coral taxa. Taxon-BRI provides a broadly applicable framework for standardization and error estimation for disparate historical records and collection of novel data, allowing for unprecedented accuracy in parameterization of mechanistic and predictive models and conservation plans.}, }
@article {pmid27047481, year = {2016}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {371}, pmid = {27047481}, issn = {1664-302X}, abstract = {It has been proposed that the chemical composition of a coral's mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26 to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed that, at lower temperatures, the main components of mucus were N-acetyl glucosamine and C6 sugars, but these constituted a significantly lower proportion of the mucus in thermally stressed corals. The change in the mucus composition coincided with a shift from a γ-Proteobacteria- to a Verrucomicrobiae- and α-Proteobacteria-dominated community in the coral mucus. Bacteria in the class Cyanobacteria also started to become prominent in the mucus when the coral was thermally stressed. The increase in the relative abundance of the Verrucomicrobiae at higher temperature was strongly associated with a change in the proportion of fucose, glucose, and mannose in the mucus. Increase in the relative abundance of α-Proteobacteria were associated with GalNAc and glucose, while the drop in relative abundance of γ-Proteobacteria at high temperature coincided with changes in fucose and mannose. Cyanobacteria were highly associated with arabinose and xylose. Changes in mucus composition and the bacterial community in the mucus layer occurred at 29°C, which were prior to visual signs of coral bleaching at 31°C. A compositional change in the coral mucus, induced by thermal stress could therefore be a key factor leading to a shift in the associated bacterial community. This, in turn, has the potential to impact the physiological function of the coral holobiont.}, }
@article {pmid27039196, year = {2016}, author = {Shapira, M}, title = {Gut Microbiotas and Host Evolution: Scaling Up Symbiosis.}, journal = {Trends in ecology &amp; evolution}, volume = {31}, number = {7}, pages = {539-549}, doi = {10.1016/j.tree.2016.03.006}, pmid = {27039196}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Microbiota ; *Symbiosis ; }, abstract = {Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.}, }
@article {pmid27036743, year = {2015}, author = {Berlanga, M}, title = {Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {18}, number = {3}, pages = {159-169}, doi = {10.2436/20.1501.01.246.}, pmid = {27036743}, issn = {1139-6709}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Cockroaches/metabolism/*microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Isoptera/metabolism/*microbiology ; Phylogeny ; Symbiosis ; Wood/metabolism/microbiology ; }, abstract = {Animal hosts typically have strong specificity for microbial symbionts and their functions. The symbiotic relationships have enhanced the limited metabolic networks of most eukaryotes by contributing several prokaryotic metabolic capabilities, such as methanogenesis, chemolithoautotrophy, nitrogen assimilation, etc. This review will examine the characteristics that determine bacterial "fidelity" to certain groups of animals (e.g., xylophagous insects, such as termites and cockroaches) over generations and throughout evolution. The hindgut bacteria of wood-feeding termites and cockroaches belong to several phyla, including Proteobacteria, especially Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, Verrucomicrobia, and Actinobacteria, as detected by 16S rRNA. Termites effectively feed on many types of lignocelluloses assisted by their gut microbial symbionts. Although the community structures differ between the hosts (termites and cockroaches), with changes in the relative abundances of particular bacterial taxa, the composition of the bacterial community could reflect at least in part the host evolution in that the microbiota may derive from the microbiota of a common ancestor. Therefore, factors other than host phylogeny, such as diet could have had strong influence in shaping the bacterial community structure.}, }
@article {pmid27034285, year = {2016}, author = {Douglas, AE and Werren, JH}, title = {Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02099}, pmid = {27034285}, issn = {2150-7511}, mesh = {Animals ; Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; *Symbiosis ; }, abstract = {The advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems. Some now question whether existing conceptual frameworks are adequate to explain microbe-host systems. One popular paradigm is the "holobiont-hologenome," which argues that a host and its microbiome evolve as a single cooperative unit of selection (i.e., a superorganism). We argue that the hologenome is based on overly restrictive assumptions which render it an approach of little research utility. A host plus its microbiome is more effectively viewed as an ecological community of organisms that encompasses a broad range of interactions (parasitic to mutualistic), patterns of transmission (horizontal to vertical), and levels of fidelity among partners. The hologenome requires high partner fidelity if it is to evolve as a unit. However, even when this is achieved by particular host-microbe pairs, it is unlikely to hold for the entire host microbiome, and therefore the community is unlikely to evolve as a hologenome. Both mutualistic and antagonistic (fitness conflict) evolution can occur among constituent members of the community, not just adaptations at the "hologenome" level, and there is abundant empirical evidence for such divergence of selective interests among members of host-microbiome communities. We believe that the concepts and methods of ecology, genetics, and evolutionary biology will continue to provide a well-grounded intellectual framework for researching host-microbiome communities, without recourse to the limiting assumption that selection acts predominantly at the holobiont level.}, }
@article {pmid27034284, year = {2016}, author = {Shropshire, JD and Bordenstein, SR}, title = {Speciation by Symbiosis: the Microbiome and Behavior.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e01785}, pmid = {27034284}, issn = {2150-7511}, mesh = {Animals ; Behavior ; Behavior, Animal ; *Genetic Speciation ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species.}, }
@article {pmid27034283, year = {2016}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Microbes Drive Evolution of Animals and Plants: the Hologenome Concept.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e01395}, pmid = {27034283}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; Recombination, Genetic ; Selection, Genetic ; *Symbiosis ; }, abstract = {The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.}, }
@article {pmid27034282, year = {2016}, author = {McFall-Ngai, M}, title = {Introduction to the Hologenome Special Series.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00371}, doi = {10.1128/mBio.00371-16}, pmid = {27034282}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; Selection, Genetic ; *Symbiosis ; }, }
@article {pmid27019410, year = {2016}, author = {Haichar, FEZ and Heulin, T and Guyonnet, JP and Achouak, W}, title = {Stable isotope probing of carbon flow in the plant holobiont.}, journal = {Current opinion in biotechnology}, volume = {41}, number = {}, pages = {9-13}, doi = {10.1016/j.copbio.2016.02.023}, pmid = {27019410}, issn = {1879-0429}, mesh = {Carbon Isotopes/*analysis ; Isotope Labeling/*methods ; Plant Roots/*metabolism/microbiology ; Plants/*metabolism/microbiology ; *Soil Microbiology ; }, abstract = {Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with [13]C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.}, }
@article {pmid27014194, year = {2016}, author = {Ding, JY and Shiu, JH and Chen, WM and Chiang, YR and Tang, SL}, title = {Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {251}, pmid = {27014194}, issn = {1664-302X}, abstract = {The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.}, }
@article {pmid26979110, year = {2016}, author = {Greer, R and Dong, X and Morgun, A and Shulzhenko, N}, title = {Investigating a holobiont: Microbiota perturbations and transkingdom networks.}, journal = {Gut microbes}, volume = {7}, number = {2}, pages = {126-135}, pmid = {26979110}, issn = {1949-0984}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; U01 AI109695/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/*microbiology ; Computational Biology ; Host-Pathogen Interactions/*drug effects ; Humans ; Microbiota/*drug effects ; }, abstract = {The scientific community has recently come to appreciate that, rather than existing as independent organisms, multicellular hosts and their microbiota comprise a complex evolving superorganism or metaorganism, termed a holobiont. This point of view leads to a re-evaluation of our understanding of different physiological processes and diseases. In this paper we focus on experimental and computational approaches which, when combined in one study, allowed us to dissect mechanisms (traditionally named host-microbiota interactions) regulating holobiont physiology. Specifically, we discuss several approaches for microbiota perturbation, such as use of antibiotics and germ-free animals, including advantages and potential caveats of their usage. We briefly review computational approaches to characterize the microbiota and, more importantly, methods to infer specific components of microbiota (such as microbes or their genes) affecting host functions. One such approach called transkingdom network analysis has been recently developed and applied in our study. (1) Finally, we also discuss common methods used to validate the computational predictions of host-microbiota interactions using in vitro and in vivo experimental systems.}, }
@article {pmid26953605, year = {2016}, author = {Glasl, B and Herndl, GJ and Frade, PR}, title = {The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2280-2292}, pmid = {26953605}, issn = {1751-7370}, support = {I 486/FWF_/Austrian Science Fund FWF/Austria ; P 23234/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Coral Reefs ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.}, }
@article {pmid26926518, year = {2016}, author = {Ryu, T and Seridi, L and Moitinho-Silva, L and Oates, M and Liew, YJ and Mavromatis, C and Wang, X and Haywood, A and Lafi, FF and Kupresanin, M and Sougrat, R and Alzahrani, MA and Giles, E and Ghosheh, Y and Schunter, C and Baumgarten, S and Berumen, ML and Gao, X and Aranda, M and Foret, S and Gough, J and Voolstra, CR and Hentschel, U and Ravasi, T}, title = {Hologenome analysis of two marine sponges with different microbiomes.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {158}, pmid = {26926518}, issn = {1471-2164}, support = {BB/G022771/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Genome ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Models, Genetic ; Molecular Sequence Annotation ; Porifera/*genetics/*microbiology ; Receptors, Scavenger/genetics ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: Sponges (Porifera) harbor distinct microbial consortia within their mesohyl interior. We herein analysed the hologenomes of Stylissa carteri and Xestospongia testudinaria, which notably differ in their microbiome content.<br><br>RESULTS: Our analysis revealed that S. carteri has an expanded repertoire of immunological domains, specifically Scavenger Receptor Cysteine-Rich (SRCR)-like domains, compared to X. testudinaria. On the microbial side, metatranscriptome analyses revealed an overrepresentation of potential symbiosis-related domains in X. testudinaria.<br><br>CONCLUSIONS: Our findings provide genomic insights into the molecular mechanisms underlying host-symbiont coevolution and may serve as a roadmap for future hologenome analyses.}, }
@article {pmid26925036, year = {2016}, author = {Zozaya-Valdés, E and Roth-Schulze, AJ and Thomas, T}, title = {Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {161}, pmid = {26925036}, issn = {1664-302X}, abstract = {In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga's chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.}, }
@article {pmid26904096, year = {2016}, author = {Negri, I and Jablonka, E}, title = {Editorial: Epigenetics as a Deep Intimate Dialogue between Host and Symbionts.}, journal = {Frontiers in genetics}, volume = {7}, number = {}, pages = {7}, pmid = {26904096}, issn = {1664-8021}, }
@article {pmid26904020, year = {2016}, author = {Fonseca-García, C and Coleman-Derr, D and Garrido, E and Visel, A and Tringe, SG and Partida-Martínez, LP}, title = {The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {150}, pmid = {26904020}, issn = {1664-302X}, abstract = {Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.}, }
@article {pmid26868597, year = {2016}, author = {Parkinson, JE and Baumgarten, S and Michell, CT and Baums, IB and LaJeunesse, TC and Voolstra, CR}, title = {Gene Expression Variation Resolves Species and Individual Strains among Coral-Associated Dinoflagellates within the Genus Symbiodinium.}, journal = {Genome biology and evolution}, volume = {8}, number = {3}, pages = {665-680}, pmid = {26868597}, issn = {1759-6653}, mesh = {Animals ; Anthozoa/*genetics/physiology ; Coral Reefs ; Dinoflagellida/*genetics/physiology ; Gene Expression Regulation ; Genotype ; Photosynthesis/genetics ; *Phylogeny ; Symbiosis/*genetics ; Transcriptome/genetics ; }, abstract = {Reef-building corals depend on symbiotic mutualisms with photosynthetic dinoflagellates in the genus Symbiodinium. This large microalgal group comprises many highly divergent lineages ("Clades A-I") and hundreds of undescribed species. Given their ecological importance, efforts have turned to genomic approaches to characterize the functional ecology of Symbiodinium. To date, investigators have only compared gene expression between representatives from separate clades-the equivalent of contrasting genera or families in other dinoflagellate groups-making it impossible to distinguish between clade-level and species-level functional differences. Here, we examined the transcriptomes of four species within one Symbiodinium clade (Clade B) at ∼20,000 orthologous genes, as well as multiple isoclonal cell lines within species (i.e., cultured strains). These species span two major adaptive radiations within Clade B, each encompassing both host-specialized and ecologically cryptic taxa. Species-specific expression differences were consistently enriched for photosynthesis-related genes, likely reflecting selection pressures driving niche diversification. Transcriptional variation among strains involved fatty acid metabolism and biosynthesis pathways. Such differences among individuals are potentially a major source of physiological variation, contributing to the functional diversity of coral holobionts composed of unique host-symbiont genotype pairings. Our findings expand the genomic resources available for this important symbiont group and emphasize the power of comparative transcriptomics as a method for studying speciation processes and interindividual variation in nonmodel organisms.}, }
@article {pmid26865302, year = {2016}, author = {Gardner, SG and Nielsen, DA and Laczka, O and Shimmon, R and Beltran, VH and Ralph, PJ and Petrou, K}, title = {Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1824}, pages = {}, pmid = {26865302}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/*physiology ; Dinoflagellida/physiology ; Glutathione/*metabolism ; *Salinity ; Species Specificity ; Stress, Physiological ; Sulfonium Compounds/*metabolism ; Superoxide Dismutase/*metabolism ; Symbiosis ; }, abstract = {Corals are among the most active producers of dimethylsulfoniopropionate (DMSP), a key molecule in marine sulfur cycling, yet the specific physiological role of DMSP in corals remains elusive. Here, we examine the oxidative stress response of three coral species (Acropora millepora, Stylophora pistillata and Pocillopora damicornis) and explore the antioxidant role of DMSP and its breakdown products under short-term hyposalinity stress. Symbiont photosynthetic activity declined with hyposalinity exposure in all three reef-building corals. This corresponded with the upregulation of superoxide dismutase and glutathione in the animal host of all three species. For the symbiont component, there were differences in antioxidant regulation, demonstrating differential responses to oxidative stress between the Symbiodinium subclades. Of the three coral species investigated, only A. millepora provided any evidence of the role of DMSP in the oxidative stress response. Our study reveals variability in antioxidant regulation in corals and highlights the influence life-history traits, and the subcladal differences can have on coral physiology. Our data expand on the emerging understanding of the role of DMSP in coral stress regulation and emphasizes the importance of exploring both the host and symbiont responses for defining the threshold of the coral holobiont to hyposalinity stress.}, }
@article {pmid26843939, year = {2016}, author = {Rouzé, H and Lecellier, G and Saulnier, D and Berteaux-Lecellier, V}, title = {Symbiodinium clades A and D differentially predispose Acropora cytherea to disease and Vibrio spp. colonization.}, journal = {Ecology and evolution}, volume = {6}, number = {2}, pages = {560-572}, pmid = {26843939}, issn = {2045-7758}, abstract = {Coral disease outbreaks have increased over the last three decades, but their causal agents remain mostly unclear (e.g., bacteria, viruses, fungi, protists). This study details a 14-month-long survey of coral colonies in which observations of the development of disease was observed in nearly half of the sampled colonies. A bimonthly qPCR method was used to quantitatively and qualitatively evaluate Symbiodinium assemblages of tagged colonies, and to detect the presence of Vibrio spp. Firstly, our data showed that predisposition to disease development in general, and, more specifically, infection by Vibrio spp. in Acropora cytherea depended on which clades of Symbiodinium were harbored. In both cases, harboring clade D rather than A was beneficial to the coral host. Secondly, the detection of Vibrio spp. in only colonies that developed disease strongly suggests opportunistic traits of the bacteria. Finally, even if sporadic cases of switching and probably shuffling were observed, this long-term survey does not suggest specific-clade recruitment in response to stressors. Altogether, our results demonstrate that the fitness of the coral holobiont depends on its initial consortium of Symbiodinium, which is distinct among colonies, rather than a temporary adaptation achieved through acquiring different Symbiodinium clades.}, }
@article {pmid26840035, year = {2016}, author = {Röthig, T and Ochsenkühn, MA and Roik, A and van der Merwe, R and Voolstra, CR}, title = {Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome.}, journal = {Molecular ecology}, volume = {25}, number = {6}, pages = {1308-1323}, pmid = {26840035}, issn = {1365-294X}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/classification ; DNA, Bacterial/genetics ; *Microbiota ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Salt Tolerance ; Symbiosis ; }, abstract = {Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.}, }
@article {pmid26818718, year = {2016}, author = {Dessaux, Y and Grandclément, C and Faure, D}, title = {Engineering the Rhizosphere.}, journal = {Trends in plant science}, volume = {21}, number = {3}, pages = {266-278}, doi = {10.1016/j.tplants.2016.01.002}, pmid = {26818718}, issn = {1878-4372}, mesh = {Botany/*methods ; Microbiota ; Plants/microbiology ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.}, }
@article {pmid26788878, year = {2016}, author = {Agler, MT and Ruhe, J and Kroll, S and Morhenn, C and Kim, ST and Weigel, D and Kemen, EM}, title = {Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation.}, journal = {PLoS biology}, volume = {14}, number = {1}, pages = {e1002352}, pmid = {26788878}, issn = {1545-7885}, mesh = {Arabidopsis/genetics/*microbiology ; Bacteria ; Basidiomycota/physiology ; Endophytes/physiology ; *Microbiota ; Oomycetes/physiology ; }, abstract = {Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe-microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial "hubs," are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on "hub" microbes, which, via microbe-microbe interactions, transmit the effects to the microbial community. We analyzed two "hub" microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial "hubs" and their importance in phyllosphere microbiome structuring has crucial implications for plant-pathogen and microbe-microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via "hub" microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome "keystone" pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.}, }
@article {pmid26779145, year = {2015}, author = {Lachnit, T and Thomas, T and Steinberg, P}, title = {Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1489}, pmid = {26779145}, issn = {1664-302X}, abstract = {Marine seaweeds are holobionts comprised of the macroalgal hosts and their associated microbiota. While the composition of the bacterial component of seaweed microbiomes is increasingly studied, almost nothing is known about the presence, diversity and composition of viruses in macroalgae in situ. In this study, we characterize for the first time the viruses associated with a red macroalga, Delisea pulchra. Using transmission electron microscopy we identified diverse morphotypes of virus-like particles in D. pulchra ranging from icosahedral to bacilliform to coiled pleomorphic as well as bacteriophages. Virome sequencing revealed the presence of a diverse group of dsRNA viruses affiliated to the genus Totivirus, known to infect plant pathogenic fungi. We further identified a ssRNA virus belonging to the order Picornavirales with a close phylogenetic relationship to a pathogenic virus infecting marine diatoms. The results of this study shed light on a so far neglected part of the seaweed holobiont, and suggest that some of the identified viruses may be possible pathogens for a host that is already known to be significantly impacted by bacterial infections.}, }
@article {pmid26774999, year = {2016}, author = {Corel, E and Lopez, P and Méheust, R and Bapteste, E}, title = {Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.}, journal = {Trends in microbiology}, volume = {24}, number = {3}, pages = {224-237}, pmid = {26774999}, issn = {1878-4380}, mesh = {Bacteria/*genetics ; *Evolution, Molecular ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genome ; *Models, Genetic ; Symbiosis ; }, abstract = {The tree model and tree-based methods have played a major, fruitful role in evolutionary studies. However, with the increasing realization of the quantitative and qualitative importance of reticulate evolutionary processes, affecting all levels of biological organization, complementary network-based models and methods are now flourishing, inviting evolutionary biology to experience a network-thinking era. We show how relatively recent comers in this field of study, that is, sequence-similarity networks, genome networks, and gene families-genomes bipartite graphs, already allow for a significantly enhanced usage of molecular datasets in comparative studies. Analyses of these networks provide tools for tackling a multitude of complex phenomena, including the evolution of gene transfer, composite genes and genomes, evolutionary transitions, and holobionts.}, }
@article {pmid26763678, year = {2016}, author = {Hacquard, S}, title = {Disentangling the factors shaping microbiota composition across the plant holobiont.}, journal = {The New phytologist}, volume = {209}, number = {2}, pages = {454-457}, doi = {10.1111/nph.13760}, pmid = {26763678}, issn = {1469-8137}, mesh = {Bacteria/genetics ; *Microbiota ; *Plants ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil Microbiology ; }, }
@article {pmid26759710, year = {2016}, author = {Lu, HL and Price, DR and Wikramanayake, A and Chang, CC and Wilson, AC}, title = {Ontogenetic differences in localization of glutamine transporter ApGLNT1 in the pea aphid demonstrate that mechanisms of host/symbiont integration are not similar in the maternal versus embryonic bacteriome.}, journal = {EvoDevo}, volume = {7}, number = {}, pages = {1}, pmid = {26759710}, issn = {2041-9139}, abstract = {BACKGROUND: Obligate intracellular symbionts of insects are metabolically and developmentally integrated with their hosts. Typically, reproduction fails in many insect nutritional endosymbioses when host insects are cured of their bacterial symbionts, and yet remarkably little is known about the processes that developmentally integrate host and symbiont. Here in the best studied insect obligate intracellular symbiosis, that of the pea aphid, Acyrthosiphon pisum, with the gammaproteobacterium Buchnera aphidicola, we tracked the expression and localization of amino acid transporter ApGLNT1 gene products during asexual embryogenesis. Recently being characterized as a glutamine transporter, ApGLNT1 has been proposed to be a key regulator of amino acid biosynthesis in A. pisum bacteriocytes. To determine when this important mediator of the symbiosis becomes expressed in aphid embryonic bacteriocytes, we applied whole-mount in situ hybridization and fluorescent immunostaining with a specific anti-ApGLNT1 antibody to detect the temporal and spatial expression of ApGLNT1 gene products during asexual embryogenesis.<br><br>RESULTS: During embryogenesis, ApGLNT1 mRNA and protein localize to the follicular epithelium that surrounds parthenogenetic viviparous embryos, where we speculate that it functions to supply developing embryos with glutamine from maternal hemolymph. Unexpectedly, in the embryonic bacteriome ApGLNT1 protein does not localize to the membrane of bacteriocytes, a pattern that leads us to conclude that the regulation of amino acid metabolism in the embryonic bacteriome mechanistically differs from that in the maternal bacteriome. Paralleling our earlier report of punctate cytoplasmic localization of ApGLNT1 in maternal bacteriocytes, we find ApGLNT1 protein localizing as cytoplasmic puncta throughout development in association with Buchnera.<br><br>CONCLUSIONS: Our work that documents ontogenetic shifts in the localization of ApGLNT1 protein in the host bacteriome demonstrates that maternal and embryonic bacteriomes are not equivalent. Significantly, the persistent punctate cytoplasmic localization of ApGLNT1 in association with Buchnera in embryos prior to bacteriocyte formation and later in both embryonic and maternal bacteriomes suggests that ApGLNT1 plays multiple roles in this symbiosis, roles that include amino acid transport and possibly nutrient sensing.}, }
@article {pmid26749251, year = {2016}, author = {Moore, A}, title = {Getting fat from an inflamed relationship? The revenge of the holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {2}, pages = {119}, doi = {10.1002/bies.201600001}, pmid = {26749251}, issn = {1521-1878}, mesh = {Anti-Bacterial Agents/adverse effects ; Food Additives/adverse effects ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/*etiology/*microbiology ; Intestines/microbiology ; Obesity/*etiology/*microbiology ; }, }
@article {pmid26739062, year = {2016}, author = {Poutahidis, T and Erdman, SE}, title = {Commensal bacteria modulate the tumor microenvironment.}, journal = {Cancer letters}, volume = {380}, number = {1}, pages = {356-358}, pmid = {26739062}, issn = {1872-7980}, support = {R01 CA108854/CA/NCI NIH HHS/United States ; U01 CA164337/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/immunology/metabolism/*pathogenicity ; *Cell Transformation, Neoplastic/immunology/metabolism/pathology ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Neoplasms/immunology/metabolism/*microbiology/pathology ; Risk Factors ; Signal Transduction ; Symbiosis ; *Tumor Microenvironment ; }, abstract = {It has been recently shown that gut microbes modulate whole host immune and hormonal factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. This raises the possibility that the tumor microenvironment interacts with broader systemic microbial-immune networks. These accumulated findings suggest novel therapeutic opportunities for holobiont engineering in emerging tumor microenvironments.}, }
@article {pmid26734000, year = {2015}, author = {Martin, M and Barbeyron, T and Martin, R and Portetelle, D and Michel, G and Vandenbol, M}, title = {The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1487}, pmid = {26734000}, issn = {1664-302X}, abstract = {Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (~25%) were found to act on at least one tested algal polysaccharide (agar, ι- or κ-carrageenan, or alginate). The isolates "active" on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren't identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies.}, }
@article {pmid26696324, year = {2016}, author = {Lema, KA and Clode, PL and Kilburn, MR and Thornton, R and Willis, BL and Bourne, DG}, title = {Imaging the uptake of nitrogen-fixing bacteria into larvae of the coral Acropora millepora.}, journal = {The ISME journal}, volume = {10}, number = {7}, pages = {1804-1808}, pmid = {26696324}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; In Situ Hybridization, Fluorescence ; Larva ; Nitrogen/*metabolism ; Nitrogen Fixation ; Nitrogen-Fixing Bacteria/*metabolism ; }, abstract = {Diazotrophic bacteria are instrumental in generating biologically usable forms of nitrogen by converting abundant dinitrogen gas (N2) into available forms, such as ammonium. Although nitrogen is crucial for coral growth, direct observation of associations between diazotrophs and corals has previously been elusive. We applied fluorescence in situ hybridization (FISH) and nanoscale secondary ion mass spectrometry to observe the uptake of (15)N-enriched diazotrophic Vibrio sp. isolated from Acropora millepora into conspecific coral larvae. Incorporation of Vibrio sp. cells was observed in coral larvae after 4-h incubation with enriched bacteria. Uptake was restricted to the aboral epidermis of larvae, where Vibrio cells clustered in elongated aggregations. Other bacterial associates were also observed in epidermal areas in FISH analyses. Although the fate and role of these bacteria requires additional investigation, this study describes a powerful approach to further explore cell associations and nutritional pathways in the early life stages of the coral holobiont.}, }
@article {pmid26659364, year = {2015}, author = {Kemp, DW and Rivers, AR and Kemp, KM and Lipp, EK and Porter, JW and Wares, JP}, title = {Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0143790}, pmid = {26659364}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Coral Reefs ; Florida ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, RNA ; }, abstract = {Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance), underside (low irradiance), and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.}, }
@article {pmid26658023, year = {2015}, author = {Fragoso Ados Santos, H and Duarte, GA and Rachid, CT and Chaloub, RM and Calderon, EN and Marangoni, LF and Bianchini, A and Nudi, AH and do Carmo, FL and van Elsas, JD and Rosado, AS and Castro, CB and Peixoto, RS}, title = {Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18268}, pmid = {26658023}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; *Biodegradation, Environmental ; *Biotransformation ; *Coral Reefs ; Hydrocarbons/metabolism ; *Microbiota ; *Petroleum Pollution ; Photochemical Processes ; *Probiotics ; Water Pollutants, Chemical ; }, abstract = {Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.}, }
@article {pmid26655037, year = {2015}, author = {Lee, KA and Kim, B and You, H and Lee, WJ}, title = {Uracil-induced signaling pathways for DUOX-dependent gut immunity.}, journal = {Fly}, volume = {9}, number = {3}, pages = {115-120}, pmid = {26655037}, issn = {1933-6942}, mesh = {Animals ; Cadherins/metabolism ; Calcium/metabolism ; Disease Resistance ; Drosophila/genetics/*immunology/metabolism ; Enterocytes/drug effects/immunology ; Gene Expression Regulation ; Hedgehog Proteins/metabolism ; MAP Kinase Signaling System ; Membrane Microdomains/metabolism/physiology ; *Models, Immunological ; NADPH Oxidases/metabolism/*physiology ; Phospholipase C beta/metabolism/physiology ; Signal Transduction ; Transcriptome/drug effects ; Uracil/*pharmacology/physiology ; }, abstract = {Intestinal dual oxidase (DUOX) activation is the first line of host defense against enteric infection in Drosophila. DUOX enzymatic activity is mainly controlled by phospholipase C-β (PLCβ)-dependent calcium mobilization, whereas DUOX gene expression is mainly controlled by the MEKK1-p38 mitogen-activated protein kinase pathway. Furthermore, bacterial-derived uracil molecules act as ligands for DUOX activation. However, our current understanding of uracil-induced signal transduction pathways remain incomplete. We have recently found that uracil stimulates Hedgehog signaling, which in turn upregulates cadherin99C (Cad99C) expression in enterocytes. Cad99C molecules, along with PLCβ and protein kinase C, induce the formation of signaling endosomes that facilitate intracellular calcium mobilization for DUOX activity. These observations illustrate the complexity of signaling cascades in uracil-induced signaling pathways. Here, we further demonstrated the role of lipid raft formation and calmodulin-dependent protein kinase-II on endosome formation and calcium mobilization, respectively. Moreover, we will provide a brief discussion on two different models for uracil recognition and uracil-induced DUOX activation in Drosophila enterocytes.}, }
@article {pmid26640464, year = {2015}, author = {Wong, AC and Holmes, A and Ponton, F and Lihoreau, M and Wilson, K and Raubenheimer, D and Simpson, SJ}, title = {Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1359}, pmid = {26640464}, issn = {1664-302X}, abstract = {The role of microbes as a part of animal systems has historically been an under-appreciated aspect of animal life histories. Recently, evidence has emerged that microbes have wide-ranging influences on animal behavior. Elucidating the complex relationships between host-microbe interactions and behavior requires an expanded ecological perspective, involving the host, the microbiome and the environment; which, in combination, is termed the holobiont. We begin by seeking insights from the literature on host-parasite interactions, then expand to consider networks of interactions between members of the microbial community. A central aspect of the environment is host nutrition. We describe how interactions between the nutrient environment, the metabolic and behavioral responses of the host and the microbiome can be studied using an integrative framework called nutritional geometry, which integrates and maps multiple aspects of the host and microbial response in multidimensional nutrient intake spaces.}, }
@article {pmid26636661, year = {2015}, author = {Moran, NA and Sloan, DB}, title = {The Hologenome Concept: Helpful or Hollow?.}, journal = {PLoS biology}, volume = {13}, number = {12}, pages = {e1002311}, pmid = {26636661}, issn = {1545-7885}, support = {R01 GM108477/GM/NIGMS NIH HHS/United States ; GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Genome ; *Genome, Microbial ; Genomics/*methods/trends ; Humans ; *Microbiota ; *Models, Genetic ; Symbiosis ; Terminology as Topic ; }, abstract = {With the increasing appreciation for the crucial roles that microbial symbionts play in the development and fitness of plant and animal hosts, there has been a recent push to interpret evolution through the lens of the "hologenome"--the collective genomic content of a host and its microbiome. But how symbionts evolve and, particularly, whether they undergo natural selection to benefit hosts are complex issues that are associated with several misconceptions about evolutionary processes in host-associated microbial communities. Microorganisms can have intimate, ancient, and/or mutualistic associations with hosts without having undergone natural selection to benefit hosts. Likewise, observing host-specific microbial community composition or greater community similarity among more closely related hosts does not imply that symbionts have coevolved with hosts, let alone that they have evolved for the benefit of the host. Although selection at the level of the symbiotic community, or hologenome, occurs in some cases, it should not be accepted as the null hypothesis for explaining features of host-symbiont associations.}, }
@article {pmid26598731, year = {2016}, author = {Eisthen, HL and Theis, KR}, title = {Animal-microbe interactions and the evolution of nervous systems.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1685}, pages = {20150052}, pmid = {26598731}, issn = {1471-2970}, mesh = {Animals ; *Bacteria ; Behavior, Animal ; *Biological Evolution ; Central Nervous System/*anatomy &amp; histology/*physiology ; Invertebrates/anatomy &amp; histology/*microbiology/physiology ; Vertebrates/anatomy &amp; histology/*microbiology/physiology ; }, abstract = {Animals ubiquitously interact with environmental and symbiotic microbes, and the effects of these interactions on animal physiology are currently the subject of intense interest. Nevertheless, the influence of microbes on nervous system evolution has been largely ignored. We illustrate here how taking microbes into account might enrich our ideas about the evolution of nervous systems. For example, microbes are involved in animals' communicative, defensive, predatory and dispersal behaviours, and have likely influenced the evolution of chemo- and photosensory systems. In addition, we speculate that the need to regulate interactions with microbes at the epithelial surface may have contributed to the evolutionary internalization of the nervous system.}, }
@article {pmid26568407, year = {2016}, author = {Mushegian, AA and Ebert, D}, title = {Rethinking "mutualism" in diverse host-symbiont communities.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {1}, pages = {100-108}, doi = {10.1002/bies.201500074}, pmid = {26568407}, issn = {1521-1878}, mesh = {Bacterial Physiological Phenomena/*genetics ; *Biological Evolution ; Ecosystem ; Eukaryota/genetics ; Microbiota/*genetics ; Symbiosis/*genetics ; }, abstract = {While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called "mutualistic" even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate. We suggest reserving the terms "mutualism" and "parasitism" for pairwise interactions where the relationship is largely independent of other species and can be verified by measuring the fitness effect experienced by both partners. In hosts with diverse microbial communities, we propose re-formulating some of the essential questions of symbiosis research - e.g. concerning specificity, transmission mode, and common evolutionary fates - as questions of community ecology and ecosystem function, allowing important biological interactions to be investigated without making assumptions about reciprocity. Understanding the fitness of host-associated bacteria is a crucial component of investigations into the role of microbes in eukaryote evolution.}, }
@article {pmid26556047, year = {2015}, author = {Shelburne, SA and Ajami, NJ and Chibucos, MC and Beird, HC and Tarrand, J and Galloway-Peña, J and Albert, N and Chemaly, RF and Ghantoji, SS and Marsh, L and Pemmaraju, N and Andreeff, M and Shpall, EJ and Wargo, JA and Rezvani, K and Alousi, A and Bruno, VM and Futreal, PA and Petrosino, JF and Kontoyiannis, DP}, title = {Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0139851}, pmid = {26556047}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01AI089891/AI/NIAID NIH HHS/United States ; R01 CA061508/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; U19AI110820/AI/NIAID NIH HHS/United States ; HHSN272200900009C//PHS HHS/United States ; HHSN272200900009C/AI/NIAID NIH HHS/United States ; R01 AI089891/AI/NIAID NIH HHS/United States ; }, mesh = {Antifungal Agents/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Chemotherapy-Induced Febrile Neutropenia ; Fungal Proteins/genetics ; Fungemia/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genome, Fungal ; Host-Pathogen Interactions ; Humans ; Leukemia, Myeloid, Acute/*complications ; Male ; Middle Aged ; Mucor/*genetics/isolation &amp; purification ; Mucormycosis/drug therapy/*microbiology ; Neoplasm Proteins/genetics ; Onychomycosis/complications ; Opportunistic Infections/drug therapy/*microbiology ; }, abstract = {Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.}, }
@article {pmid26555246, year = {2016}, author = {Hester, ER and Barott, KL and Nulton, J and Vermeij, MJ and Rohwer, FL}, title = {Stable and sporadic symbiotic communities of coral and algal holobionts.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1157-1169}, pmid = {26555246}, issn = {1751-7370}, mesh = {Algorithms ; Animals ; Anthozoa/*microbiology ; Archaea/*classification ; Bacteria/classification ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/analysis ; Environment ; Evolution, Molecular ; Fungi/classification ; *Microbiota ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Viruses/classification ; }, abstract = {Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial-temporally stable or species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadic symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution.}, }
@article {pmid26547794, year = {2016}, author = {Berg, G and Rybakova, D and Grube, M and Köberl, M}, title = {The plant microbiome explored: implications for experimental botany.}, journal = {Journal of experimental botany}, volume = {67}, number = {4}, pages = {995-1002}, pmid = {26547794}, issn = {1460-2431}, support = {J 3638/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Botany/*trends ; *Microbiota ; Plants/*microbiology ; }, abstract = {The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.}, }
@article {pmid26539166, year = {2015}, author = {Kuang, W and Li, J and Zhang, S and Long, L}, title = {Diversity and distribution of Actinobacteria associated with reef coral Porites lutea.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1094}, pmid = {26539166}, issn = {1664-302X}, abstract = {Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater.}, }
@article {pmid26536917, year = {2015}, author = {Zhang, Y and Ling, J and Yang, Q and Wen, C and Yan, Q and Sun, H and Van Nostrand, JD and Shi, Z and Zhou, J and Dong, J}, title = {The functional gene composition and metabolic potential of coral-associated microbial communities.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16191}, pmid = {26536917}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*genetics/*metabolism ; Carbon/metabolism ; Ecosystem ; Genetic Variation/genetics ; Homeostasis/genetics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems.}, }
@article {pmid26511052, year = {2015}, author = {Cardini, U and Bednarz, VN and Naumann, MS and van Hoytema, N and Rix, L and Foster, RA and Al-Rshaidat, MM and Wild, C}, title = {Functional significance of dinitrogen fixation in sustaining coral productivity under oligotrophic conditions.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1818}, pages = {20152257}, pmid = {26511052}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Chlorophyll/analysis ; Chlorophyll A ; Coral Reefs ; Dinoflagellida/*metabolism ; Indian Ocean ; Light ; Nitrogen/metabolism ; *Nitrogen Fixation ; Photosynthesis/physiology ; Seasons ; Symbiosis ; Temperature ; }, abstract = {Functional traits define species by their ecological role in the ecosystem. Animals themselves are host-microbe ecosystems (holobionts), and the application of ecophysiological approaches can help to understand their functioning. In hard coral holobionts, communities of dinitrogen (N2)-fixing prokaryotes (diazotrophs) may contribute a functional trait by providing bioavailable nitrogen (N) that could sustain coral productivity under oligotrophic conditions. This study quantified N2 fixation by diazotrophs associated with four genera of hermatypic corals on a northern Red Sea fringing reef exposed to high seasonality. We found N2 fixation activity to be 5- to 10-fold higher in summer, when inorganic nutrient concentrations were lowest and water temperature and light availability highest. Concurrently, coral gross primary productivity remained stable despite lower Symbiodinium densities and tissue chlorophyll a contents. In contrast, chlorophyll a content per Symbiodinium cell increased from spring to summer, suggesting that algal cells overcame limitation of N, an essential element for chlorophyll synthesis. In fact, N2 fixation was positively correlated with coral productivity in summer, when its contribution was estimated to meet 11% of the Symbiodinium N requirements. These results provide evidence of an important functional role of diazotrophs in sustaining coral productivity when alternative external N sources are scarce.}, }
@article {pmid26510159, year = {2015}, author = {Kaniewska, P and Chan, CK and Kline, D and Ling, EY and Rosic, N and Edwards, D and Hoegh-Guldberg, O and Dove, S}, title = {Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139223}, pmid = {26510159}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; Anthozoa/*genetics/*physiology ; Carbon Dioxide/analysis ; *Climate Change ; Gene Expression Profiling ; Gene Ontology ; *Oceans and Seas ; Protein Binding ; Protein Interaction Maps ; Seawater ; Temperature ; Transcriptome/*genetics ; }, abstract = {Tropical reef-building coral stress levels will intensify with the predicted rising atmospheric CO2 resulting in ocean temperature and acidification increase. Most studies to date have focused on the destabilization of coral-dinoflagellate symbioses due to warming oceans, or declining calcification due to ocean acidification. In our study, pH and temperature conditions consistent with the end-of-century scenarios of the Intergovernmental Panel on Climate Change (IPCC) caused major changes in photosynthesis and respiration, in addition to decreased calcification rates in the coral Acropora millepora. Population density of symbiotic dinoflagellates (Symbiodinium) under high levels of ocean acidification and temperature (Representative Concentration Pathway, RCP8.5) decreased to half of that found under present day conditions, with photosynthetic and respiratory rates also being reduced by 40%. These physiological changes were accompanied by evidence for gene regulation of calcium and bicarbonate transporters along with components of the organic matrix. Metatranscriptomic RNA-Seq data analyses showed an overall down regulation of metabolic transcripts, and an increased abundance of transcripts involved in circadian clock control, controlling the damage of oxidative stress, calcium signaling/homeostasis, cytoskeletal interactions, transcription regulation, DNA repair, Wnt signaling and apoptosis/immunity/ toxins. We suggest that increased maintenance costs under ocean acidification and warming, and diversion of cellular ATP to pH homeostasis, oxidative stress response, UPR and DNA repair, along with metabolic suppression, may underpin why Acroporid species tend not to thrive under future environmental stress. Our study highlights the potential increased energy demand when the coral holobiont is exposed to high levels of ocean warming and acidification.}, }
@article {pmid26497873, year = {2015}, author = {Parkinson, JE and Banaszak, AT and Altman, NS and LaJeunesse, TC and Baums, IB}, title = {Intraspecific diversity among partners drives functional variation in coral symbioses.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {15667}, pmid = {26497873}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/genetics/*physiology ; Climate ; *Cold Temperature ; Cold-Shock Response/genetics/*physiology ; Coral Reefs ; Dinoflagellida/chemistry/genetics/*physiology ; Gene Expression Regulation/*physiology ; Genetic Variation/genetics ; Microsatellite Repeats/genetics ; Photochemistry ; Symbiosis/*physiology ; }, abstract = {The capacity of coral-dinoflagellate mutualisms to adapt to a changing climate relies in part on standing variation in host and symbiont populations, but rarely have the interactions between symbiotic partners been considered at the level of individuals. Here, we tested the importance of inter-individual variation with respect to the physiology of coral holobionts. We identified six genetically distinct Acropora palmata coral colonies that all shared the same isoclonal Symbiodinium 'fitti' dinoflagellate strain. No other Symbiodinium could be detected in host tissues. We exposed fragments of each colony to extreme cold and found that the stress-induced change in symbiont photochemical efficiency varied up to 3.6-fold depending on host genetic background. The S. 'fitti' strain was least stressed when associating with hosts that significantly altered the expression of 184 genes under cold shock; it was most stressed in hosts that only adjusted 14 genes. Key expression differences among hosts were related to redox signaling and iron availability pathways. Fine-scale interactions among unique host colonies and symbiont strains provide an underappreciated source of raw material for natural selection in coral symbioses.}, }
@article {pmid26483769, year = {2015}, author = {Moreira, AP and Meirelles, PM and Santos, Ede O and Amado-Filho, GM and Francini-Filho, RB and Thompson, CC and Thompson, FL}, title = {Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1038}, pmid = {26483769}, issn = {1664-302X}, abstract = {The aim of this study was to investigate the planktonic and the holobiont Madracis decactis (Scleractinia) microbial diversity along a turbulence-driven upwelling event, in the world's most isolated tropical island, St Peter and St Paul Archipelago (SPSPA, Brazil). Twenty one metagenomes were obtained for seawater (N = 12), healthy and bleached holobionts (N = 9) before, during and after the episode of high seawater turbulence and upwelling. Microbial assemblages differed between low turbulence-low nutrient (LLR) and high-turbulence-high nutrient (HHR) regimes in seawater. During LLR there was a balance between autotrophy and heterotrophy in the bacterioplankton and the ratio cyanobacteria:heterotrophs ~1 (C:H). Prochlorales, unclassified Alphaproteobacteria and Euryarchaeota were the dominant bacteria and archaea, respectively. Basic metabolisms and cyanobacterial phages characterized the LLR. During HHR C:H < < 0.05 and Gammaproteobacteria approximated 50% of the most abundant organisms in seawater. Alteromonadales, Oceanospirillales, and Thaumarchaeota were the dominant bacteria and archaea. Prevailing metabolisms were related to membrane transport, virulence, disease, and defense. Phages targeting heterotrophs and virulence factor genes characterized HHR. Shifts were also observed in coral microbiomes, according to both annotation-indepent and -dependent methods. HHR bleached corals metagenomes were the most dissimilar and could be distinguished by their di- and tetranucleotides frequencies, Iron Acquision metabolism and virulence genes, such as V. cholerae-related virulence factors. The healthy coral holobiont was shown to be less sensitive to transient seawater-related perturbations than the diseased animals. A conceptual model for the turbulence-induced shifts is put forward.}, }
@article {pmid26478771, year = {2015}, author = {Hunt, T}, title = {The Microcosm within: An interview with William B. Miller, Jr., on the Extended Hologenome theory of evolution.}, journal = {Communicative &amp; integrative biology}, volume = {8}, number = {3}, pages = {e1000711}, pmid = {26478771}, issn = {1942-0889}, abstract = {There is a singular unifying reality underlying every biologic interaction on our planet. In immunology, that which does not kill you makes you different. -William B. Miller, Jr. We are experiencing a revolution in our understanding of inner space on a par with our exponentially increasing understanding of outer space. In biology, we are learning that the genetic and epigenetic complexity within organisms is far deeper than suspected. This is a key theme in William B. Miller Jr.'s book, The Microcosm Within: Evolution and Extinction in the Hologenome. We are learning also that a focus on the human genome alone is misleading when it comes to who we really are as biological entities, and in terms of how we and other creatures have evolved. Rather than being defined by the human genome alone, we are instead defined by the "hologenome," the sum of the human genome and the far larger genetic endowment of the microbiome and symbiotic communities that reside within and around us. Miller is a medical doctor previously in private practice in Pennsylvania and Phoenix, Arizona. This book is his first foray into evolutionary theory. His book could have been titled "The Origin of Variation" because this is his primary focus. He accepts that natural selection plays a role in evolution, but he demotes this mechanism to a less important role than the Modern Synthesis suggests. His main gripe, however, concerns random variation. He argues that random variation is unable to explain the origin and evolution of biological forms that we see in the world around us and in the historical record. Miller suggests that, rather than random variation as the engine of novelty, there is a creative impulse at the heart of cellular life, and even at the level of the genetic aggregate, that generates novelty on a regular basis. I probe this assertion in the interview below. He also highlights the strong role of "exogenous genetic assault" in variation and in his immunological model of evolution.}, }
@article {pmid26468740, year = {2015}, author = {Park, DY and Lee, WJ and Jang, IH and Lee, WJ}, title = {Got Lactobacillus? Commensals Power Growth.}, journal = {Cell host &amp; microbe}, volume = {18}, number = {4}, pages = {388-390}, doi = {10.1016/j.chom.2015.09.012}, pmid = {26468740}, issn = {1934-6069}, mesh = {Animals ; *Antibiosis ; Drosophila/*growth &amp; development/*microbiology ; Lactobacillus plantarum/*enzymology/*physiology ; Peptide Hydrolases/*metabolism ; *Symbiosis ; }, abstract = {Although Lactobacilli are generally considered probiotic agents in metazoans, the underlying molecular mechanisms are largely unknown. In this issue of Cell Host &amp; Microbe, Erkosar et al. (2015) reveal that a Drosophila gut commensal, Lactobacillus plantarum(WJL), promotes animal growth by enhancing the host's capacity for protein degradation.}, }
@article {pmid26451236, year = {2015}, author = {Meyer, JL and Dillard, BA and Rodgers, JM and Ritchie, KB and Paul, VJ and Teplitski, M}, title = {Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {75}, pmid = {26451236}, issn = {1944-3277}, abstract = {Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.}, }
@article {pmid26442023, year = {2015}, author = {Smith, DL and Subramanian, S and Lamont, JR and Bywater-Ekegärd, M}, title = {Signaling in the phytomicrobiome: breadth and potential.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {709}, pmid = {26442023}, issn = {1664-462X}, abstract = {Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.}, }
@article {pmid26441903, year = {2015}, author = {Minard, G and Tran, FH and Van, VT and Goubert, C and Bellet, C and Lambert, G and Kim, KL and Thuy, TH and Mavingui, P and Valiente Moro, C}, title = {French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {970}, pmid = {26441903}, issn = {1664-302X}, abstract = {The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.}, }
@article {pmid26414414, year = {2015}, author = {Blackall, LL and Wilson, B and van Oppen, MJ}, title = {Coral-the world's most diverse symbiotic ecosystem.}, journal = {Molecular ecology}, volume = {24}, number = {21}, pages = {5330-5347}, doi = {10.1111/mec.13400}, pmid = {26414414}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/genetics/*microbiology ; Archaea/classification ; Bacteria/*classification ; Biodiversity ; *Coral Reefs ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Dinoflagellida/*classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Zooxanthellate corals (i.e. those harbouring Symbiodinium) are the main builders of the world's shallow-water marine coral reefs. They represent intimate diverse symbioses between coral animals, single-celled photosynthetic dinoflagellates (Symbiodinium spp.), other microscopic eukaryotes, prokaryotes and viruses. Crabs and other crustaceans, worms, sponges, bivalves and hydrozoans, fishes, sea urchins, octopuses and sea stars are itinerant members of these 'rainforests of the sea'. This review focuses on the biodiversity of scleractinian coral animals and their best studied microscopic epi- and endosymbionts. In relation to coral-associated species diversity, Symbiodinium internal transcribed spacer region sequence types tally 10(2) -10(3) or up to ~15 different operational taxonomic units (OTUs, or putative species at the 97% sequence identity level; this cut-off was chosen based on intragenomic sequence diversity observed in monoclonal cultures) and prokaryotes (mostly bacterial) total 10(2) -10(4) OTUs. We analysed all publically accessible 16S rRNA gene sequence data and found Gammaproteobacteria were extremely abundant, followed by Alphaproteobacteria. Notably, Archaea were poorly represented and 'unassigned OTUs' were abundant in data generated by high-throughput DNA sequencing studies of corals. We outline and compare model systems that could be used in future studies of the coral holobiont. In our future directions, we recommend a global coral sampling effort including substantial attention being paid to method of coral tissue acquisition, which compartments (mucus, tissue, skeleton) to explore, broadening the holobiont members considered and linking biodiversity with functional investigations.}, }
@article {pmid26388838, year = {2015}, author = {Har, JY and Helbig, T and Lim, JH and Fernando, SC and Reitzel, AM and Penn, K and Thompson, JR}, title = {Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {818}, pmid = {26388838}, issn = {1664-302X}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; }, abstract = {We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.}, }
@article {pmid26311127, year = {2016}, author = {Meisterhans, G and Raymond, N and Girault, E and Lambert, C and Bourrasseau, L and de Montaudouin, X and Garabetian, F and Jude-Lemeilleur, F}, title = {Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {194-206}, pmid = {26311127}, issn = {1432-184X}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bivalvia/*microbiology ; *Microbiota ; Shellfish/*microbiology ; }, abstract = {Marine invertebrate microbiota has a key function in host physiology and health. To date, knowledge about bivalve microbiota is poorly documented except public health concerns. This study used a molecular approach to characterize the microbiota associated with the bivalve Manila clam (Ruditapes philippinarum) by determining (1) the difference among organs either or not under the influence of host habitat, (2) small-scale variability of microbiota, and (3) the experimental response of the Manila clam microbiota submitted to different lateral transmissions. These questions were investigated by sampling two groups of individuals living in contrasting habitats and carrying out a transplant experiment. Manila clam microbiota (i.e., bacterial community structure) was determined at organ-scale (gills, gut, and a pool of remaining tissues) by capillary electrophoresis DNA fingerprinting (CE fingerprinting). The Manila clam microbiota structure differed among organs indicating a selection of Manila clam microbiota at organ scale. Habitat strongly influenced gill and gut microbiota. In contrast, microbiota associated with remaining tissues was similar between group individuals suggesting that these communities are mostly autochthonous, i.e., Manila clam specific. Transplant experiment showed that improving living condition did not induce any change in microbiota associated with remaining tissues. In contrast, the reduction in individual habitat quality led to individuals in declining health as strongly suggested by the increase in phagocytosis activity and decrease in condition index together with the change in internal organ microbiota. This study provides a first description of the Manila clam holobiont which can withstand disturbance and respond opportunistically to improved environmental conditions.}, }
@article {pmid26310029, year = {2015}, author = {Provoro, NA and Tikhonovich, IA and Vorobyov, NI}, title = {[Symbiogenesis and Synthetic Evolutionary Theory: The Third Synthesis].}, journal = {Genetika}, volume = {51}, number = {6}, pages = {658-667}, pmid = {26310029}, issn = {0016-6758}, mesh = {*Evolution, Molecular ; *Genome, Plant ; Rhizobium/genetics ; Symbiosis/*genetics ; }, abstract = {Integration of the concepts of symbiogenesis and synthetic evolutionary theory is the main path for the development of evolutionary biology. It is based on the analysis of cooperative adaptations that evolve under the impact of symbiotic-specific selective pressures responsible for the formation of super-species hereditary systems--metagenomes, symbiogenomes, and hologenomes. The genetic integration of nonrelated organisms (symbiogenesis) is determined by the inheritance of microsymbionts by hosts resulted in the complication of mutualistic interactions according to the scheme: pleiotropic symbiosis --> mutual partner's exploitation --> interspecies altruism. This evolution may result in the loss of genetic individuality in microsymbionts; this loss is expressed as a deep reduction in their genomes. A significant number of these may be exported to the host, resulting in the transformation of symbiotic systems into novel, genetically integral organisms.}, }
@article {pmid26300848, year = {2015}, author = {Voss, JD and Leon, JC and Dhurandhar, NV and Robb, FT}, title = {Pawnobiome: manipulation of the hologenome within one host generation and beyond.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {697}, pmid = {26300848}, issn = {1664-302X}, }
@article {pmid26293603, year = {2016}, author = {Nogales, A and Nobre, T and Valadas, V and Ragonezi, C and Döring, M and Polidoros, A and Arnholdt-Schmitt, B}, title = {Can functional hologenomics aid tackling current challenges in plant breeding?.}, journal = {Briefings in functional genomics}, volume = {15}, number = {4}, pages = {288-297}, doi = {10.1093/bfgp/elv030}, pmid = {26293603}, issn = {2041-2657}, mesh = {Genomics/*methods ; Phenotype ; *Plant Breeding ; Plants/*genetics ; *Quantitative Trait Loci ; }, abstract = {Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs.}, }
@article {pmid26291447, year = {2015}, author = {Krediet, CJ and DeNofrio, JC and Caruso, C and Burriesci, MS and Cella, K and Pringle, JR}, title = {Rapid, Precise, and Accurate Counts of Symbiodinium Cells Using the Guava Flow Cytometer, and a Comparison to Other Methods.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135725}, pmid = {26291447}, issn = {1932-6203}, mesh = {Animals ; Cnidaria/cytology ; Dinoflagellida/cytology ; Flow Cytometry/*methods ; Symbiosis/physiology ; }, abstract = {In studies of both the establishment and breakdown of cnidarian-dinoflagellate symbiosis, it is often necessary to determine the number of Symbiodinium cells relative to the quantity of host tissue. Ideally, the methods used should be rapid, precise, and accurate. In this study, we systematically evaluated methods for sample preparation and storage and the counting of algal cells using the hemocytometer, a custom image-analysis program for automated counting of the fluorescent algal cells, the Coulter Counter, or the Millipore Guava flow-cytometer. We found that although other methods may have value in particular applications, for most purposes, the Guava flow cytometer provided by far the best combination of precision, accuracy, and efficient use of investigator time (due to the instrument's automated sample handling), while also allowing counts of algal numbers over a wide range and in small volumes of tissue homogenate. We also found that either of two assays of total homogenate protein provided a precise and seemingly accurate basis for normalization of algal counts to the total amount of holobiont tissue.}, }
@article {pmid26284777, year = {2015}, author = {Bordenstein, SR and Theis, KR}, title = {Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.}, journal = {PLoS biology}, volume = {13}, number = {8}, pages = {e1002226}, pmid = {26284777}, issn = {1545-7885}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Humans ; *Metagenome ; Microbiota/*genetics ; Mutation ; Plants/genetics ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., "holobionts." As such, their collective genomes forge a "hologenome," and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.}, }
@article {pmid29587997, year = {2015}, author = {Schwarz, RS and Huang, Q and Evans, JD}, title = {Hologenome theory and the honey bee pathosphere.}, journal = {Current opinion in insect science}, volume = {10}, number = {}, pages = {1-7}, doi = {10.1016/j.cois.2015.04.006}, pmid = {29587997}, issn = {2214-5753}, abstract = {Recent research has provided improved genome-level views of diversity across global honey bee populations, the gut microbiota residing within them, and the expanding pathosphere challenging honey bees. Different combinations of bee/microbiota/pathosphere genome complexes may explain regional variation in apiculture productivity and mortality. To understand this, we must consider management and research approaches in light of a hologenome paradigm: that honey bee fitness is determined by the composite bee and microbiota genomes. Only by considering the hologenome can we truly interpret and address impacts from the pathosphere, pesticides, toxins, nutrition, climate and other stressors affecting bee health.}, }
@article {pmid26177948, year = {2015}, author = {Kramer, P and Bressan, P}, title = {Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {10}, number = {4}, pages = {464-481}, doi = {10.1177/1745691615583131}, pmid = {26177948}, issn = {1745-6924}, mesh = {Animals ; Behavior/*physiology ; Brain/*microbiology/parasitology/*virology ; *Genomic Imprinting ; Humans ; *Microbiota ; *Viruses ; }, abstract = {Psychologists and psychiatrists tend to be little aware that (a) microbes in our brains and guts are capable of altering our behavior; (b) viral DNA that was incorporated into our DNA millions of years ago is implicated in mental disorders; (c) many of us carry the cells of another human in our brains; and (d) under the regulation of viruslike elements, the paternally inherited and maternally inherited copies of some genes compete for domination in the offspring, on whom they have opposite physical and behavioral effects. This article provides a broad overview, aimed at a wide readership, of the consequences of our coexistence with these selfish entities. The overarching message is that we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are.}, }
@article {pmid26148974, year = {2015}, author = {Marzinelli, EM and Campbell, AH and Zozaya Valdes, E and Vergés, A and Nielsen, S and Wernberg, T and de Bettignies, T and Bennett, S and Caporaso, JG and Thomas, T and Steinberg, PD}, title = {Continental-scale variation in seaweed host-associated bacterial communities is a function of host condition, not geography.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {4078-4088}, doi = {10.1111/1462-2920.12972}, pmid = {26148974}, issn = {1462-2920}, mesh = {Archaea/*classification/genetics ; Australia ; Bacteria/*classification/genetics ; Ecosystem ; Environment ; Geography ; Humans ; Kelp/*microbiology ; Microbiota/*genetics/physiology ; Phenotype ; Phylogeny ; Plankton/*microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Interactions between hosts and associated microbial communities can fundamentally shape the development and ecology of 'holobionts', from humans to marine habitat-forming organisms such as seaweeds. In marine systems, planktonic microbial community structure is mainly driven by geography and related environmental factors, but the large-scale drivers of host-associated microbial communities are largely unknown. Using 16S-rRNA gene sequencing, we characterized 260 seaweed-associated bacterial and archaeal communities on the kelp Ecklonia radiata from three biogeographical provinces spanning 10° of latitude and 35° of longitude across the Australian continent. These phylogenetically and taxonomically diverse communities were more strongly and consistently associated with host condition than geographical location or environmental variables, and a 'core' microbial community characteristic of healthy kelps appears to be lost when hosts become stressed. Microbial communities on stressed individuals were more similar to each other among locations than those on healthy hosts. In contrast to biogeographical patterns of planktonic marine microbial communities, host traits emerge as critical determinants of associated microbial community structure of these holobionts, even at a continental scale.}, }
@article {pmid26099965, year = {2015}, author = {Aires, T and Moalic, Y and Serrao, EA and Arnaud-Haond, S}, title = {Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa).}, journal = {FEMS microbiology ecology}, volume = {91}, number = {7}, pages = {}, doi = {10.1093/femsec/fiv067}, pmid = {26099965}, issn = {1574-6941}, mesh = {Animals ; Anthozoa ; Bacteria/*genetics ; Biodiversity ; Caulerpa/genetics/*microbiology ; Endophytes/*genetics ; Mediterranean Sea ; Microbial Consortia/*genetics ; Plants ; Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts (< 1% of the total community), (2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, which might represent environmentally acquired bacteria and (3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.}, }
@article {pmid26097896, year = {2015}, author = {Zhao, Y and Lukiw, WJ}, title = {Microbiome-generated amyloid and potential impact on amyloidogenesis in Alzheimer's disease (AD).}, journal = {Journal of nature and science}, volume = {1}, number = {7}, pages = {}, pmid = {26097896}, issn = {2377-2700}, support = {R01 AG018031/AG/NIA NIH HHS/United States ; R01 AG038834/AG/NIA NIH HHS/United States ; R01 EY006311/EY/NEI NIH HHS/United States ; }, abstract = {According to the 'amyloid cascade hypothesis of Alzheimer's disease' first proposed about 16 years ago, the accumulation of Aβ peptides in the human central nervous system (CNS) is the primary influence driving Alzheimer's disease (AD) pathogenesis, and Aβ peptide accretion is the result of an imbalance between Aβ peptide production and clearance. In the last 18 months multiple laboratories have reported two particularly important observations: (i) that because the microbes of the human microbiome naturally secrete large amounts of amyloid, lipopolysaccharides (LPS) and other related pro-inflammatory pathogenic signals, these may contribute to both the systemic and CNS amyloid burden in aging humans; and (ii) that the clearance of Aβ peptides appears to be intrinsically impaired by deficits in the microglial plasma-membrane enriched triggering receptor expressed in microglial/myeloid-2 cells (TREM2). This brief general commentary-perspective paper: (i) will highlight some of these very recent findings on microbiome-secreted amyloids and LPS and the potential contribution of these microbial-derived pro-inflammatory and neurotoxic exudates to age-related inflammatory and AD-type neurodegeneration in the host; and (ii) will discuss the contribution of a defective microglial-based TREM2 transmembrane sensor-receptor system to amyloidogenesis in AD that is in contrast to the normal, homeostatic clearance of Aβ peptides from the human CNS.}, }
@article {pmid26064625, year = {2015}, author = {Pinzón, JH and Kamel, B and Burge, CA and Harvell, CD and Medina, M and Weil, E and Mydlarz, LD}, title = {Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral.}, journal = {Royal Society open science}, volume = {2}, number = {4}, pages = {140214}, pmid = {26064625}, issn = {2054-5703}, abstract = {Climate change is negatively affecting the stability of natural ecosystems, especially coral reefs. The dissociation of the symbiosis between reef-building corals and their algal symbiont, or coral bleaching, has been linked to increased sea surface temperatures. Coral bleaching has significant impacts on corals, including an increase in disease outbreaks that can permanently change the entire reef ecosystem. Yet, little is known about the impacts of coral bleaching on the coral immune system. In this study, whole transcriptome analysis of the coral holobiont and each of the associate components (i.e. coral host, algal symbiont and other associated microorganisms) was used to determine changes in gene expression in corals affected by a natural bleaching event as well as during the recovery phase. The main findings include evidence that the coral holobiont and the coral host have different responses to bleaching, and the host immune system appears suppressed even a year after a bleaching event. These results support the hypothesis that coral bleaching changes the expression of innate immune genes of corals, and these effects can last even after recovery of symbiont populations. Research on the role of immunity on coral's resistance to stressors can help make informed predictions on the future of corals and coral reefs.}, }
@article {pmid26047662, year = {2016}, author = {Stilling, RM and Dinan, TG and Cryan, JF}, title = {The brain's Geppetto-microbes as puppeteers of neural function and behaviour?.}, journal = {Journal of neurovirology}, volume = {22}, number = {1}, pages = {14-21}, pmid = {26047662}, issn = {1538-2443}, mesh = {Animals ; *Behavior ; Behavior, Animal ; Biological Evolution ; Brain/*microbiology/parasitology/physiopathology/virology ; Diet ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology/parasitology/physiopathology/virology ; *Host-Pathogen Interactions ; Humans ; Symbiosis/physiology ; }, abstract = {Research on the microbiome and its interaction with various host organs, including the brain, is increasingly gaining momentum. With more evidence establishing a comprehensive microbiota-gut-brain axis, questions have been raised as to the extent to which microbes influence brain physiology and behaviour. In parallel, there is a growing literature showing active behavioural manipulation in favour of the microbe for certain parasites. However, it seems unclear where the hidden majority of microbes are localised on the parasitism-mutualism spectrum. A long evolutionary history intimately connects host and microbiota, which complicates this classification. In this conceptual minireview, we discuss current hypotheses on host-microbe interaction and argue that novel experimental approaches and theoretical concepts, such as the hologenome theory, are necessary to incorporate transgenerational epigenetic inheritance of the microbiome into evolutionary theories.}, }
@article {pmid26039986, year = {2015}, author = {Wilson, AC and Duncan, RP}, title = {Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10255-10261}, pmid = {26039986}, issn = {1091-6490}, mesh = {Amino Acids/chemistry ; Amino Acids, Branched-Chain/chemistry ; Animals ; Bacteria/genetics ; Buchnera/genetics ; Cell Lineage ; Cytoplasm/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Hemiptera/*genetics/*microbiology ; Pantothenic Acid/chemistry ; *Symbiosis ; }, abstract = {The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.}, }
@article {pmid26028424, year = {2015}, author = {Price, DR and Wilson, AC and Luetje, CW}, title = {Proton-dependent glutamine uptake by aphid bacteriocyte amino acid transporter ApGLNT1.}, journal = {Biochimica et biophysica acta}, volume = {1848}, number = {10 Pt A}, pages = {2085-2091}, doi = {10.1016/j.bbamem.2015.05.019}, pmid = {26028424}, issn = {0006-3002}, support = {DC011091/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Aphids/*microbiology ; Buchnera/*metabolism ; Cells, Cultured ; Glutamine/*pharmacokinetics ; Ion Channel Gating/*physiology ; Membrane Potentials/*physiology ; Oocytes/*physiology ; Protons ; Xenopus laevis ; }, abstract = {Aphids house large populations of the gammaproteobacterial symbiont Buchnera aphidicola in specialized bacteriocyte cells. The combined biosynthetic capability of the holobiont (Acyrthosiphon pisum and Buchnera) is sufficient for biosynthesis of all twenty protein coding amino acids, including amino acids that animals alone cannot synthesize; and that are present at low concentrations in A. pisum's plant phloem sap diet. Collaborative holobiont amino acid biosynthesis depends on glutamine import into bacteriocytes, which serves as a nitrogen-rich amino donor for biosynthesis of other amino acids. Recently, we characterized A. pisum glutamine transporter 1 (ApGLNT1), a member of the amino acid/auxin permease family, as the dominant bacteriocyte plasma membrane glutamine transporter. Here we show ApGLNT1 to be structurally and functionally related to mammalian proton-dependent amino acid transporters (PATs 1-4). Using functional expression in Xenopus laevis oocytes, combined with two-electrode voltage clamp electrophysiology we demonstrate that ApGLNT1 is electrogenic and that glutamine induces large inward currents. ApGLNT1 glutamine induced currents are dependent on external glutamine concentration, proton (H+) gradient across the membrane, and membrane potential. Based on these transport properties, ApGLNT1-mediated glutamine uptake into A. pisum bacteriocytes can be regulated by changes in either proton gradients across the plasma membrane or membrane potential.}, }
@article {pmid32846714, year = {2015}, author = {Lewis, Z and Lizé, A}, title = {Insect behaviour and the microbiome.}, journal = {Current opinion in insect science}, volume = {9}, number = {}, pages = {86-90}, doi = {10.1016/j.cois.2015.03.003}, pmid = {32846714}, issn = {2214-5753}, abstract = {Increasingly we are coming to understand the role of the microbiome in determining host physiological, behavioural, and evolutionary processes. Indeed it is now widely accepted that the host genome should be considered from a hologenomic point of view, with it also including the genomes of its symbiotic microbiota. Some of the most remarkable phenomena in the insect world relate to behavioural manipulation by the microorganisms associated with a host, and we here review recent progress in the study of these phenomena. The effects of the microbiome on insect hosts have important evolutionary consequences, and we are at the forefront of an exciting time in the study of manipulated insects.}, }
@article {pmid26026593, year = {2015}, author = {Dheilly, NM and Poulin, R and Thomas, F}, title = {Biological warfare: Microorganisms as drivers of host-parasite interactions.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {34}, number = {}, pages = {251-259}, doi = {10.1016/j.meegid.2015.05.027}, pmid = {26026593}, issn = {1567-7257}, mesh = {Animals ; *Biological Warfare ; *Host-Parasite Interactions ; Humans ; Microbiota ; Parasitic Diseases/*microbiology/parasitology ; Symbiosis ; }, abstract = {Understanding parasite strategies for evasion, manipulation or exploitation of hosts is crucial for many fields, from ecology to medical sciences. Generally, research has focused on either the host response to parasitic infection, or the parasite virulence mechanisms. More recently, integrated studies of host-parasite interactions have allowed significant advances in theoretical and applied biology. However, these studies still provide a simplistic view of these as mere two-player interactions. Host and parasite are associated with a myriad of microorganisms that could benefit from the improved fitness of their partner. Illustrations of such complex multi-player interactions have emerged recently from studies performed in various taxa. In this conceptual article, we propose how these associated microorganisms may participate in the phenotypic alterations induced by parasites and hence in host-parasite interactions, from an ecological and evolutionary perspective. Host- and parasite-associated microorganisms may participate in the host-parasite interaction by interacting directly or indirectly with the other partner. As a result, parasites may develop (i) the disruptive strategy in which the parasite alters the host microbiota to its advantage, and (ii) the biological weapon strategy where the parasite-associated microorganism contributes to or modulates the parasite's virulence. Some phenotypic alterations induced by parasite may also arise from conflicts of interests between the host or parasite and its associated microorganism. For each situation, we review the literature and propose new directions for future research. Specifically, investigating the role of host- and parasite-associated microorganisms in host-parasite interactions at the individual, local and regional level will lead to a holistic understanding of how the co-evolution of the different partners influences how the other ones respond, both ecologically and evolutionary. The conceptual framework we propose here is important and relevant to understand the proximate basis of parasite strategies, to predict their evolutionary dynamics and potentially to prevent therapeutic failures.}, }
@article {pmid26020776, year = {2015}, author = {Gudenkauf, BM and Hewson, I}, title = {Metatranscriptomic Analysis of Pycnopodia helianthoides (Asteroidea) Affected by Sea Star Wasting Disease.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0128150}, pmid = {26020776}, issn = {1932-6203}, mesh = {Animals ; *Energy Metabolism ; *Gene Expression Regulation ; Starfish/genetics/*metabolism ; *Transcriptome ; Wasting Syndrome/genetics/*metabolism/pathology/*veterinary ; }, abstract = {Sea star wasting disease (SSWD) describes a suite of symptoms reported in asteroids of the North American Pacific Coast. We performed a metatranscriptomic survey of asymptomatic and symptomatic sunflower star (Pycnopodia helianthoides) body wall tissues to understand holobiont gene expression in tissues affected by SSWD. Metatranscriptomes were highly variable between replicate libraries, and most differentially expressed genes represented either transcripts of associated microorganisms (particularly Pseudomonas and Vibrio relatives) or low-level echinoderm transcripts of unknown function. However, the pattern of annotated host functional genes reflects enhanced apoptotic and tissue degradation processes and decreased energy metabolism, while signalling of death-related proteins was greater in asymptomatic and symptomatic tissues. Our results suggest that the body wall tissues of SSWD-affected asteroids may undergo structural changes during disease progression, and that they are stimulated to undergo autocatalytic cell death processes.}, }
@article {pmid26018191, year = {2015}, author = {Roder, C and Bayer, T and Aranda, M and Kruse, M and Voolstra, CR}, title = {Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences.}, journal = {Molecular ecology}, volume = {24}, number = {13}, pages = {3501-3511}, pmid = {26018191}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Biodiversity ; Coral Reefs ; *Environment ; Indian Ocean ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; }, abstract = {The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species' preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.}, }
@article {pmid25989369, year = {2015}, author = {Baker, DM and Freeman, CJ and Knowlton, N and Thacker, RW and Kim, K and Fogel, ML}, title = {Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses.}, journal = {The ISME journal}, volume = {9}, number = {12}, pages = {2620-2629}, pmid = {25989369}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Carbon Cycle ; Caribbean Region ; Dinoflagellida/classification/genetics/isolation &amp; purification/*physiology ; Photosynthesis ; Phylogeny ; *Symbiosis ; }, abstract = {Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean. While current research has focused on the phylo- and population genetics of gorgonian symbiont types and their photo-physiology, relatively less work has focused on biogeochemical benefits conferred to the host and how these benefits vary across host species. Here we examine this symbiosis among 11 gorgonian species collected in Bocas del Toro, Panama. By coupling light and dark bottle incubations (P/R) with (13)C-bicarbonate tracers, we quantified the link between holobiont oxygen metabolism with carbon assimilation and translocation from symbiont to host. Our data show that P/R varied among species, and was correlated with colony morphology and polyp size. Sea fans and sea plumes were net autotrophs (P/R>1.5), while nine species of sea rods were net heterotrophs with most below compensation (P/R<1.0). (13)C assimilation corroborated the P/R results, and maximum δ(13)Chost values were strongly correlated with polyp size, indicating higher productivity by colonies with high polyp SA:V. A survey of gorgonian-Symbiodinium associations revealed that productive species maintain specialized, obligate symbioses and are more resistant to coral bleaching, whereas generalist and facultative associations are common among sea rods that have higher bleaching sensitivities. Overall, productivity and polyp size had strong phylogenetic signals with carbon fixation and polyp size showing evidence of trait covariance.}, }
@article {pmid25977840, year = {2015}, author = {Zhao, Y and Dua, P and Lukiw, WJ}, title = {Microbial Sources of Amyloid and Relevance to Amyloidogenesis and Alzheimer's Disease (AD).}, journal = {Journal of Alzheimer's disease &amp; Parkinsonism}, volume = {5}, number = {1}, pages = {177}, pmid = {25977840}, issn = {2161-0460}, support = {R01 EY006311/EY/NEI NIH HHS/United States ; R01 AG018031/AG/NIA NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; R01 AG038834/AG/NIA NIH HHS/United States ; P30 GM103340/GM/NIGMS NIH HHS/United States ; }, abstract = {Since the inception of the human microbiome project (HMP) by the US National Institutes of Health (NIH) in 2007 there has been a keen resurgence in our recognition of the human microbiome and its contribution to development, immunity, neurophysiology, metabolic and nutritive support to central nervous system (CNS) health and disease. What is not generally appreciated is that (i) the ~10[14] microbial cells that comprise the human microbiome outnumber human host cells by approximately one hundred-to-one; (ii) together the microbial genes of the microbiome outnumber human host genes by about one hundred-and-fifty to one; (iii) collectively these microbes constitute the largest 'diffuse organ system' in the human body, more metabolically active than the liver; strongly influencing host nutritive-, innate-immune, neuroinflammatory-, neuromodulatory- and neurotransmission-functions; and (iv) that these microbes actively secrete highly complex, immunogenic mixtures of lipopolysaccharide (LPS) and amyloid from their outer membranes into their immediate environment. While secreted LPS and amyloids are generally quite soluble as monomers over time they form into highly insoluble fibrous protein aggregates that are implicated in the progressive degenerative neuropathology of several common, age-related disorders of the human CNS including Alzheimer's disease (AD). This general commentary-perspective paper will highlight some recent findings on microbial-derived secreted LPS and amyloids and the potential contribution of these neurotoxic and proinflammatory microbial exudates to age-related inflammatory amyloidogenesis and neurodegeneration, with specific reference to AD wherever possible.}, }
@article {pmid25972851, year = {2015}, author = {Fiore, CL and Labrie, M and Jarett, JK and Lesser, MP}, title = {Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {364}, pmid = {25972851}, issn = {1664-302X}, abstract = {Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.}, }
@article {pmid28357290, year = {2015}, author = {Zarraonaindia, I and Gilbert, JA}, title = {Understanding grapevine-microbiome interactions: implications for viticulture industry.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {5}, pages = {171-173}, doi = {10.15698/mic2015.05.204}, pmid = {28357290}, issn = {2311-2638}, abstract = {Until recently, the analysis of complex communities such as that of the grapevine-microbe holobiont has been limited by the fact that most microbes are not culturable under laboratory conditions (less than 1%). However, metagenomics, the study of the genetic material recovered directly from environmental samples without the need for enrichment or of culturing, has led to open an unprecedented era in the field of microbiology. Importantly, this technological advance has now become so pervasive that it is being regularly applied to explore soils and plants of agricultural interest. Interestingly, many large companies are taking notice, with significant financial investment being used to exploring ways to manipulate the productivity, disease resistance and stress tolerance for crops by influencing the microbiome. To understand which microbes one needs to manipulate to influence this valuable characteristics, we need to sequence the microbiome and capture the genetic and hence functional metabolic information contained therein. For viticulture and other agricultural fields where the crop is also associated to particular flavor properties that may also be manipulated, understanding how the bacteria, fungi and viruses influence the development and hence chemical makeup of the crop is essential.}, }
@article {pmid25903335, year = {2015}, author = {Roossinck, MJ}, title = {Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts.}, journal = {Journal of virology}, volume = {89}, number = {13}, pages = {6532-6535}, pmid = {25903335}, issn = {1098-5514}, mesh = {Animals ; Bacteria/*virology ; Insecta/*virology ; Mammals/*virology ; Plants/*virology ; *Symbiosis ; *Virus Physiological Phenomena ; Viruses/*growth &amp; development ; }, abstract = {Viruses are being redefined as more than just pathogens. They are also critical symbiotic partners in the health of their hosts. In some cases, viruses have fused with their hosts in symbiogenetic relationships. Mutualistic interactions are found in plant, insect, and mammalian viruses, as well as with eukaryotic and prokaryotic microbes, and some interactions involve multiple players of the holobiont. With increased virus discovery, more mutualistic interactions are being described and more will undoubtedly be discovered.}, }
@article {pmid25894127, year = {2015}, author = {Land, WG}, title = {How evolution tells us to induce allotolerance.}, journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation}, volume = {13 Suppl 1}, number = {}, pages = {46-54}, pmid = {25894127}, issn = {2146-8427}, mesh = {Animals ; Bacteria/immunology ; *Evolution, Molecular ; Female ; Graft Rejection/*immunology/metabolism/prevention &amp; control ; *Graft Survival ; Host-Pathogen Interactions ; Humans ; Immunity, Innate ; Immunity, Mucosal ; Intestines/immunology/microbiology ; Models, Immunological ; Organ Transplantation/*adverse effects ; Placenta/immunology ; Pregnancy ; Signal Transduction ; *Transplantation Tolerance ; Treatment Outcome ; }, abstract = {Modern immunology, in many ways, is based on 3 major paradigms: the clonal selection theory (Medawar, Burnet; 1953/1959), the pattern recognition theory (Janeway; 1989), and the danger/injury theory (Matzinger, Land; 1994). The last theory holds that any cell stress and tissue injury including allograft injury, via induction of damage-associated molecular patterns, induces immunity including alloimmunity leading to allograft rejection. On the other hand, the concept precludes that "non-self " per se induces immunity as proposed by the two former theories. Today, the danger/injury model has been largely accepted by immunologists, as documented by a steadily increasing number of publications. In particular, overwhelming evidence in support of the correctness of the model has come from recent studies on the gut microbiota representing a huge assemblage of "non-self. " Here, harmless noninjurious commensal microbes are protected by innate immunity-based immune tolerance whereas intestinal injury-causing pathogenic microbes are immunology attacked. The ability of the immune system to discriminate between harmless beneficial "non-self " to induce tolerance and harmful life-threatening "non-self " to induce immunity has apparently emerged during evolution: Protection of innate immunity-controlled beneficial "non-self " (eg, as reflected by microbiotas but also by the fetus of placental mammals) as well as immune defense responses to injuring/injured "non-self " (eg, as reflected by plant resistance to biotic and abiotic stress and allograft rejection in mammals) evolved under pressure across the tree of life, that is, in plants, lower and higher invertebrates as well as lower and higher vertebrates. And evolution tells us why the overall existence of protected microbiotas really makes sense: It is the formation of the "holobiont, " - a metaorganism - that is, the host plus all of its associated microorganisms that - in terms of a strong unit of selection in evolution - provides that kind of fitness to all species on earth to successfully live, survive and reproduce. In other words: "We all evolve, develop, grow, and reproduce as multigenomic ecosystems! Regarding reproduction, another impressive example of active immunologic protection of "nonself " refers to pregnancy in placental mammals that emerged about 400 millions of years ago. Similar to "non-self " microbiotas, pregnancy in placental mammals reflects an evolution-driven phenomenon on the basis of innate immunity-controlled tolerance induction to semiallogeneic non-injuring/non-injured "non-self " aiming to ensure reproduction! Altogether, the lesson learned from evolution of how to avoid allograft rejection is clear: prevent allograft injury to induce allotolerance, in other words: create a "transplant holobiont. ".}, }
@article {pmid25873456, year = {2015}, author = {Rua, CP and Gregoracci, GB and Santos, EO and Soares, AC and Francini-Filho, RB and Thompson, F}, title = {Potential metabolic strategies of widely distributed holobionts in the oceanic archipelago of St Peter and St Paul (Brazil).}, journal = {FEMS microbiology ecology}, volume = {91}, number = {6}, pages = {}, doi = {10.1093/femsec/fiv043}, pmid = {25873456}, issn = {1574-6941}, mesh = {Animals ; Bacteriophages/genetics/isolation &amp; purification ; Base Sequence ; Brazil ; Carbon/metabolism ; Hydrocarbons, Aromatic/metabolism ; Metagenomics ; Microbiota/*genetics ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Principal Component Analysis ; Sequence Analysis, DNA ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are one of the most complex symbiotic communities and while the taxonomic composition of associated microbes has been determined, the biggest challenge now is to uncover their functional role in symbiosis. We investigated the microbiota of two widely distributed sponge species, regarding both their taxonomic composition and their functional roles. Samples of Didiscus oxeata and Scopalina ruetzleri were collected in the oceanic archipelago of St Peter and St Paul and analysed through metagenomics. Sequences generated by 454 pyrosequencing and Ion Torrent were taxonomically and functionally annotated on the MG-RAST server using the GenBank and SEED databases, respectively. Both communities exhibit equivalence in core functions, interestingly played by the most abundant taxa in each community. Conversely, the microbial communities differ in composition, taxonomic diversity and potential metabolic strategies. Functional annotation indirectly suggests differences in preferential pathways of carbon, nitrogen and sulphur metabolisms, which may indicate different metabolic strategies.}, }
@article {pmid25868684, year = {2015}, author = {Rädecker, N and Pogoreutz, C and Voolstra, CR and Wiedenmann, J and Wild, C}, title = {Nitrogen cycling in corals: the key to understanding holobiont functioning?.}, journal = {Trends in microbiology}, volume = {23}, number = {8}, pages = {490-497}, doi = {10.1016/j.tim.2015.03.008}, pmid = {25868684}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*metabolism/*microbiology ; Archaea/growth &amp; development/metabolism ; Bacteria/growth &amp; development/metabolism ; Dinoflagellida/*metabolism/physiology ; Fungi/growth &amp; development/metabolism ; Nitrogen/*metabolism ; *Nitrogen Cycle ; *Symbiosis ; }, abstract = {Corals are animals that form close mutualistic associations with endosymbiotic photosynthetic algae of the genus Symbiodinium. Together they provide the calcium carbonate framework of coral reef ecosystems. The importance of the microbiome (i.e., bacteria, archaea, fungi, and viruses) to holobiont functioning has only recently been recognized. Given that growth and density of Symbiodinium within the coral host is highly dependent on nitrogen availability, nitrogen-cycling microbes may be of fundamental importance to the stability of the coral-algae symbiosis and holobiont functioning, in particular under nutrient-enriched and -depleted scenarios. We summarize what is known about nitrogen cycling in corals and conclude that disturbance of microbial nitrogen cycling may be tightly linked to coral bleaching and disease.}, }
@article {pmid25852650, year = {2015}, author = {Balzano, S and Corre, E and Decelle, J and Sierra, R and Wincker, P and Da Silva, C and Poulain, J and Pawlowski, J and Not, F}, title = {Transcriptome analyses to investigate symbiotic relationships between marine protists.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {98}, pmid = {25852650}, issn = {1664-302X}, abstract = {Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.}, }
@article {pmid25786308, year = {2014}, author = {Provorov, NA and Tikhonovich, IA}, title = {[Super-species genetic systems].}, journal = {Zhurnal obshchei biologii}, volume = {75}, number = {4}, pages = {247-260}, pmid = {25786308}, issn = {0044-4596}, mesh = {Gene Transfer, Horizontal/*physiology ; Metagenome/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; Quorum Sensing/physiology ; Symbiosis/physiology ; }, abstract = {Genetic integration of diverse organisms results in generation of three types of the super-species systems of heredity: metagenome (set of genetic factors of the microbial community which occupies a certain ecological niche), symbiogenome (functionally integrated system of the partners' symbiotic genes) and hologenome (entire hereditary system of a symbiotically originated organism). The integrity of metagenome is based on the cross-regulation and horizontal transfer of genes in co-evolving organisms which in the soil microbial communities are accompanied by maintenance of the stable extracellular DNA pool. Formation of symbiogenome is related to the highly specific partners' signaling interactions which are responsible for development of the joint metabolic pathways based on the specialized cellular and tissue structures. Transitions of symbiogenome into hologenome are due to the endosymbiotic gene transfer from microsymbionts to their hosts. In symbiotic bacteria, these transitions are coupled with establishments of multi-component, reduced and rudimentary genomes revealed for the ecologically obligatory symbionts, genetically obligatory symbionts, and cellular organelles, respectively. Their evolution is related to the stringency of transmission of microsymbionts by hosts increased from pseudo-vertical (via environment) to the trans-embryonic (via embryos and the surrounding tissues) and trans-ovarian transmission (via germ cells) which are culminated in the cytoplasmic inheritance of cellular organelles. We suggest the hypothesis about generation of endophytic plant symbiogenome on the basis of soil metagenome subjected to the control of host by its involvement into the quorum sensing auto-regulation of microbial community.}, }
@article {pmid25773891, year = {2015}, author = {Metian, M and Hédouin, L and Ferrier-Pagès, C and Teyssié, JL and Oberhansli, F and Buschiazzo, E and Warnau, M}, title = {Metal bioconcentration in the scleractinian coral Stylophora pistillata: investigating the role of different components of the holobiont using radiotracers.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {4}, pages = {178}, pmid = {25773891}, issn = {1573-2959}, mesh = {Animals ; Anthozoa/*chemistry/physiology ; Environment ; Environmental Monitoring/*methods ; Metals/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bioconcentration kinetics of five metals (Ag, Cd, Co, Mn, and Zn) were determined in the scleractinian coral Stylophora pistillata (entire symbiotic association vs. cultured symbionts), using radiotracer techniques. Among contrasting element behaviors observed in S. pistillata, the highest efficiency of concentration and retention was observed for Ag in the symbiotic association (CFss reaching 5000 and T b½>1 year). Predominant proportion of this metal was found associated with the skeleton whereas the other metals were mainly present in the coral tissues (including host tissues and symbionts). A 96-h exposure of cultured symbionts (isolated zooxantellae from S. pistillata) indicated that they displayed a very high potential for metal bioconcentration (higher by 1 to 3 orders of magnitude compared to the skeleton). In addition, among the five elements investigated, Ag had the highest concentration factor in the cultured symbionts. Contrasting kinetic characteristics of skeleton vs. tissues offer interesting implications for biomonitoring purposes. Indeed, the skeleton was shown to display stable metal concentrations after an exposure (long retention time) and thereby allows recording contamination event on the long term, whereas the concentrations within coral tissues rapidly increased during the exposure and dropped when non-contaminating conditions were restored, allowing information on the current (short term) contamination status. The present study confirms that the coral can be seen as a two-compartment box model for metal bioconcentration: the tissues sensus latto as a first box governing metal entrance (with a crucial role played by the symbionts) and the skeleton as a second box where metal detoxification (storage) is taking place; the first box also depurates toward the environment when non-contaminating conditions are restored.}, }
@article {pmid25756121, year = {2014}, author = {Nguyen-Kim, H and Bouvier, T and Bouvier, C and Doan-Nhu, H and Nguyen-Ngoc, L and Rochelle-Newall, E and Baudoux, AC and Desnues, C and Reynaud, S and Ferrier-Pages, C and Bettarel, Y}, title = {High occurrence of viruses in the mucus layer of scleractinian corals.}, journal = {Environmental microbiology reports}, volume = {6}, number = {6}, pages = {675-682}, doi = {10.1111/1758-2229.12185}, pmid = {25756121}, issn = {1758-2229}, mesh = {Animals ; Anthozoa/*virology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Molecular Sequence Data ; Phylogeny ; Viruses/classification/genetics/*isolation &amp; purification ; }, abstract = {Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m = 24.8%) than in water (m = 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.}, }
@article {pmid25745427, year = {2015}, author = {Wichard, T and Charrier, B and Mineur, F and Bothwell, JH and Clerck, OD and Coates, JC}, title = {The green seaweed Ulva: a model system to study morphogenesis.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {72}, pmid = {25745427}, issn = {1664-462X}, abstract = {Green macroalgae, mostly represented by the Ulvophyceae, the main multicellular branch of the Chlorophyceae, constitute important primary producers of marine and brackish coastal ecosystems. Ulva or sea lettuce species are some of the most abundant representatives, being ubiquitous in coastal benthic communities around the world. Nonetheless the genus also remains largely understudied. This review highlights Ulva as an exciting novel model organism for studies of algal growth, development and morphogenesis as well as mutualistic interactions. The key reasons that Ulva is potentially such a good model system are: (i) patterns of Ulva development can drive ecologically important events, such as the increasing number of green tides observed worldwide as a result of eutrophication of coastal waters, (ii) Ulva growth is symbiotic, with proper development requiring close association with bacterial epiphytes, (iii) Ulva is extremely developmentally plastic, which can shed light on the transition from simple to complex multicellularity and (iv) Ulva will provide additional information about the evolution of the green lineage.}, }
@article {pmid25737238, year = {2015}, author = {Wang, J and Kalyan, S and Steck, N and Turner, LM and Harr, B and Künzel, S and Vallier, M and Häsler, R and Franke, A and Oberg, HH and Ibrahim, SM and Grassl, GA and Kabelitz, D and Baines, JF}, title = {Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6440}, pmid = {25737238}, issn = {2041-1723}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Crosses, Genetic ; DNA Primers/genetics ; Flow Cytometry ; Gastrointestinal Microbiome/*genetics ; Genetics, Population ; Genome/*genetics ; Germany ; Hybridization, Genetic/*genetics ; Mice/*genetics/microbiology ; *Models, Genetic ; Molecular Sequence Data ; Quantitative Trait Loci ; Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Recent evidence suggests that natural selection operating on hosts to maintain their microbiome contributes to the emergence of new species, that is, the 'hologenomic basis of speciation'. Here we analyse the gut microbiota of two house mice subspecies, Mus musculus musculus and M. m. domesticus, across their Central European hybrid zone, in addition to hybrids generated in the lab. Hybrid mice display widespread transgressive phenotypes (that is, exceed or fall short of parental values) in a variety of measures of bacterial community structure, which reveals the importance of stabilizing selection operating on the intestinal microbiome within species. Further genetic and immunological analyses reveal genetic incompatibilities, aberrant immune gene expression and increased intestinal pathology associated with altered community structure among hybrids. These results provide unique insight into the consequences of evolutionary divergence in a vertebrate 'hologenome', which may be an unrecognized contributing factor to reproductive isolation in this taxonomic group.}, }
@article {pmid25732740, year = {2015}, author = {Bosch, TC and Grasis, JA and Lachnit, T}, title = {Microbial ecology in Hydra: why viruses matter.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {53}, number = {3}, pages = {193-200}, pmid = {25732740}, issn = {1976-3794}, support = {5F32AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*physiology ; Biological Evolution ; Cnidaria/*virology ; Hydra/*virology ; Hydrobiology ; Microbiota/physiology ; Species Specificity ; *Symbiosis ; *Virus Physiological Phenomena ; }, abstract = {While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.}, }
@article {pmid25724277, year = {2015}, author = {Peterson, BF and Stewart, HL and Scharf, ME}, title = {Quantification of symbiotic contributions to lower termite lignocellulose digestion using antimicrobial treatments.}, journal = {Insect biochemistry and molecular biology}, volume = {59}, number = {}, pages = {80-88}, doi = {10.1016/j.ibmb.2015.02.009}, pmid = {25724277}, issn = {1879-0240}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Isoptera/*drug effects/metabolism/microbiology ; Lignin/*metabolism ; Symbiosis ; }, abstract = {Animal-microbe co-evolution and symbiosis are broadly distributed across the animal kingdom. Insects form a myriad of associations with microbes ranging from vectoring of pathogens to intracellular, mutualistic relationships. Lower termites are key models for insect-microbe symbiosis because of the diversity, complexity and functionality of their unique tripartite symbiosis. This collaboration allows termites to live on a diet of nitrogen-poor lignocellulose. Recent functional investigations of lignocellulose digestion in lower termites have primarily focused on the contributions of the eukaryotic members of the termite holobiont (termite and protist). Here, using multiple antimicrobial treatments, we induced differing degrees of dysbiosis in the termite gut, leading to variably altered symbiont abundance and diversity, and lignocellulolytic capacity. Although protists are clearly affected by antimicrobial treatments, our findings provide novel evidence that the removal of distinct groups of bacteria partially reduces, but does not abolish, the saccharolytic potential of the termite gut holobiont. This is specifically manifested by reductions of 23-47% and 30-52% in glucose and xylose yields respectively from complex lignocellulose. Thus, all members of the lower termite holobiont (termite, protist and prokaryotes) are involved in the process of efficient, sustained lignocellulase activity. This unprecedented quantification of the relative importance of prokaryotes in this system emphasizes the collaborative nature of the termite holobiont, and the relevance of lower termites as models for inter-domain symbioses.}, }
@article {pmid25678260, year = {2015}, author = {Steinert, G and Taylor, MW and Schupp, PJ}, title = {Diversity of Actinobacteria Associated with the Marine Ascidian Eudistoma toealensis.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {17}, number = {4}, pages = {377-385}, pmid = {25678260}, issn = {1436-2236}, support = {S06-GM-44796/GM/NIGMS NIH HHS/United States ; }, mesh = {Actinobacteria/*genetics/metabolism ; Animals ; Base Sequence ; *Biodiversity ; DNA Primers/genetics ; Microbiota/*genetics ; Micronesia ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; Staurosporine/biosynthesis ; Urochordata/*microbiology ; }, abstract = {Ascidians have yielded a wide variety of bioactive natural products. The colonial ascidian Eudistoma toealensis from Micronesia has been identified as the source of a series of staurosporine derivatives, though the exact origin of these derivatives is still unknown. To identify known staurosporine-producing microbes associated with E. toealensis, we analyzed with 16S rRNA gene tag pyrosequencing the overall bacterial community and focused on potential symbiotic bacteria already known from other ascidians or other marine hosts, such as sponges. The described microbiota was one of very high diversity, comprising 43 phyla: two from archaea, 34 described bacterial phyla, and seven candidate bacterial phyla. Many bacteria, which are renowned community members of other ascidians and marine holobionts, such as sponges and corals, were also part of the E. toealensis microbial community. Furthermore, two known producers of indolocarbazoles, Salinispora and Verrucosispora, were found with high abundance exclusively in the ascidian tissue, suggesting that microbial symbionts and not the organism itself may be the true producers of the staurosporines in E. toealensis.}, }
@article {pmid25673681, year = {2015}, author = {Dheilly, NM and Maure, F and Ravallec, M and Galinier, R and Doyon, J and Duval, D and Leger, L and Volkoff, AN and Missé, D and Nidelet, S and Demolombe, V and Brodeur, J and Gourbal, B and Thomas, F and Mitta, G}, title = {Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1803}, pages = {20142773}, pmid = {25673681}, issn = {1471-2954}, mesh = {Animals ; Coleoptera/*parasitology/physiology/*virology ; Female ; Host-Parasite Interactions ; Larva/parasitology/virology ; Molecular Sequence Data ; Oviducts/virology ; RNA Viruses/*physiology ; Wasps/physiology/*virology ; }, abstract = {Many parasites modify their host behaviour to improve their own transmission and survival, but the proximate mechanisms remain poorly understood. An original model consists of the parasitoid Dinocampus coccinellae and its coccinellid host, Coleomegilla maculata; during the behaviour manipulation, the parasitoid is not in contact with its host anymore. We report herein the discovery and characterization of a new RNA virus of the parasitoid (D. coccinellae paralysis virus, DcPV). Using a combination of RT-qPCR and transmission electron microscopy, we demonstrate that DcPV is stored in the oviduct of parasitoid females, replicates in parasitoid larvae and is transmitted to the host during larval development. Next, DcPV replication in the host's nervous tissue induces a severe neuropathy and antiviral immune response that correlate with the paralytic symptoms characterizing the behaviour manipulation. Remarkably, virus clearance correlates with recovery of normal coccinellid behaviour. These results provide evidence that changes in ladybeetle behaviour most likely result from DcPV replication in the cerebral ganglia rather than by manipulation by the parasitoid. This offers stimulating prospects for research on parasitic manipulation by suggesting for the first time that behaviour manipulation could be symbiont-mediated.}, }
@article {pmid25668159, year = {2015}, author = {Pantos, O and Bongaerts, P and Dennis, PG and Tyson, GW and Hoegh-Guldberg, O}, title = {Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {1916-1927}, pmid = {25668159}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/genetics ; Australia ; *Coral Reefs ; Gammaproteobacteria/genetics ; Genotype ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics ; }, abstract = {Reef-building corals form complex relationships with a range of microorganisms including bacteria, archaea, fungi and the unicellular microalgae of the genus Symbiodinium, which together form the coral holobiont. These symbionts are known to have both beneficial and deleterious effects on their coral host, but little is known about what the governing factors of these relationships are, or the interactions that exist between the different members of the holobiont and their environment. Here we used 16S ribosomal RNA gene amplicon sequencing to investigate how archaeal and bacterial communities associated with the widespread scleractinian coral Seriatopora hystrix are influenced by extrinsic (reef habitat and geographic location) and intrinsic (host genotype and Symbiodinium subclade) factors. Bacteria dominate the microbiome of S. hystrix, with members of the Alphaproteobacteria, Gammaproteobacteria and Bacteriodetes being the most predominant in all samples. The richness and evenness of these communities varied between reef habitats, but there was no significant difference between distinct coral host lineages or corals hosting distinct Symbiodinium subclades. The coral microbiomes correlated to reef habitat (depth) and geographic location, with a negative correlation between Alpha- and Gammaproteobacteria, driven by the key members of both groups (Rhodobacteraceae and Hahellaceae, respectively), which showed significant differences between location and depth. This study suggests that the control of microbial communities associated with the scleractinian coral S. hystrix is driven primarily by external environmental conditions rather than by those directly associated with the coral holobiont.}, }
@article {pmid25655016, year = {2015}, author = {Vandenkoornhuyse, P and Quaiser, A and Duhamel, M and Le Van, A and Dufresne, A}, title = {The importance of the microbiome of the plant holobiont.}, journal = {The New phytologist}, volume = {206}, number = {4}, pages = {1196-1206}, doi = {10.1111/nph.13312}, pmid = {25655016}, issn = {1469-8137}, mesh = {Biological Evolution ; *Microbiota ; Plants/*microbiology ; }, abstract = {Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.}, }
@article {pmid25621279, year = {2014}, author = {Thompson, JR and Rivera, HE and Closek, CJ and Medina, M}, title = {Microbes in the coral holobiont: partners through evolution, development, and ecological interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {176}, pmid = {25621279}, issn = {2235-2988}, mesh = {Animals ; Anthozoa/genetics/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biological Evolution ; *Ecosystem ; Symbiosis ; }, abstract = {In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health-not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.}, }
@article {pmid25615440, year = {2015}, author = {Tout, J and Jeffries, TC and Petrou, K and Tyson, GW and Webster, NS and Garren, M and Stocker, R and Ralph, PJ and Seymour, JR}, title = {Chemotaxis by natural populations of coral reef bacteria.}, journal = {The ISME journal}, volume = {9}, number = {8}, pages = {1764-1777}, pmid = {25615440}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*drug effects/genetics ; Chemotactic Factors/pharmacology ; Chemotaxis/*drug effects ; *Coral Reefs ; DNA, Bacterial/analysis ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfonium Compounds/pharmacology ; Vibrio/genetics ; }, abstract = {Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.}, }
@article {pmid25586521, year = {2015}, author = {Hasnain, SE and O'Toole, RF and Grover, S and Ehtesham, NZ}, title = {Whole genome sequencing: a new paradigm in the surveillance and control of human tuberculosis.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {95}, number = {2}, pages = {91-94}, doi = {10.1016/j.tube.2014.12.007}, pmid = {25586521}, issn = {1873-281X}, mesh = {Bacterial Typing Techniques/methods ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Humans ; Molecular Typing/methods ; Mycobacterium tuberculosis/*genetics ; Population Surveillance/methods ; Tuberculosis/epidemiology/*microbiology/prevention &amp; control ; }, abstract = {Whole Genome Sequencing (WGS) is emerging as a very powerful tool for the management, outbreak analyses, surveillance and determining drug resistance of human infectious pathogens including Mycobacterium tuberculosis and MRSA. WGS can also discriminate relapse TB from re-infection and the resolution provided by WGS has no comparison to conventional technologies. With current cost coming down to <£70 per bacterial genome, WGS has emerged as an alternative to all the existing technologies put together. We discuss the advantage and disadvantages of WGS and whether it can become a point of care tool in not just developed countries but also in developing countries which have a huge TB burden. The likely utility of WGS for other pathogens and also in characterizing holobionts is also discussed.}, }
@article {pmid25548731, year = {2014}, author = {Freeman, CJ and Easson, CG and Baker, DM}, title = {Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e695}, pmid = {25548731}, issn = {2167-8359}, abstract = {Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEA c ]) and assessing the relative placement of common sponge species in bivariate (δ (13)C and δ (15)N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.}, }
@article {pmid25477868, year = {2014}, author = {Hardoim, CC and Cardinale, M and Cúcio, AC and Esteves, AI and Berg, G and Xavier, JR and Cox, CJ and Costa, R}, title = {Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {611}, pmid = {25477868}, issn = {1664-302X}, abstract = {Complex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.}, }
@article {pmid25467196, year = {2014}, author = {Rosic, N and Kaniewska, P and Chan, CK and Ling, EY and Edwards, D and Dove, S and Hoegh-Guldberg, O}, title = {Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {1052}, pmid = {25467196}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/*genetics/metabolism ; Computational Biology ; Coral Reefs ; Energy Metabolism ; Gene Expression Profiling ; *Gene Expression Regulation ; Molecular Sequence Annotation ; Oxidation-Reduction ; Photosynthesis ; Stress, Physiological/*genetics ; Temperature ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality. Understanding how elevated temperatures and nutrient concentration affect early transcriptional changes in corals and their algal endosymbionts is critically important for evaluating the responses of coral reefs to global changes happening in the environment. Here, we investigated the expression of genes in colonies of the reef-building coral Acropora aspera exposed to short-term sub-lethal levels of thermal (+6°C) and nutrient stress (ammonium-enrichment: 20 μM).<br><br>RESULTS: The RNA-Seq data provided hundreds of differentially expressed genes (DEGs) corresponding to various stress regimes, with 115 up- and 78 down-regulated genes common to all stress regimes. A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels. Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. Gene ontology analyses revealed enriched pathways, which led to changes in the dynamics of protein networks affecting growth, cellular processes, and energy requirement.<br><br>CONCLUSIONS: In corals with preserved symbiont physiological performance (based on Fv/Fm, photo-pigment and symbiont density), transcriptomic changes and DEGs provided important insight into early stages of the stress response in the coral holobiont. Although there were no signs of coral bleaching after exposure to short-term thermal and nutrient stress conditions, we managed to detect oxidative stress and apoptotic changes on a molecular level and provide a list of prospective stress biomarkers for both partners in symbiosis. Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.}, }
@article {pmid25467066, year = {2015}, author = {Iluz, D and Dubinsky, Z}, title = {Coral photobiology: new light on old views.}, journal = {Zoology (Jena, Germany)}, volume = {118}, number = {2}, pages = {71-78}, doi = {10.1016/j.zool.2014.08.003}, pmid = {25467066}, issn = {1873-2720}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/*physiology ; Calcification, Physiologic/physiology ; Chlorophyta/physiology ; Energy Metabolism ; *Light ; Photobiology ; Photosynthesis/physiology ; *Symbiosis ; }, abstract = {The relationship between reef-building corals and light-harvesting pigments of zooxanthellae (Symbiodinium sp.) has been acknowledged for decades. The photosynthetic activity of the algal endocellular symbionts may provide up to 90% of the energy needed for the coral holobiont. This relationship limits the bathymetric distribution of coral reefs to the upper 100 m of tropical shorelines. However, even corals growing under high light intensities have to supplement the photosynthates translocated from the algae by predation on nutrient-rich zooplankton. New information has revealed how the fate of carbon acquired through photosynthesis differs from that secured by predation, whose rates are controlled by light-induced tentacular extension. The Goreau paradigm of "light-enhanced calcification" is being reevaluated, based on evidence that blue light stimulates coral calcification independently from photosynthesis rates. Furthermore, under dim light, calcification rates were stoichiometrically uncoupled from photosynthesis. The rates of photosynthesis of the zooxanthellae exhibit a clear endogenous rhythmicity maintained by light patterns. This daily pattern is concomitant with a periodicity of all the antioxidant protective mechanisms that wax and wane to meet the concomitant fluctuation in oxygen evolution. The phases of the moon are involved in the triggering of coral reproduction and control the spectacular annual mass-spawning events taking place in several reefs. The intensity and directionality of the underwater light field affect the architecture of coral colonies, leading to an optimization of the exposure of the zooxanthellae to light. We present a summary of major gaps in our understanding of the relationship between light and corals as a roadmap for future research.}, }
@article {pmid25431341, year = {2015}, author = {Hoppers, A and Stoudenmire, J and Wu, S and Lopanik, NB}, title = {Antibiotic activity and microbial community of the temperate sponge, Haliclona sp.}, journal = {Journal of applied microbiology}, volume = {118}, number = {2}, pages = {419-430}, doi = {10.1111/jam.12709}, pmid = {25431341}, issn = {1365-2672}, mesh = {Animals ; Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Bacteria/genetics/isolation &amp; purification ; Haliclona/chemistry/genetics/*microbiology ; Seawater/microbiology ; }, abstract = {AIMS: Sessile marine invertebrates engage in a diverse array of beneficial interactions with bacterial symbionts. One feature of some of these relationships is the presence of bioactive natural products that can defend the holobiont from predation, competition or disease. In this study, we investigated the antimicrobial activity and microbial community of a common temperate sponge from coastal North Carolina.<br><br>METHODS AND RESULTS: The sponge was identified as a member of the genus Haliclona, a prolific source of bioactive natural products, based on its 18S rRNA gene sequence. The crude chemical extract and methanol partition had broad activity against the assayed Gram-negative and Gram-positive pathogenic bacteria. Further fractionation resulted in two groups of compounds with differing antimicrobial activity, primarily against Gram-positive test organisms. There was, however, notable activity against the Gram-negative marine pathogen, Vibrio parahaemolyticus. Microbial community analysis of the sponge and surrounding sea water via denaturing gradient gel electrophoresis (DGGE) indicates that it harbours a distinct group of bacterial associates.<br><br>CONCLUSIONS: The common temperate sponge, Haliclona sp., is a source of multiple antimicrobial compounds and has some consistent microbial community members that may play a role in secondary metabolite production.<br><br>These data suggest that common temperate sponges can be a source of bioactive chemical and microbial diversity. Further studies may reveal the importance of the microbial associates to the sponge and natural product biosynthesis.}, }
@article {pmid25430522, year = {2016}, author = {Salvucci, E}, title = {Microbiome, holobiont and the net of life.}, journal = {Critical reviews in microbiology}, volume = {42}, number = {3}, pages = {485-494}, doi = {10.3109/1040841X.2014.962478}, pmid = {25430522}, issn = {1549-7828}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biological Evolution ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.}, }
@article {pmid25401092, year = {2014}, author = {Stilling, RM and Bordenstein, SR and Dinan, TG and Cryan, JF}, title = {Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {147}, pmid = {25401092}, issn = {2235-2988}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01GM085163/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Animals ; Behavior ; *Biological Evolution ; Brain/*physiology ; Epigenesis, Genetic ; Gene-Environment Interaction ; Host-Pathogen Interactions/*physiology ; Humans ; Microbiota ; Symbiosis ; }, abstract = {The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a "social triangle" that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.}, }
@article {pmid25387109, year = {2015}, author = {Denman, SE and McSweeney, CS}, title = {The early impact of genomics and metagenomics on ruminal microbiology.}, journal = {Annual review of animal biosciences}, volume = {3}, number = {}, pages = {447-465}, doi = {10.1146/annurev-animal-022114-110705}, pmid = {25387109}, issn = {2165-8110}, mesh = {Animals ; Dietary Fiber/metabolism ; Genomics ; Methane/biosynthesis ; Microbiota/*genetics ; Phylogeny ; Rumen/*microbiology ; Ruminants/*microbiology ; }, abstract = {Knowledge gained from early and recent studies that define the functions of microbial populations within the rumen microbiome is essential to allow for directed rumen manipulation strategies. A large number of omic studies have focused on carbohydrate active enzymes either for improved fiber digestion within the animal or for use in industries such as biofuels. Studies of the rumen microbiome with respect to methane production and abatement strategies have led to initiatives for defining the microbiome of low- and high-methane-emitting animals while ensuring optimal feed conversion. With advances in omic technologies, the ability to link host genetics and the rumen microbiome by studying all the biological components (holobiont) through the use of hologenomics has begun. However, a program to culture and isolate microbial species for the purpose of standard microbial characterization to aid in assigning function to genomic data remains critical, especially for genes of unknown function.}, }
@article {pmid25360746, year = {2014}, author = {Schrameyer, V and Wangpraseurt, D and Hill, R and Kühl, M and Larkum, AW and Ralph, PJ}, title = {Light respiratory processes and gross photosynthesis in two scleractinian corals.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110814}, pmid = {25360746}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*metabolism/physiology/*radiation effects ; Biological Transport/radiation effects ; Carbon Dioxide/metabolism ; *Light ; Oxygen/metabolism ; Photosynthesis/*radiation effects ; Respiration/*radiation effects ; Symbiosis/radiation effects ; }, abstract = {The light dependency of respiratory activity of two scleractinian corals was examined using O2 microsensors and CO2 exchange measurements. Light respiration increased strongly but asymptotically with elevated irradiance in both species. Light respiration in Pocillopora damicornis was higher than in Pavona decussata under low irradiance, indicating species-specific differences in light-dependent metabolic processes. Overall, the coral P. decussata exhibited higher CO2 uptake rates than P. damicornis over the experimental irradiance range. P. decussata also harboured twice as many algal symbionts and higher total protein biomass compared to P. damicornis, possibly resulting in self-shading of the symbionts and/or changes in host tissue specific light distribution. Differences in light respiration and CO2 availability could be due to host-specific characteristics that modulate the symbiont microenvironment, its photosynthesis, and hence the overall performance of the coral holobiont.}, }
@article {pmid25343582, year = {2014}, author = {Grasis, JA and Lachnit, T and Anton-Erxleben, F and Lim, YW and Schmieder, R and Fraune, S and Franzenburg, S and Insua, S and Machado, G and Haynes, M and Little, M and Kimble, R and Rosenstiel, P and Rohwer, FL and Bosch, TC}, title = {Species-specific viromes in the ancestral holobiont Hydra.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109952}, pmid = {25343582}, issn = {1932-6203}, support = {R21 AI094534/AI/NIAID NIH HHS/United States ; 1F32AI098518/AI/NIAID NIH HHS/United States ; 1R21AI094534/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/isolation &amp; purification/virology ; Bacteriophages/genetics/isolation &amp; purification/metabolism ; Hydra/metabolism/microbiology/ultrastructure/*virology ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Viruses/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.}, }
@article {pmid25309882, year = {2014}, author = {Apidianakis, Y and Ferrandon, D}, title = {Modeling hologenome imbalances in inflammation and cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {134}, pmid = {25309882}, issn = {2235-2988}, mesh = {Animals ; Humans ; Inflammation/*complications/*etiology ; Neoplasms/*complications/*etiology ; }, }
@article {pmid25278474, year = {2014}, author = {Grover, R and Ferrier-Pagès, C and Maguer, JF and Ezzat, L and Fine, M}, title = {Nitrogen fixation in the mucus of Red Sea corals.}, journal = {The Journal of experimental biology}, volume = {217}, number = {Pt 22}, pages = {3962-3963}, doi = {10.1242/jeb.111591}, pmid = {25278474}, issn = {1477-9145}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida/*metabolism ; Indian Ocean ; Mucus ; Nitrogen/*analysis ; *Nitrogen Fixation ; Nitrogen Isotopes ; Seawater/*chemistry ; Symbiosis ; }, abstract = {Scleractinian corals are essential constituents of tropical reef ecological diversity. They live in close association with diazotrophs [dinitrogen (N2)-fixing microbes], which can fix high rates of N2. Whether corals benefit from this extrinsic nitrogen source is still under debate. Until now, N2 fixation rates have been indirectly estimated using the acetylene reduction assay, which does not permit assessment of the amount of nitrogen incorporated into the different compartments of the coral holobiont. In the present study, the (15)N2 technique was applied for the first time on three Red Sea coral species. Significant (15)N enrichment was measured in particles released by corals to the surrounding seawater. N2 fixation rates were species specific and as high as 1.6-2 ng N day(-1) l(-1). However, no significant enrichment was measured in the symbiotic dinoflagellates or the coral host tissues, suggesting that corals do not benefit from diazotrophic N2 fixation.}, }
@article {pmid25272328, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.}, journal = {Marine drugs}, volume = {12}, number = {10}, pages = {5089-5122}, pmid = {25272328}, issn = {1660-3397}, mesh = {Animals ; Archaea/physiology ; Bacteria/metabolism ; Fungi/physiology ; Humans ; Porifera/*microbiology ; Quorum Sensing/*physiology ; Symbiosis/*physiology ; }, abstract = {Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.}, }
@article {pmid25222772, year = {2014}, author = {Singh, Y and Hasnain, SE}, title = {Holobionts: emerging strategy for interventions against infectious diseases, metabolic disorders &amp; cancer.}, journal = {The Indian journal of medical research}, volume = {140}, number = {1}, pages = {11-14}, pmid = {25222772}, issn = {0975-9174}, mesh = {*Biological Evolution ; Communicable Diseases/microbiology/*therapy ; *Ecosystem ; Genome, Human/*genetics ; Humans ; Metabolic Diseases/microbiology/*therapy ; Microbiota/*genetics ; Neoplasms/microbiology/*therapy ; }, }
@article {pmid25213651, year = {2015}, author = {Fernando, SC and Wang, J and Sparling, K and Garcia, GD and Francini-Filho, RB and de Moura, RL and Paranhos, R and Thompson, FL and Thompson, JR}, title = {Microbiota of the major South Atlantic reef building coral Mussismilia.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {267-280}, pmid = {25213651}, issn = {1432-184X}, support = {P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Brazil ; Cloning, Molecular ; Coral Reefs ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gene Library ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation.}, }
@article {pmid25205353, year = {2014}, author = {Bosch, TC and Adamska, M and Augustin, R and Domazet-Loso, T and Foret, S and Fraune, S and Funayama, N and Grasis, J and Hamada, M and Hatta, M and Hobmayer, B and Kawai, K and Klimovich, A and Manuel, M and Shinzato, C and Technau, U and Yum, S and Miller, DJ}, title = {How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {12}, pages = {1185-1194}, pmid = {25205353}, issn = {1521-1878}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cnidaria/classification/genetics/*growth &amp; development ; Ecosystem ; Extinction, Biological ; Gene Expression Regulation, Developmental ; *Gene-Environment Interaction ; Life Cycle Stages/*genetics ; Metamorphosis, Biological/genetics ; Phylogeny ; Porifera/classification/genetics/*growth &amp; development ; Signal Transduction ; }, abstract = {Ecological developmental biology (eco-devo) explores the mechanistic relationships between the processes of individual development and environmental factors. Recent studies imply that some of these relationships have deep evolutionary origins, and may even pre-date the divergences of the simplest extant animals, including cnidarians and sponges. Development of these early diverging metazoans is often sensitive to environmental factors, and these interactions occur in the context of conserved signaling pathways and mechanisms of tissue homeostasis whose detailed molecular logic remain elusive. Efficient methods for transgenesis in cnidarians together with the ease of experimental manipulation in cnidarians and sponges make them ideal models for understanding causal relationships between environmental factors and developmental mechanisms. Here, we identify major questions at the interface between animal evolution and development and outline a road map for research aimed at identifying the mechanisms that link environmental factors to developmental mechanisms in early diverging metazoans. Also watch the Video Abstract.}, }
@article {pmid25202306, year = {2014}, author = {Parkinson, JE and Baums, IB}, title = {The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral-algal associations.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {445}, pmid = {25202306}, issn = {1664-302X}, abstract = {Reef-building corals owe much of their success to a symbiosis with dinoflagellate microalgae in the genus Symbiodinium. In this association, the performance of each organism is tied to that of its partner, and together the partners form a holobiont that can be subject to selection. Climate change affects coral reefs, which are declining globally as a result. Yet the extent to which coral holobionts will be able to acclimate or evolve to handle climate change and other stressors remains unclear. Selection acts on individuals and evidence from terrestrial systems demonstrates that intraspecific genetic diversity plays a significant role in symbiosis ecology and evolution. However, we have a limited understanding of the effects of such diversity in corals. As molecular methods have advanced, so too has our recognition of the taxonomic and functional diversity of holobiont partners. Resolving the major components of the holobiont to the level of the individual will help us assess the importance of intraspecific diversity and partner interactions in coral-algal symbioses. Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. Our synthesis is derived from reviewing existing evidence and presenting novel data. By incorporating the effects of holobiont extended phenotypes into predictive models, we may refine our understanding of the evolutionary trajectory of corals and reef communities responding to climate change.}, }
@article {pmid25202301, year = {2014}, author = {Roth, MS}, title = {The engine of the reef: photobiology of the coral-algal symbiosis.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {422}, pmid = {25202301}, issn = {1664-302X}, abstract = {Coral reef ecosystems thrive in tropical oligotrophic oceans because of the relationship between corals and endosymbiotic dinoflagellate algae called Symbiodinium. Symbiodinium convert sunlight and carbon dioxide into organic carbon and oxygen to fuel coral growth and calcification, creating habitat for these diverse and productive ecosystems. Light is thus a key regulating factor shaping the productivity, physiology, and ecology of the coral holobiont. Similar to all oxygenic photoautotrophs, Symbiodinium must safely harvest sunlight for photosynthesis and dissipate excess energy to prevent oxidative stress. Oxidative stress is caused by environmental stressors such as those associated with global climate change, and ultimately leads to breakdown of the coral-algal symbiosis known as coral bleaching. Recently, large-scale coral bleaching events have become pervasive and frequent threatening and endangering coral reefs. Because the coral-algal symbiosis is the biological engine producing the reef, the future of coral reef ecosystems depends on the ecophysiology of the symbiosis. This review examines the photobiology of the coral-algal symbiosis with particular focus on the photophysiological responses and timescales of corals and Symbiodinium. Additionally, this review summarizes the light environment and its dynamics, the vulnerability of the symbiosis to oxidative stress, the abiotic and biotic factors influencing photosynthesis, the diversity of the coral-algal symbiosis, and recent advances in the field. Studies integrating physiology with the developing "omics" fields will provide new insights into the coral-algal symbiosis. Greater physiological and ecological understanding of the coral-algal symbiosis is needed for protection and conservation of coral reefs.}, }
@article {pmid25199498, year = {2014}, author = {Pillai, P and Gouhier, TC and Vollmer, SV}, title = {The cryptic role of biodiversity in the emergence of host-microbial mutualisms.}, journal = {Ecology letters}, volume = {17}, number = {11}, pages = {1437-1446}, doi = {10.1111/ele.12349}, pmid = {25199498}, issn = {1461-0248}, mesh = {*Biodiversity ; Ecosystem ; Genetic Fitness ; Microbiota ; *Models, Biological ; *Symbiosis ; }, abstract = {The persistence of mutualisms in host-microbial - or holobiont - systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist 'cheater' species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host-microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales.}, }
@article {pmid25191338, year = {2014}, author = {Gilbert, SF}, title = {A holobiont birth narrative: the epigenetic transmission of the human microbiome.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {282}, pmid = {25191338}, issn = {1664-8021}, abstract = {This essay plans to explore, expand, and re-tell the human birth narrative. Usually, human birth narratives focus on the origins of a new individual, focusing on the mother and fetus. This essay discusses birth as the origin of a new community. For not only is the eukaryotic body being reproduced, but so also are the bodies of its symbiotic microbes and so is the set of relationships between these organic components. Several parts of the new narrative are surprising: (1) bacterial symbionts might cause some of the characteristics of pregnancy and prepare a symbiotic community for transfer; (2) the first bacterial colonizers of the mammalian organism my enter the fetus prior to the lysing of the amniotic membrane and birth; (3) the same signals that often cause immunological attack against a microbe may serve under these conditions to signal homeostatic stability between symbiont and host; and (4) the mother may actively provide substances that promote the growth and settlement of helpful bacteria. The birth of the holobiont exemplifies principles of co-evolution, co-development, niche construction, and scaffolding. Birth is nothing less than the passage from one set of symbiotic relationships to another.}, }
@article {pmid25190333, year = {2014}, author = {Li, J and Dong, JD and Yang, J and Luo, XM and Zhang, S}, title = {Detection of polyketide synthase and nonribosomal peptide synthetase biosynthetic genes from antimicrobial coral-associated actinomycetes.}, journal = {Antonie van Leeuwenhoek}, volume = {106}, number = {4}, pages = {623-635}, doi = {10.1007/s10482-014-0233-1}, pmid = {25190333}, issn = {1572-9699}, mesh = {Actinobacteria/*classification/*enzymology/genetics ; Animals ; Anthozoa/*microbiology ; *Biodiversity ; China ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Genes, Bacterial ; Molecular Sequence Data ; Peptide Synthases/*genetics ; Phylogeny ; Polyketide Synthases/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The diversity and properties of actinobacteria, predominant residents in coral holobionts, have been rarely documented. In this study, we aimed to explore the species diversity, antimicrobial activities and biosynthetic potential of culturable actinomycetes within the tissues of the scleractinian corals Porites lutea, Galaxea fascicularis and Acropora millepora from the South China Sea. A total of 70 strains representing 13 families and 15 genera of actinobacteria were isolated. The antimicrobial activity and biosynthetic potential of fifteen representative filamentous actinomycetes were estimated. Crude fermentation extracts of 6 strains exhibited comparable or greater activities against Vibrio alginolyticus than ciprofloxacin. Seven of the 15 actinomycetes strains possess type I polyketide synthases (PKS-I) and/or nonribosomal peptide synthetases (NRPS) genes. Nine tested strains possess type II polyketide synthases (PKS-II). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these PKS and NRPS gene screening positive strains belong to genera Nocardiopsis, Pseudonocardia, Streptomyces, Micromonospora, Amycolatopsis and Prauserella. One PKS-I and four NRPS fragments showed <70% similarity to their closest relatives, which suggested the novelty of these genes. This study helps uncover the genetic capacity of stony coral-associated actinomycetes to produce bioactive molecules.}, }
@article {pmid25178787, year = {2014}, author = {Watson, J and Degnan, B and Degnan, S and Krömer, JO}, title = {Determining the biomass composition of a sponge holobiont for flux analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1191}, number = {}, pages = {107-125}, doi = {10.1007/978-1-4939-1170-7_7}, pmid = {25178787}, issn = {1940-6029}, mesh = {Animals ; Biomass ; Bisbenzimidazole ; DNA/*analysis ; Fluorometry/methods ; Metabolic Flux Analysis/*methods ; *Models, Biological ; Porifera/anatomy &amp; histology/growth &amp; development/*metabolism/*microbiology ; Proteins/analysis ; Species Specificity ; *Symbiosis ; }, abstract = {The first step on the path of flux analysis of a new organism with little available literature is the determination of the biomass composition. Once the content of the macromolecular components (protein, RNA, DNA, carbohydrates, lipids) and their composition is known, this composition can be converted into a biomass equation. The biomass equation is an important part of metabolic flux analysis. This equation provides the information about the precursor and energy needs for growth. In many experiments the determination of the growth rate is the simplest flux to be determined, yet this rate determines the net fluxes of a whole range of anabolic pathways in the system and often is used as the objective function in FBA analysis. The challenge for the scientist is to create a biomass equation that represents the organisms of choice under the conditions studied. This chapter outlines basic protocols that can be applied to the quantification of the macromolecular components, using the marine demosponge Amphimedon queenslandica as a case study. As is true for all other sponges and indeed marine animals, A. queenslandica is a holobiont, comprising an animal host plus symbiotic and other associated microbial cells. We show how this complexity can be overcome by developing a fast, yet robust, method for biomass quantification of sponges using the displacement volume. The analytical protocols we describe herein are widely applicable not only to other organisms sampled from complex environments but also to cell cultures. The second part of the chapter highlights the procedures needed to convert a macromolecular composition into a biomass equation.}, }
@article {pmid26988195, year = {2014}, author = {Probert, I and Siano, R and Poirier, C and Decelle, J and Biard, T and Tuji, A and Suzuki, N and Not, F}, title = {Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians.}, journal = {Journal of phycology}, volume = {50}, number = {2}, pages = {388-399}, doi = {10.1111/jpy.12174}, pmid = {26988195}, issn = {1529-8817}, abstract = {Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.}, }
@article {pmid25729239, year = {2014}, author = {Torday, JS}, title = {On the evolution of development.}, journal = {Trends in developmental biology}, volume = {8}, number = {}, pages = {17-37}, pmid = {25729239}, issn = {0972-8422}, support = {R01 HL055268/HL/NHLBI NIH HHS/United States ; }, abstract = {Perhaps development is more than just morphogenesis. We now recognize that the conceptus expresses epigenetic marks that heritably affect it phenotypically, indicating that the offspring are to some degree genetically autonomous, and that ontogeny and phylogeny may coordinately determine the fate of such marks. This scenario mechanistically links ecology, ontogeny and phylogeny together as an integrated mechanism for evolution for the first time. As a functional example, the Parathyroid Hormone-related Protein (PTHrP) signaling duplicated during the Phanerozoic water-land transition. The PTHrP signaling pathway was critical for the evolution of the skeleton, skin barrier, and lung function, based on experimental evidence, inferring that physiologic stress can profoundly affect adaptation through internal selection, giving seminal insights to how and why vertebrates were able to evolve from water to land. By viewing evolution from its inception in unicellular organisms, driven by competition between pro- and eukaryotes, the emergence of complex biologic traits from the unicellular cell membrane offers a novel way of thinking about the process of evolution from its beginnings, rather than from its consequences as is traditionally done. And by focusing on the epistatic balancing mechanisms for calcium and lipid homeostasis, the evolution of unicellular organisms, driven by competition between pro- and eukaryotes, gave rise to the emergence of complex biologic traits derived from the unicellular plasma lemma, offering a unique way of thinking about the process of evolution. By exploiting the cellular-molecular mechanisms of lung evolution as ontogeny and phylogeny, the sequence of events for the evolution of the skin, kidney and skeleton become more transparent. This novel approach to the evolution question offers equally novel insights to the primacy of the unicellular state, hologenomics and even a priori bioethical decisions.}, }
@article {pmid26925190, year = {2013}, author = {Paz-Y-Miño-C, G and Espinosa, A}, title = {Galapagos III World Evolution Summit: why evolution matters.}, journal = {Evolution}, volume = {6}, number = {}, pages = {}, pmid = {26925190}, issn = {1936-6426}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; }, abstract = {There is no place on Earth like the Galapagos Islands and no better destination to discuss the reality of evolution. Under the theme 'Why Does Evolution Matter', the University San Francisco of Quito (USFQ), Ecuador, and its Galapagos Institute for the Arts and Sciences (GAIAS), organized the III World Evolution Summit in San Cristóbal Island. The 200-attendee meeting took place on 1 to 5 June 2013; it included 12 keynote speakers, 20 oral presentations by international scholars, and 31 posters by faculty, postdocs, and graduate and undergraduate students. The Summit encompassed five sessions: evolution and society, pre-cellular evolution and the RNA world, behavior and environment, genome, and microbes and diseases. USFQ and GAIAS launched officially the Lynn Margulis Center for Evolutionary Biology and showcased the Galapagos Science Center, in San Cristóbal, an impressive research facility conceptualized in partnership with the University of North Carolina at Chapel Hill, USA. USFQ and GAIAS excelled at managing the conference with exceptional vision and at highlighting the relevance of Galapagos in the history of modern evolutionary thinking; Charles Darwin's visit to this volcanic archipelago in 1835 unfolded unprecedented scientific interest in what today is a matchless World Heritage.}, }
@article {pmid32214633, year = {2012}, author = {Hewson, I and Brown, JM and Burge, CA and Couch, CS and LaBarre, BA and Mouchka, ME and Naito, M and Harvell, CD}, title = {Description of viral assemblages associated with the Gorgonia ventalina holobiont.}, journal = {Coral reefs (Online)}, volume = {31}, number = {2}, pages = {487-491}, pmid = {32214633}, issn = {1432-0975}, abstract = {The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.}, }
@article {pmid25171444, year = {2015}, author = {Bettarel, Y and Bouvier, T and Nguyen, HK and Thu, PT}, title = {The versatile nature of coral-associated viruses.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3433-3439}, doi = {10.1111/1462-2920.12579}, pmid = {25171444}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/microbiology/*virology ; Bacteria/*virology ; Bacteriophages/growth &amp; development ; Coral Reefs ; Dinoflagellida/*virology ; Phycodnaviridae/*growth &amp; development ; }, abstract = {A recent hypothesis considers that many coral pathologies are the result of a sudden structural alteration of the epibiotic bacterial communities in response to environmental disturbances. However, the ecological mechanisms that lead to shifts in their composition are still unclear. In the ocean, viruses represent a major bactericidal agent but little is known on their occurrence within the coral holobiont. Recent reports have revealed that viruses are abundant and diversified within the coral mucus and therefore could be decisive for coral health. However, their mode of action is still unknown, and there is now an urgent need to shed light on the nature of the relationships they might have with the other prokaryotic and eukaryotic members of the holobiont. In this opinion letter, we are putting forward the hypothesis that coral-associated viruses (mostly bacterial and algal viruses), depending on the environmental conditions might either reinforce coral stability or conversely fasten their decline. We propose that these processes are presumably based on an environmentally driven shift in infection strategies allowing viruses to regulate, circumstantially, both coral symbionts (bacteria or Symbiodinium) and surrounding pathogens.}, }
@article {pmid25170145, year = {2014}, author = {Brucker, RM and Bordenstein, SR}, title = {Response to Comment on "The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia".}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6200}, pages = {1011}, doi = {10.1126/science.1256708}, pmid = {25170145}, issn = {1095-9203}, mesh = {Animals ; Bacteria/*classification ; Gastrointestinal Tract/*microbiology ; Germ-Free Life/*physiology ; Hymenoptera/*microbiology/*physiology ; *Symbiosis ; }, abstract = {Chandler and Turelli postulate that intrinsic hybrid dysfunction underscores hybrid lethality in Nasonia. Although it is a suitable conception for examining hybrid incompatibilities, their account of the evidence is factually inaccurate and leaves out the evolutionary process for why lethality became conditional on nuclear-microbe interactions. Hybrid incompatibilities in the context of phylosymbiosis are resolved by hologenomic principles and exemplify this emerging postmodern synthesis.}, }
@article {pmid25170144, year = {2014}, author = {Chandler, JA and Turelli, M}, title = {Comment on "The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia".}, journal = {Science (New York, N.Y.)}, volume = {345}, number = {6200}, pages = {1011}, pmid = {25170144}, issn = {1095-9203}, support = {R01 GM104325/GM/NIGMS NIH HHS/United States ; R01-GM-104325-01/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*classification ; Gastrointestinal Tract/*microbiology ; Germ-Free Life/*physiology ; Hymenoptera/*microbiology/*physiology ; *Symbiosis ; }, abstract = {Brucker and Bordenstein (Reports, 9 August 2013, p. 667) claim that adaptive codivergence of gut bacteria with hosts contributes to hybrid lethality. Yet, they provide no evidence for coadaptation of bacteria and Nasonia hosts. Their data on hybrid viability suggest that bacteria contribute to inviability only because intrinsic hybrid dysfunction increases susceptibility to free-living bacteria. Hologenomic speciation remains testable speculation without experimental support.}, }
@article {pmid25156176, year = {2014}, author = {Lema, KA and Bourne, DG and Willis, BL}, title = {Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora.}, journal = {Molecular ecology}, volume = {23}, number = {19}, pages = {4682-4695}, doi = {10.1111/mec.12899}, pmid = {25156176}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; Bacteria/*classification/genetics ; Genes, Bacterial ; Life Cycle Stages ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Early establishment of coral-microbial symbioses is fundamental to the fitness of corals, but comparatively little is known about the onset and succession of bacterial communities in their early life history stages. In this study, bacterial associates of the coral Acropora millepora were characterized throughout the first year of life, from larvae and 1-week-old juveniles reared in laboratory conditions in the absence of the dinoflagellate endosymbiont Symbiodinium to field-outplanted juveniles with established Symbiodinium symbioses, and sampled at 2 weeks and at 3, 6 and 12 months. Using an amplicon pyrosequencing approach, the diversity of both nitrogen-fixing bacteria and of bacterial communities overall was assessed through analysis of nifH and 16S rRNA genes, respectively. The consistent presence of sequences affiliated with diazotrophs of the order Rhizobiales (23-58% of retrieved nifH sequences; 2-12% of 16S rRNA sequences), across all samples from larvae to 12-month-old coral juveniles, highlights the likely functional importance of this nitrogen-fixing order to the coral holobiont. Dominance of Roseobacter-affiliated sequences (>55% of retrieved 16S rRNA sequences) in larvae and 1-week-old juveniles, and the consistent presence of sequences related to Oceanospirillales and Altermonadales throughout all early life history stages, signifies their potential importance as coral associates. Increased diversity of bacterial communities once juveniles were transferred to the field, particularly of Cyanobacteria and Deltaproteobacteria, demonstrates horizontal (environmental) uptake of coral-associated bacterial communities. Although overall bacterial communities were dynamic, bacteria with likely important functional roles remain stable throughout early life stages of Acropora millepora.}, }
@article {pmid25120558, year = {2014}, author = {Dittami, SM and Barbeyron, T and Boyen, C and Cambefort, J and Collet, G and Delage, L and Gobet, A and Groisillier, A and Leblanc, C and Michel, G and Scornet, D and Siegel, A and Tapia, JE and Tonon, T}, title = {Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {241}, pmid = {25120558}, issn = {1664-8021}, abstract = {Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The "Ca. P. ectocarpi" genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, "Ca. P. ectocarpi" has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus "Phaeomarinobacter" may comprise several species, which may colonize different niches.}, }
@article {pmid25117532, year = {2015}, author = {Davis, TS}, title = {The ecology of yeasts in the bark beetle holobiont: a century of research revisited.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {723-732}, pmid = {25117532}, issn = {1432-184X}, mesh = {Animals ; Larva/growth &amp; development/microbiology ; Ovum/growth &amp; development/microbiology ; Pheromones/physiology ; Pupa/growth &amp; development/microbiology ; *Symbiosis ; Weevils/growth &amp; development/*microbiology ; Yeasts/*physiology ; }, abstract = {Yeasts are extremely common associates of scolytine bark beetles, yet the basic ecology of yeasts in the bark beetle holobiont remains poorly understood. Yeasts are present in all beetle life stages and consistently isolated from adult, larval, and pupal integuments and mycangial structures, but yeasts are also found in oviposition galleries, pupal chambers, larval and adult digestive tracts, as well as phloem and xylem tissues. Yeasts in the Saccharomycetaceae family are the most prevalent associates, and most individual beetles are associated with only one or several yeast species. Kuraishia capsulata and Ogataea pini are the most commonly encountered yeast species in surveys of Dendroctonus and Ips beetles; most beetles that have been surveyed are vectors for one or both yeasts. Yeasts have significant but often overlooked functional roles in bark beetle ecology. Infochemicals resulting from volatile production by yeast have wide-ranging bioactivity for arthropods: Yeast emissions attract beetles at low concentrations but repel beetles at high concentrations, and yeast emissions can also serve as cues to predators and parasites of bark beetles. In some cases, yeasts can modify tree chemistry over time or metabolize toxic terpenoids, though potential consequences for beetle performance or the growth of nutritional fungi remain to be demonstrated. Also, the presence of yeast species can restrict or promote the establishment and growth of filamentous fungi, including mutualists, entomopathogens, and opportunistic saprophytes. The role of yeasts as nutritional symbionts has received mixed support, though a nutritional hypothesis has not been extensively tested. Continued research on the functional ecology of bark beetle-yeast associations is needed to better understand the emergent properties of these complex symbiont assemblages.}, }
@article {pmid25071729, year = {2014}, author = {Zchori-Fein, E and Lahav, T and Freilich, S}, title = {Variations in the identity and complexity of endosymbiont combinations in whitefly hosts.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {310}, pmid = {25071729}, issn = {1664-302X}, abstract = {The target of natural selection is suggested to be the holobiont - the organism together with its associated symbiotic microorganisms. The well-defined endosymbiotic communities of insects make them a useful model for exploring the role of symbiotic interactions in shaping the functional repertoire of plants and animals. Here, we studied the variations in the symbiotic communities of the sweet potato whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) by compiling a dataset of over 2000 individuals derived from several independent screenings. The secondary endosymbionts harbored by each individual were clustered into entities termed Facultative Endosymbiont Combinations (FECs), each representing a natural assemblage of co-occurring bacterial genera. The association of FECs with whitefly individuals stratified the otherwise homogeneous population into holobiont units. We both identified bacterial assemblages that are specific to whitefly groups sharing unique genetic backgrounds, and characterized the FEC variations within these groups. The analysis revealed that FEC complexity is positively correlated with both distance from the equator and specificity of the genetic clade of the host insect. These findings highlight the importance of symbiotic combinations in shaping the distribution patterns of B. tabaci and possibly other insect species.}, }
@article {pmid25070863, year = {2014}, author = {Doo, SS and Fujita, K and Byrne, M and Uthicke, S}, title = {Fate of calcifying tropical symbiont-bearing large benthic foraminifera: living sands in a changing ocean.}, journal = {The Biological bulletin}, volume = {226}, number = {3}, pages = {169-186}, doi = {10.1086/BBLv226n3p169}, pmid = {25070863}, issn = {1939-8697}, mesh = {Animals ; Calcification, Physiologic ; Climate Change ; Coral Reefs ; Foraminifera/*physiology ; Geologic Sediments ; Oceans and Seas ; *Symbiosis ; Tropical Climate ; }, abstract = {Concerns regarding the response of calcifiers in future warmer and more acidic oceans have been raised in many studies. Tropical large benthic foraminifera (LBF) are important carbonate producers that reside in coral reefs worldwide. Similar to corals, these organisms live in symbioses with microalgae, which promote high calcification rates. The contribution of LBFs to reef sediments is under threat due to climate change. In this review, we synthesize research conducted on the effects of increased temperature and acidification on these organisms, and assess the potential impacts on reef carbonate production. A meta-analysis of all available experimental data (18 publications, 84 individual experiments) on the effects of ocean warming and acidification on LBF holobiont health was performed using log-transformed response ratios (LnRR) comparing present-day ambient and projected future scenarios. For the latter, we used Representative Concentration Pathway 8.5 from the Intergovernmental Panel on Climate Change, which projects changes of +4 °C and -0.3 pH units by the year 2100. Overall, a general negative trend on holobiont growth was observed across most species of LBFs in response to both stressors. The only exception was the hyaline species (porous CaCO3 test composed of interlocking microcrystals) that have diatom symbionts. Species in this group appear resilient to future ocean acidification scenarios. Differences in the response of LBF species to warming and acidifying oceans may be due to (1) differences in the carbonate species' use in formation of the CaCO3 skeleton (CO2 vs. CO3(2-)), (2) varied responses of the symbiont types (diatom, dinoflagellate, rhodophyte) to stressors, or (3) the degree of nutritional dependence of the host to its symbiont. We also summarize current estimates of carbonate production by LBFs to provide a context of their contribution to reefs. Finally, we outline major gaps in knowledge in addressing the potential for LBF species persistence in a changing ocean.}, }
@article {pmid25058318, year = {2014}, author = {Moree, WJ and McConnell, OJ and Nguyen, DD and Sanchez, LM and Yang, YL and Zhao, X and Liu, WT and Boudreau, PD and Srinivasan, J and Atencio, L and Ballesteros, J and Gavilán, RG and Torres-Mendoza, D and Guzmán, HM and Gerwick, WH and Gutiérrez, M and Dorrestein, PC}, title = {Microbiota of healthy corals are active against fungi in a light-dependent manner.}, journal = {ACS chemical biology}, volume = {9}, number = {10}, pages = {2300-2308}, pmid = {25058318}, issn = {1554-8937}, support = {S10RR029121/RR/NCRR NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 TW006634/TW/FIC NIH HHS/United States ; AI095125/AI/NIAID NIH HHS/United States ; TW006634/TW/FIC NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Antifungal Agents/isolation &amp; purification/*pharmacology ; Fungi/*drug effects ; *Light ; *Microbiota ; Molecular Sequence Data ; Pseudoalteromonas/growth &amp; development/*isolation &amp; purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Symbiosis/*physiology ; }, abstract = {Coral reefs are intricate ecosystems that harbor diverse organisms, including 25% of all marine fish. Healthy corals exhibit a complex symbiosis between coral polyps, endosymbiotic alga, and an array of microorganisms, called the coral holobiont. Secretion of specialized metabolites by coral microbiota is thought to contribute to the defense of this sessile organism against harmful biotic and abiotic factors. While few causative agents of coral diseases have been unequivocally identified, fungi have been implicated in the massive destruction of some soft corals worldwide. Because corals are nocturnal feeders, they may be more vulnerable to fungal infection at night, and we hypothesized that the coral microbiota would have the capability to enhance their defenses against fungi in the dark. A Pseudoalteromonas sp. isolated from a healthy octocoral displayed light-dependent antifungal properties when grown adjacent to Penicillium citrinum (P. citrinum) isolated from a diseased Gorgonian octocoral. Microbial MALDI-imaging mass spectrometry (IMS) coupled with molecular network analyses revealed that Pseudoalteromonas produced higher levels of antifungal polyketide alteramides in the dark than in the light. The alteramides were inactivated by light through a photoinduced intramolecular cyclization. Further NMR studies led to a revision of the stereochemical structure of the alteramides. Alteramide A exhibited antifungal properties and elicited changes in fungal metabolite distributions of mycotoxin citrinin and citrinadins. These data support the hypothesis that coral microbiota use abiotic factors such as light to regulate the production of metabolites with specialized functions to combat opportunistic pathogens at night.}, }
@article {pmid25050199, year = {2014}, author = {Erdman, SE and Poutahidis, T}, title = {The microbiome modulates the tumor macroenvironment.}, journal = {Oncoimmunology}, volume = {3}, number = {}, pages = {e28271}, pmid = {25050199}, issn = {2162-4011}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; U01 CA164337/CA/NCI NIH HHS/United States ; }, abstract = {Earlier investigations of the tumor microenvironment unveiled systemic networks presenting novel therapeutic opportunities. It has been recently shown that gut microbes modulate whole host immune and neuroendocrine factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. These findings establish a new paradigm of holobiont therapeutic engineering in emerging tumor macroenvironments.}, }
@article {pmid25044878, year = {2014}, author = {Grottoli, AG and Warner, ME and Levas, SJ and Aschaffenburg, MD and Schoepf, V and McGinley, M and Baumann, J and Matsui, Y}, title = {The cumulative impact of annual coral bleaching can turn some coral species winners into losers.}, journal = {Global change biology}, volume = {20}, number = {12}, pages = {3823-3833}, doi = {10.1111/gcb.12658}, pmid = {25044878}, issn = {1365-2486}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Animals ; Anthozoa/*microbiology/*physiology ; Caribbean Region ; Dinoflagellida/*physiology ; Photosynthesis/physiology ; Species Specificity ; Stress, Physiological/*physiology ; *Symbiosis ; *Temperature ; }, abstract = {Mass coral bleaching events caused by elevated seawater temperatures result in extensive coral loss throughout the tropics, and are projected to increase in frequency and severity. If bleaching becomes an annual event later in this century, more than 90% of coral reefs worldwide may be at risk of long-term degradation. While corals can recover from single isolated bleaching and can acclimate to recurring bleaching events that are separated by multiple years, it is currently unknown if and how they will survive and possibly acclimatize to annual coral bleaching. Here, we demonstrate for the first time that annual coral bleaching can dramatically alter thermal tolerance in Caribbean corals. We found that high coral energy reserves and changes in the dominant algal endosymbiont type (Symbiodinium spp.) facilitated rapid acclimation in Porites divaricata, whereas low energy reserves and a lack of algal phenotypic plasticity significantly increased susceptibility in Porites astreoides to bleaching the following year. Phenotypic plasticity in the dominant endosymbiont type of Orbicella faveolata did not prevent repeat bleaching, but may have facilitated rapid recovery. Thus, coral holobiont response to an isolated single bleaching event is not an accurate predictor of its response to bleaching the following year. Rather, the cumulative impact of annual coral bleaching can turn some coral species 'winners' into 'losers', and can also facilitate acclimation and turn some coral species 'losers' into 'winners'. Overall, these findings indicate that cumulative impact of annual coral bleaching could result in some species becoming increasingly susceptible to bleaching and face a long-term decline, while phenotypically plastic coral species will acclimatize and persist. Thus, annual coral bleaching and recovery could contribute to the selective loss of coral diversity as well as the overall decline of coral reefs in the Caribbean.}, }
@article {pmid25016412, year = {2014}, author = {Gust, KA and Najar, FZ and Habib, T and Lotufo, GR and Piggot, AM and Fouke, BW and Laird, JG and Wilbanks, MS and Rawat, A and Indest, KJ and Roe, BA and Perkins, EJ}, title = {Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress.}, journal = {BMC genomics}, volume = {15}, number = {1}, pages = {591}, pmid = {25016412}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/drug effects/*genetics/metabolism ; Dinoflagellida/drug effects/*genetics/metabolism ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Stress, Physiological ; Symbiosis ; Transcriptome/*drug effects ; Triazines/*pharmacology ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {BACKGROUND: Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater).<br><br>RESULTS: RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5. Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral/zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (i.e. cytochrome P450 and UDP glucuronosyltransferase 2 family) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal.<br><br>CONCLUSIONS: Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts.}, }
@article {pmid24995875, year = {2014}, author = {McFall-Ngai, MJ}, title = {The importance of microbes in animal development: lessons from the squid-vibrio symbiosis.}, journal = {Annual review of microbiology}, volume = {68}, number = {}, pages = {177-194}, pmid = {24995875}, issn = {1545-3251}, support = {R01 AI050661/AI/NIAID NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Decapodiformes/*growth &amp; development/*microbiology/physiology ; *Symbiosis ; Vibrio/*physiology ; }, abstract = {Developmental biology is among the many subdisciplines of the life sciences being transformed by our increasing awareness of the role of coevolved microbial symbionts in health and disease. Most symbioses are horizontally acquired, i.e., they begin anew each generation. In such associations, the embryonic period prepares the animal to engage with the coevolved partner(s) with fidelity following birth or hatching. Once interactions are underway, the microbial partners drive maturation of tissues that are either directly associated with or distant from the symbiont populations. Animal alliances often involve complex microbial communities, such as those in the vertebrate gastrointestinal tract. A series of simpler-model systems is providing insight into the basic rules and principles that govern the establishment and maintenance of stable animal-microbe partnerships. This review focuses on what biologists have learned about the developmental trajectory of horizontally acquired symbioses through the study of the binary squid-vibrio model.}, }
@article {pmid24992663, year = {2014}, author = {Dheilly, NM}, title = {Holobiont-Holobiont interactions: redefining host-parasite interactions.}, journal = {PLoS pathogens}, volume = {10}, number = {7}, pages = {e1004093}, pmid = {24992663}, issn = {1553-7374}, mesh = {Animals ; *Host-Pathogen Interactions ; Humans ; Plant Diseases ; Plants ; }, }
@article {pmid24983638, year = {2014}, author = {Leal, MC and Sheridan, C and Osinga, R and Dionísio, G and Rocha, RJ and Silva, B and Rosa, R and Calado, R}, title = {Marine microorganism-invertebrate assemblages: perspectives to solve the "supply problem" in the initial steps of drug discovery.}, journal = {Marine drugs}, volume = {12}, number = {7}, pages = {3929-3952}, pmid = {24983638}, issn = {1660-3397}, mesh = {Animals ; Aquaculture ; *Biological Products ; Cnidaria/metabolism ; *Drug Discovery ; Invertebrates/*metabolism ; *Marine Biology ; Mollusca/metabolism ; Porifera/metabolism ; *Water Microbiology ; }, abstract = {The chemical diversity associated with marine natural products (MNP) is unanimously acknowledged as the "blue gold" in the urgent quest for new drugs. Consequently, a significant increase in the discovery of MNP published in the literature has been observed in the past decades, particularly from marine invertebrates. However, it remains unclear whether target metabolites originate from the marine invertebrates themselves or from their microbial symbionts. This issue underlines critical challenges associated with the lack of biomass required to supply the early stages of the drug discovery pipeline. The present review discusses potential solutions for such challenges, with particular emphasis on innovative approaches to culture invertebrate holobionts (microorganism-invertebrate assemblages) through in toto aquaculture, together with methods for the discovery and initial production of bioactive compounds from these microbial symbionts.}, }
@article {pmid24982156, year = {2014}, author = {Kelly, LW and Williams, GJ and Barott, KL and Carlson, CA and Dinsdale, EA and Edwards, RA and Haas, AF and Haynes, M and Lim, YW and McDole, T and Nelson, CE and Sala, E and Sandin, SA and Smith, JE and Vermeij, MJ and Youle, M and Rohwer, F}, title = {Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10227-10232}, pmid = {24982156}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; *Bacteria/genetics/metabolism ; *Coral Reefs ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; Pacific Ocean ; *Water Pollution ; }, abstract = {Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.}, }
@article {pmid24960461, year = {2014}, author = {Watson, JR and Brennan, TC and Degnan, BM and Degnan, SM and Krömer, JO}, title = {Analysis of the biomass composition of the demosponge Amphimedon queenslandica on Heron Island Reef, Australia.}, journal = {Marine drugs}, volume = {12}, number = {6}, pages = {3733-3753}, pmid = {24960461}, issn = {1660-3397}, mesh = {Amino Acids/chemistry/isolation &amp; purification ; Animals ; Australia ; *Biomass ; Fatty Acids/chemistry/isolation &amp; purification ; Genome ; Genomics/*methods ; Models, Genetic ; Porifera/genetics/*metabolism ; }, abstract = {Marine sponges are a potential source of important pharmaceutical drugs, the commercialisation of which is restricted by the difficulties of obtaining a sufficient and regular supply of biomass. One way to optimize commercial cell lines for production is the in-depth characterization and target identification through genome scale metabolic modeling and flux analysis. By applying these tools to a sponge, we hope to gain insights into how biomass is formed. We chose Amphimedon queenslandica as it has an assembled and annotated genome, a prerequisite for genome scale modeling. The first stepping stone on the way to metabolic flux analysis in a sponge holobiont, is the characterization of its biomass composition. In this study we quantified the macromolecular composition and investigated the variation between and within sponges of a single population. We found lipids and protein to be the most abundant macromolecules, while carbohydrates were the most variable. We also analysed the composition and abundance of the fatty acids and amino acids, the important building blocks required to synthesise the abundant macromolecule types, lipids, and protein. These data complement the extensive genomic information available for A. queenslandica and lay the basis for genome scale modelling and flux analysis.}, }
@article {pmid24950107, year = {2014}, author = {Closek, CJ and Sunagawa, S and DeSalvo, MK and Piceno, YM and DeSantis, TZ and Brodie, EL and Weber, MX and Voolstra, CR and Andersen, GL and Medina, M}, title = {Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.}, journal = {The ISME journal}, volume = {8}, number = {12}, pages = {2411-2422}, pmid = {24950107}, issn = {1751-7370}, mesh = {Alveolata/classification/isolation &amp; purification ; Animals ; Anthozoa/*genetics/metabolism/*microbiology ; Bacteria/*classification/isolation &amp; purification ; *Transcriptome ; }, abstract = {Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.}, }
@article {pmid24926286, year = {2014}, author = {Berg, G and Grube, M and Schloter, M and Smalla, K}, title = {Unraveling the plant microbiome: looking back and future perspectives.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {148}, pmid = {24926286}, issn = {1664-302X}, support = {I 183/FWF_/Austrian Science Fund FWF/Austria ; I 882/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {Most eukaryotes develop close interactions with microorganisms that are essential for their performance and survival. Thus, eukaryotes and prokaryotes in nature can be considered as meta-organisms or holobionts. Consequently, microorganisms that colonize different plant compartments contain the plant's second genome. In this respect, many studies in the last decades have shown that plant-microbe interactions are not only crucial for better understanding plant growth and health, but also for sustainable crop production in a changing world. This mini-review acting as editorial presents retrospectives and future perspectives for plant microbiome studies as well as information gaps in this emerging research field. In addition, the contribution of this research topic to the solution of various issues is discussed.}, }
@article {pmid24860565, year = {2014}, author = {Yarden, O}, title = {Fungal association with sessile marine invertebrates.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {228}, pmid = {24860565}, issn = {1664-302X}, abstract = {The presence and association of fungi with sessile marine animals such as coral and sponges has been well established, yet information on the extent of diversity of the associated fungi is still in its infancy. Culture - as well as metagenomic - and transcriptomic-based analyses have shown that fungal presence in association with these animals can be dynamic and can include "core" residents as well as shifts in fungal communities. Evidence for detrimental and beneficial interactions between fungi and their marine hosts is accumulating and current challenges include the elucidation of the chemical and cellular crosstalk between fungi and their associates within the holobionts. The ecological function of fungi in association with sessile marine animals is complex and is founded on a combination of factors such as fungal origin, host health, environmental conditions and the presence of other resident or invasive microorganisms in the host. Based on evidence from the much more studied terrestrial systems, the evaluation of marine animal-fungal symbioses under varying environmental conditions may well prove to be critical in predicting ecosystem response to global change, including effects on the health of sessile marine animals.}, }
@article {pmid24860563, year = {2014}, author = {Luter, HM and Gibb, K and Webster, NS}, title = {Eutrophication has no short-term effect on the Cymbastela stipitata holobiont.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {216}, pmid = {24860563}, issn = {1664-302X}, abstract = {Levels of nitrogen in coastal areas have been rapidly increasing due to accumulative inputs of sewage and terrigenous sediments carrying fertilizers. Sponges have an immense filtering capacity and may be directly impacted (positively or negatively) by elevated concentrations of nitrogen. Sponges also host a wide diversity of microbes involved in nitrogen metabolism, yet little is known about the effects of nitrogen loading on these symbiotic partnerships. Manipulative experiments were undertaken to examine the potential effects of excess nitrogen (up to 240 μM) on microbial symbiosis in the abundant sponge species Cymbastela stipitata. Microbial composition and activity were examined using 454-pyrotag sequencing of DNA- and RNA-derived samples. Despite the high levels of nitrogen exposure (up to 124-fold above ambient), sponges appeared visibly unaffected at all treatment concentrations. At the phylum level, the microbial community was consistent between all sponge samples regardless of nitrogen treatment, with Cyanobacteria and Thaumarchaeota being the dominant taxa. Higher microbial diversity was observed at the operational taxonomic units (OTU) level (97% sequence similarity), with only 40% of OTUs shared between samples from all treatments. However, a single cyanobacterial OTU dominated the community of all individuals (average 73.5%) and this OTU did not vary with nitrogen treatment. The conserved microbial community in all sponges irrespective of nitrogen treatment highlights the stability of the sponge-microbe relationship and indicates that the holobiont is resistant to short pulses of nitrogen at levels mimicking sewage effluent.}, }
@article {pmid24847321, year = {2014}, author = {Weynberg, KD and Wood-Charlson, EM and Suttle, CA and van Oppen, MJ}, title = {Generating viral metagenomes from the coral holobiont.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {206}, pmid = {24847321}, issn = {1664-302X}, abstract = {Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis.}, }
@article {pmid24814756, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus.}, journal = {Molecular ecology}, volume = {23}, number = {12}, pages = {3097-3112}, doi = {10.1111/mec.12789}, pmid = {24814756}, issn = {1365-294X}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {In spite of their putative relevance to host functioning, in-depth knowledge of sponge microbiome stability over time is scarce. This study tackles the temporal maintenance of bacterial and archaeal assemblages in the model host Sarcotragus spinosulus along three successive years. Prokaryotic communities were profiled by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and 454-pyrosequencing of S. spinosulus-derived 16S rRNA gene amplicons. Prevailing bacterial phyla were Actinobacteria, Acidobacteria, Proteobacteria, Poribacteria, PAUC34f, Chloroflexi and Bacteroidetes, with Bacteroidetes, Chloroflexi and Poribacteria showing different abundances over the years. At the approximate species level (operational taxonomic units, OTUs, defined at 97% sequence similarity), no major changes in bacterial richness and composition were found through time. Nearly 50% of all detected bacterial symbionts (96 in 205 OTUs) were recovered from all sampling years, whereas a taxonomically equivalent community of less dominant bacteria characterized the transient sponge microbiota. Despite the evidence for temporal symbiont maintenance, an intriguing cumulative degree of variation between individuals was unravelled, with all the surveyed sponge specimens sharing only 27 bacterial OTUs. Archaeal communities were dominated by one single symbiont of the candidate genus Nitrosopumilus (Thaumarchaeota), known for its ability to aerobically oxidize ammonia to nitrite. Only few bacterial ammonia oxidizers consistently occurred in S. spinosulus across the years as documented by PCR-DGGE fingerprinting. In conclusion, prokaryotic symbionts of S. spinosulus display a state of dynamic stability shaped by the interplay between the maintenance of dominant players and turnover of less prevalent community members, in time and across host individuals, with no apparent consequences to holobiont functioning.}, }
@article {pmid24782852, year = {2014}, author = {Webster, NS}, title = {Cooperation, communication, and co-evolution: grand challenges in microbial symbiosis research.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {164}, pmid = {24782852}, issn = {1664-302X}, }
@article {pmid24778636, year = {2014}, author = {Poutahidis, T and Kleinewietfeld, M and Erdman, SE}, title = {Gut microbiota and the paradox of cancer immunotherapy.}, journal = {Frontiers in immunology}, volume = {5}, number = {}, pages = {157}, pmid = {24778636}, issn = {1664-3224}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; R01 CA108854/CA/NCI NIH HHS/United States ; U01 CA164337/CA/NCI NIH HHS/United States ; }, abstract = {It is recently shown that beneficial environmental microbes stimulate integrated immune and neuroendocrine factors throughout the body, consequently modulating regulatory T-lymphocyte phenotypes, maintaining systemic immune balance, and determining the fate of preneoplastic lesions toward regression while sustaining whole body good health. Stimulated by a gut microbiota-centric systemic homeostasis hypothesis, we set out to explore the influence of the gut microbiome to explain the paradoxical roles of regulatory T-lymphocytes in cancer development and growth. This paradigm shift places cancer prevention and treatment into a new broader context of holobiont engineering to cultivate a tumor-suppressive macroenvironment.}, }
@article {pmid24769774, year = {2014}, author = {Rivest, EB and Hofmann, GE}, title = {Responses of the metabolism of the larvae of Pocillopora damicornis to ocean acidification and warming.}, journal = {PloS one}, volume = {9}, number = {4}, pages = {e96172}, pmid = {24769774}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*metabolism ; Carbon Dioxide/chemistry ; Citrate (si)-Synthase/metabolism ; Global Warming ; Hydrogen-Ion Concentration ; Larva/metabolism ; Oxygen Consumption ; Pacific Ocean ; Temperature ; }, abstract = {Ocean acidification and warming are expected to threaten the persistence of tropical coral reef ecosystems. As coral reefs face multiple stressors, the distribution and abundance of corals will depend on the successful dispersal and settlement of coral larvae under changing environmental conditions. To explore this scenario, we used metabolic rate, at holobiont and molecular levels, as an index for assessing the physiological plasticity of Pocillopora damicornis larvae from this site to conditions of ocean acidity and warming. Larvae were incubated for 6 hours in seawater containing combinations of CO2 concentration (450 and 950 µatm) and temperature (28 and 30°C). Rates of larval oxygen consumption were higher at elevated temperatures. In contrast, high CO2 levels elicited depressed metabolic rates, especially for larvae released later in the spawning period. Rates of citrate synthase, a rate-limiting enzyme in aerobic metabolism, suggested a biochemical limit for increasing oxidative capacity in coral larvae in a warming, acidifying ocean. Biological responses were also compared between larvae released from adult colonies on the same day (cohorts). The metabolic physiology of Pocillopora damicornis larvae varied significantly by day of release. Additionally, we used environmental data collected on a reef in Moorea, French Polynesia to provide information about what adult corals and larvae may currently experience in the field. An autonomous pH sensor provided a continuous time series of pH on the natal fringing reef. In February/March, 2011, pH values averaged 8.075 ± 0.023. Our results suggest that without adaptation or acclimatization, only a portion of naïve Pocillopora damicornis larvae may have suitable metabolic phenotypes for maintaining function and fitness in an end-of-the century ocean.}, }
@article {pmid24736967, year = {2014}, author = {Stazi, MA and Toccaceli, V}, title = {[Genome and microbiome: hologenome. Is epigenetics their link?].}, journal = {Epidemiologia e prevenzione}, volume = {38}, number = {1}, pages = {67-68}, pmid = {24736967}, issn = {1120-9763}, mesh = {Animals ; *Epigenomics ; Gene Transfer, Horizontal ; *Genome ; Germ-Free Life ; Humans ; Intestines/microbiology ; Mice ; MicroRNAs/genetics ; *Microbiota ; }, }
@article {pmid24736154, year = {2014}, author = {Gilbert, SF}, title = {Symbiosis as the way of eukaryotic life: the dependent co-origination of the body.}, journal = {Journal of biosciences}, volume = {39}, number = {2}, pages = {201-209}, pmid = {24736154}, issn = {0973-7138}, mesh = {Animals ; Biological Evolution ; Genetic Variation ; Humans ; Microbiota/immunology ; Selection, Genetic ; *Symbiosis ; }, abstract = {Molecular analyses of symbiotic relationships are challenging our biological definitions of individuality and supplanting them with a new notion of normal part-whole relationships. This new notion is that of a 'holobiont', a consortium of organisms that becomes a functionally integrated 'whole'. This holobiont includes the zoological organism (the 'animal') as well as its persistent microbial symbionts. This new individuality is seen on anatomical and physiological levels, where a diversity of symbionts form a new 'organ system' within the zoological organism and become integrated into its metabolism and development. Moreover, as in normal development, there are reciprocal interactions between the 'host' organism and its symbionts that alter gene expression in both sets of cells. The immune system, instead of being seen as functioning solely to keep microbes out of the body, is also found to develop, in part, in dialogue with symbionts. Moreover, the immune system is actively involved in the colonization of the zoological organism, functioning as a mechanism for integrating microbes into the animal-cell community. Symbionts have also been found to constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. We develop, grow and evolve as multi-genomic consortia/teams/ecosystems.}, }
@article {pmid24594773, year = {2014}, author = {Fujita, K and Okai, T and Hosono, T}, title = {Oxygen metabolic responses of three species of large benthic foraminifers with algal symbionts to temperature stress.}, journal = {PloS one}, volume = {9}, number = {3}, pages = {e90304}, pmid = {24594773}, issn = {1932-6203}, mesh = {Climate Change ; Foraminifera/*metabolism/physiology ; Microalgae/*metabolism/physiology ; Oxygen/*metabolism ; *Stress, Physiological ; *Symbiosis ; *Temperature ; }, abstract = {Water temperature affects the physiology of large benthic foraminifers (LBFs) with algal symbionts dwelling in coral reef environments. However, the detailed physiological responses of LBF holobionts to temperature ranges occurring in their habitats are not known. We report net oxygen (O2) production and respiration rates of three LBF holobionts (Baculogypsina sphaerulata and Calcarina gaudichaudii hosting diatom symbionts, and Amphisorus kudakajimensis hosting dinoflagellate symbionts) measured in the laboratory at water temperatures ranging from 5°C to 45°C in 2.5°C or 5°C intervals and with light saturation levels of ∼500 µmol m(-2) s(-1). In addition, the recovery of net O2 production and respiration rates after exposure to temperature stress was assessed. The net O2 production and respiration rates of the three LBF holobionts peaked at ∼30°C, indicating their optimal temperature for a short exposure period. At extreme high temperatures (≥40°C), the net O2 production rates of all three LBF holobionts declined to less than zero and the respiration rates slightly decreased, indicating that photosynthesis of algal symbionts was inactivated. At extreme low temperatures (≤10°C for two calcarinid species and ≤5°C for A. kudakajimensis), the net O2 production and respiration rates were near zero, indicating a weakening of holobiont activity. After exposure to extreme high or low temperature, the net O2 production rates did not recover until the following day, whereas the respiration rates recovered rapidly, suggesting that a longer time (days) is required for recovery from damage to the photosystem by temperature stress compared to the respiration system. These results indicate that the oxygen metabolism of LBF holobionts can generally cope well with conditions that fluctuate diurnally and seasonally in their habitats. However, temporal heat and cold stresses with high light levels may induce severe damage to algal symbionts and also damage to host foraminifers.}, }
@article {pmid24577740, year = {2014}, author = {He, L and Liu, F and Karuppiah, V and Ren, Y and Li, Z}, title = {Comparisons of the fungal and protistan communities among different marine sponge holobionts by pyrosequencing.}, journal = {Microbial ecology}, volume = {67}, number = {4}, pages = {951-961}, pmid = {24577740}, issn = {1432-184X}, mesh = {Animals ; China ; DNA, Fungal/genetics ; DNA, Protozoan/genetics ; Eukaryota/genetics/physiology ; Fungi/genetics/physiology ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*microbiology/*parasitology ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; Symbiosis ; }, abstract = {To date, the knowledge of eukaryotic communities associated with sponges remains limited compared with prokaryotic communities. In a manner similar to prokaryotes, it could be hypothesized that sponge holobionts have phylogenetically diverse eukaryotic symbionts, and the eukaryotic community structures in different sponge holobionts were probably different. In order to test this hypothesis, the communities of eukaryota associated with 11 species of South China Sea sponges were compared with the V4 region of 18S ribosomal ribonucleic acid gene using 454 pyrosequencing. Consequently, 135 and 721 unique operational taxonomic units (OTUs) of fungi and protists were obtained at 97 % sequence similarity, respectively. These sequences were assigned to 2 phyla of fungi (Ascomycota and Basidiomycota) and 9 phyla of protists including 5 algal phyla (Chlorophyta, Haptophyta, Streptophyta, Rhodophyta, and Stramenopiles) and 4 protozoal phyla (Alveolata, Cercozoa, Haplosporidia, and Radiolaria) including 47 orders (12 fungi, 35 protists). Entorrhizales of fungi and 18 orders of protists were detected in marine sponges for the first time. Particularly, Tilletiales of fungi and Chlorocystidales of protists were detected for the first time in marine habitats. Though Ascomycota, Alveolata, and Radiolaria were detected in all the 11 sponge species, sponge holobionts have different fungi and protistan communities according to OTU comparison and principal component analysis at the order level. This study provided the first insights into the fungal and protistan communities associated with different marine sponge holobionts using pyrosequencing, thus further extending the knowledge on sponge-associated eukaryotic diversity.}, }
@article {pmid24568029, year = {2013}, author = {Guerrero, R and Margulis, L and Berlanga, M}, title = {Symbiogenesis: the holobiont as a unit of evolution.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {16}, number = {3}, pages = {133-143}, doi = {10.2436/20.1501.01.188}, pmid = {24568029}, issn = {1139-6709}, mesh = {Animals ; Bacteria/*genetics ; *Biological Evolution ; Insecta/*genetics/*microbiology/physiology ; *Microbiota ; Selection, Genetic ; *Symbiosis ; }, abstract = {Symbiogenesis is the result of the permanent coexistence of various bionts to form the holobiont (namely, the host and its microbiota). The holobiome is the sum total of the component genomes in a eukaryotic organism; it comprises the genome of an individual member of a given taxon (the host genome) and the microbiome (the genomes of the symbiotic microbiota). The latter is made up of the genes of a variety of microbial communities that persist over time and are not eliminated by natural selection. Therefore, the holobiome can also be considered as the genomic reflection of the complex network of symbiotic interactions that link an individual member of a given taxon with its associated microbiome. Eukaryotic individuals can be analyzed as coevolved, tightly integrated, prokaryotic communities; in this view, natural selection acts on the holobiont as if it were an integrated unit. The best studied holobionts are those that emerged from symbioses involving insects. The presence of symbiotic associations throughout most of the evolutionary history of insects suggests that they were a driving force in the diversification of this group. Support for the evolutionary importance of symbiogenesis comes from the observation that the gradual passage from an ancestral to a descendant species by the accumulation of random mutations has not been demonstrated in the field, nor in the laboratory, nor in the fossil record. Instead, symbiogenesis expands the view of the point-mutation-only as the unique mechanisms of evolution and offers an explanation for the discontinuities in the fossil record ("punctuated equilibrium"). As such, it challenges conventional paradigms in biology. This review describes the relationships between xylophagous insects and their microbiota in an attempt to understand the characteristics that have determined bacterial fidelity over generations and throughout evolutionary history.}, }
@article {pmid24463735, year = {2014}, author = {Li, ZY and Wang, YZ and He, LM and Zheng, HJ}, title = {Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics.}, journal = {Scientific reports}, volume = {4}, number = {}, pages = {3895}, pmid = {24463735}, issn = {2045-2322}, mesh = {Animals ; Carbon Monoxide/metabolism ; *Metagenomics ; Nitrogen/metabolism ; Phylogeny ; Porifera/chemistry/*genetics/metabolism ; Symbiosis ; }, abstract = {The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi [corrected] . at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi [corrected]. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi [corrected].}, }
@article {pmid24454815, year = {2014}, author = {Shinzato, C and Inoue, M and Kusakabe, M}, title = {A snapshot of a coral "holobiont": a transcriptome assembly of the scleractinian coral, porites, captures a wide variety of genes from both the host and symbiotic zooxanthellae.}, journal = {PloS one}, volume = {9}, number = {1}, pages = {e85182}, pmid = {24454815}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*genetics ; Polymorphism, Genetic ; *Symbiosis ; *Transcriptome ; }, abstract = {Massive scleractinian corals of the genus Porites are important reef builders in the Indo-Pacific, and they are more resistant to thermal stress than other stony corals, such as the genus Acropora. Because coral health and survival largely depend on the interaction between a coral host and its symbionts, it is important to understand the molecular interactions of an entire "coral holobiont". We simultaneously sequenced transcriptomes of Porites australiensis and its symbionts using the Illumina Hiseq2000 platform. We obtained 14.3 Gbp of sequencing data and assembled it into 74,997 contigs (average: 1,263 bp, N50 size: 2,037 bp). We successfully distinguished contigs originating from the host (Porites) and the symbiont (Symbiodinium) by aligning nucleotide sequences with the decoded Acropora digitifera and Symbiodinium minutum genomes. In contrast to previous coral transcriptome studies, at least 35% of the sequences were found to have originated from the symbionts, indicating that it is possible to analyze both host and symbiont transcriptomes simultaneously. Conserved protein domain and KEGG analyses showed that the dataset contains broad gene repertoires of both Porites and Symbiodinium. Effective utilization of sequence reads revealed that the polymorphism rate in P. australiensis is 1.0% and identified the major symbiotic Symbiodinium as Type C15. Analyses of amino acid biosynthetic pathways suggested that this Porites holobiont is probably able to synthesize most of the common amino acids and that Symbiodinium is potentially able to provide essential amino acids to its host. We believe this to be the first molecular evidence of complementarity in amino acid metabolism between coral hosts and their symbionts. We successfully assembled genes originating from both the host coral and the symbiotic Symbiodinium to create a snapshot of the coral holobiont transcriptome. This dataset will facilitate a deeper understanding of molecular mechanisms of coral symbioses and stress responses.}, }
@article {pmid24454551, year = {2014}, author = {Reusch, TB}, title = {Climate change in the oceans: evolutionary versus phenotypically plastic responses of marine animals and plants.}, journal = {Evolutionary applications}, volume = {7}, number = {1}, pages = {104-122}, pmid = {24454551}, issn = {1752-4571}, abstract = {I summarize marine studies on plastic versus adaptive responses to global change. Due to the lack of time series, this review focuses largely on the potential for adaptive evolution in marine animals and plants. The approaches were mainly synchronic comparisons of phenotypically divergent populations, substituting spatial contrasts in temperature or CO2 environments for temporal changes, or in assessments of adaptive genetic diversity within populations for traits important under global change. The available literature is biased towards gastropods, crustaceans, cnidarians and macroalgae. Focal traits were mostly environmental tolerances, which correspond to phenotypic buffering, a plasticity type that maintains a functional phenotype despite external disturbance. Almost all studies address coastal species that are already today exposed to fluctuations in temperature, pH and oxygen levels. Recommendations for future research include (i) initiation and analyses of observational and experimental temporal studies encompassing diverse phenotypic traits (including diapausing cues, dispersal traits, reproductive timing, morphology) (ii) quantification of nongenetic trans-generational effects along with components of additive genetic variance (iii) adaptive changes in microbe-host associations under the holobiont model in response to global change (iv) evolution of plasticity patterns under increasingly fluctuating environments and extreme conditions and (v) joint consideration of demography and evolutionary adaptation in evolutionary rescue approaches.}, }
@article {pmid24452239, year = {2014}, author = {Sela, DA and Mills, DA}, title = {The marriage of nutrigenomics with the microbiome: the case of infant-associated bifidobacteria and milk.}, journal = {The American journal of clinical nutrition}, volume = {99}, number = {3}, pages = {697S-703S}, pmid = {24452239}, issn = {1938-3207}, support = {R01 AT007079/AT/NCCIH NIH HHS/United States ; }, mesh = {Animals ; Bifidobacterium/*growth &amp; development/metabolism ; Biomedical Research/trends ; *Child Development ; *Evidence-Based Medicine ; Humans ; Infant ; Infant Formula ; *Infant Nutritional Physiological Phenomena ; Infant, Newborn ; Intestines/growth &amp; development/*microbiology ; Milk ; *Milk, Human ; Nutrigenomics/methods/trends ; *Symbiosis ; }, abstract = {Broadly, nutrigenomics examines the association of exogenous nutrients and molecular responses to maintain homeostasis in an individual. Phenotypic expression profiling, often transcriptomics, has been applied to identify markers and metabolic consequences of suboptimal diet, lifestyle, or both. The decade after the Human Genome Project has been marked with advances in high-throughput analysis of biological polymers and metabolites, prompting a rapid increase in characterization of the profound nature by which our symbiotic microbiota influences human physiology. Although the technology is widely accessible to assess microbiome composition, genetic potential, and global function, nutrigenomics studies often exclude the microbial contribution to host responses to ingested nutritive molecules. Perhaps a hallmark of coevolution, milk provides a dramatic example of a diet that promotes a particular microbial community structure, because the lower infant gastrointestinal tract is often dominated by bifidobacteria that flourish on milk glycans. Systems-level approaches should continue to be applied to examine the microbial communities in the context of their host's dietary habits and metabolic status. In addition, studies of isolated microbiota species should be encouraged to inform clinical studies and interventions as well as community studies. Whereas nutrigenomics research is beginning to account for resident microbiota, the need remains to consistently consider our microscopic partners in the human holobiont.}, }
@article {pmid24447216, year = {2014}, author = {Dittami, SM and Eveillard, D and Tonon, T}, title = {A metabolic approach to study algal-bacterial interactions in changing environments.}, journal = {Molecular ecology}, volume = {23}, number = {7}, pages = {1656-1660}, doi = {10.1111/mec.12670}, pmid = {24447216}, issn = {1365-294X}, mesh = {Acclimatization ; Bacteria/*metabolism ; Biological Evolution ; Chlorophyta/*metabolism/*microbiology ; *Environment ; Models, Biological ; }, abstract = {Increasing evidence exists that bacterial communities interact with and shape the biology of algae and that their evolutionary histories are connected. Despite these findings, physiological studies were and still are generally carried out with axenic or at least antibiotic-treated cultures. Here, we argue that considering interactions between algae and associated bacteria is key to understanding their biology and evolution. To deal with the complexity of the resulting 'holobiont' system, a metabolism-centred approach that uses combined metabolic models for algae and associated bacteria is proposed. We believe that these models will be valuable tools both to study algal-bacterial interactions and to elucidate processes important for the acclimation of the holobiont to environmental changes.}, }
@article {pmid24373029, year = {2014}, author = {Lema, KA and Willis, BL and Bourne, DG}, title = {Amplicon pyrosequencing reveals spatial and temporal consistency in diazotroph assemblages of the Acropora millepora microbiome.}, journal = {Environmental microbiology}, volume = {16}, number = {10}, pages = {3345-3359}, doi = {10.1111/1462-2920.12366}, pmid = {24373029}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; *Microbiota/genetics ; *Nitrogen Fixation/genetics ; Oxidoreductases/genetics ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Diazotrophic bacteria potentially play an important functional role in supplying fixed nitrogen to the coral holobiont, but the value of such a partnership depends on the stability of the association. Here we evaluate the composition of diazotroph assemblages associated with the coral Acropora millepora throughout four seasons and at two reefs, an inshore and an offshore (mid-shelf) reef on the Great Barrier Reef, Australia. Amplicon pyrosequencing of the nifH gene revealed that diazotrophs are ubiquitous members of the bacterial community associated with A. millepora. Rhizobia (65% of the overall nifH sequences retrieved) and particularly Bradyrhizobia sp.-affiliated sequences (> 50% of rhizobia sequences) dominated diazotrophic assemblages across all coral samples from the two sites throughout the year. In contrast to this consistency in the spatial and temporal patterns of occurrence of diazotroph assemblages, the overall coral-associated bacterial community, assessed through amplicon sequencing of the general bacterial 16S ribosomal RNA gene, differed between inshore and mid-shelf reef locations. Sequences associated with the Oceanospirillales family, particularly with Endozoicomonas sp., dominated bacterial communities associated with inshore corals. Although rhizobia represented a variable and generally small fraction of the overall bacterial community associated with A. millepora, consistency in the structure of these diazotrophic assemblages suggests that they have a functional role in the coral holobiont.}, }
@article {pmid24372150, year = {2014}, author = {Foster, C and Portman, N and Chen, M and Šlapeta, J}, title = {Increased growth and pigment content of Chromera velia in mixotrophic culture.}, journal = {FEMS microbiology ecology}, volume = {88}, number = {1}, pages = {121-128}, doi = {10.1111/1574-6941.12275}, pmid = {24372150}, issn = {1574-6941}, mesh = {Alveolata/*growth &amp; development/isolation &amp; purification/physiology ; Animals ; Anthozoa/physiology ; Chlorophyll/metabolism ; *Coral Reefs ; Culture Media/chemistry ; Photosynthesis ; }, abstract = {The alveolate microalga Chromera velia is an evolutionarily significant organism, representing the closest photosynthetic relative of the parasitic Apicomplexa. Chromera velia has been detected in and isolated from several stony corals and can be readily cultured in vitro under strictly autotrophic conditions. However, little is known about the ecology of this organism in the coral holobiont, an environment in which it could potentially access abundant organic carbon sources. To understand the response of C. velia to ecologically relevant organic compounds in vitro, we tested a mixotrophic culture strategy by supplementing inorganic f-medium with sugars, sugar-alcohols, organic acids and amino acids. For 15 of the 18 tested growth media, culture growth rate was significantly higher than that of strictly autotrophic cultures, and in three of these, a significant increase in maximum culture density was observed. In cultures supplemented with glutamate or glycine, the chlorophyll content per cell was up to 11-fold higher than cultures grown in standard inorganic media. Together, the in vitro culture growth and pigment responses demonstrate an ability to respond to nutritional resources when available. We propose that C. velia is a facultative opportunist in environments similarly enriched in such organic compounds, such as the coral holobiont.}, }
@article {pmid24370863, year = {2014}, author = {Frydenborg, BR and Krediet, CJ and Teplitski, M and Ritchie, KB}, title = {Temperature-dependent inhibition of opportunistic Vibrio pathogens by native coral commensal bacteria.}, journal = {Microbial ecology}, volume = {67}, number = {2}, pages = {392-401}, pmid = {24370863}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Chitinases/metabolism ; Coculture Techniques ; Glycoside Hydrolases/metabolism ; Peptide Hydrolases/metabolism ; Symbiosis ; *Temperature ; Vibrio/*growth &amp; development/isolation &amp; purification/*metabolism ; Virulence Factors/metabolism ; }, abstract = {Bacteria living within the surface mucus layer of corals compete for nutrients and space. A number of stresses affect the outcome of this competition. The interactions between native microorganisms and opportunistic pathogens largely determine the coral holobiont's overall health and fitness. In this study, we tested the hypothesis that commensal bacteria isolated from the mucus layer of a healthy elkhorn coral, Acropora palmata, are capable of inhibition of opportunistic pathogens, Vibrio shiloi AK1 and Vibrio coralliilyticus. These vibrios are known to cause disease in corals and their virulence is temperature dependent. Elevated temperature (30 °C) increased the cell numbers of one commensal and both Vibrio pathogens in monocultures. We further tested the hypothesis that elevated temperature favors pathogenic organisms by simultaneously increasing the fitness of vibrios and decreasing the fitness of commensals by measuring growth of each species within a co-culture over the course of 1 week. In competition experiments between vibrios and commensals, the proportion of Vibrio spp. increased significantly under elevated temperature. We finished by investigating several temperature-dependent mechanisms that could influence co-culture differences via changes in competitive fitness. The ability of Vibrio spp. to utilize glycoproteins found in A. palmata mucus increased or remained stable when exposed to elevated temperature, while commensals' tended to decrease utilization. In both vibrios and commensals, protease activity increased at 30 °C, while chiA expression increased under elevated temperatures for Vibrio spp. These results provide insight into potential mechanisms through which elevated temperature may select for pathogenic bacterial dominance and lead to disease or a decrease in coral fitness.}, }
@article {pmid24350609, year = {2014}, author = {Roder, C and Arif, C and Daniels, C and Weil, E and Voolstra, CR}, title = {Bacterial profiling of White Plague Disease across corals and oceans indicates a conserved and distinct disease microbiome.}, journal = {Molecular ecology}, volume = {23}, number = {4}, pages = {965-974}, pmid = {24350609}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics ; Caribbean Region ; DNA, Bacterial/genetics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral diseases are characterized by microbial community shifts in coral mucus and tissue, but causes and consequences of these changes are vaguely understood due to the complexity and dynamics of coral-associated bacteria. We used 16S rRNA gene microarrays to assay differences in bacterial assemblages of healthy and diseased colonies displaying White Plague Disease (WPD) signs from two closely related Caribbean coral species, Orbicella faveolata and Orbicella franksi. Analysis of differentially abundant operational taxonomic units (OTUs) revealed strong differences between healthy and diseased specimens, but not between coral species. A subsequent comparison to data from two Indo-Pacific coral species (Pavona duerdeni and Porites lutea) revealed distinct microbial community patterns associated with ocean basin, coral species and health state. Coral species were clearly separated by site, but also, the relatedness of the underlying bacterial community structures resembled the phylogenetic relationship of the coral hosts. In diseased samples, bacterial richness increased and putatively opportunistic bacteria were consistently more abundant highlighting the role of opportunistic conditions in structuring microbial community patterns during disease. Our comparative analysis shows that it is possible to derive conserved bacterial footprints of diseased coral holobionts that might help in identifying key bacterial species related to the underlying etiopathology. Furthermore, our data demonstrate that similar-appearing disease phenotypes produce microbial community patterns that are consistent over coral species and oceans, irrespective of the putative underlying pathogen. Consequently, profiling coral diseases by microbial community structure over multiple coral species might allow the development of a comparative disease framework that can inform on cause and relatedness of coral diseases.}, }
@article {pmid24334358, year = {2013}, author = {Pratte, ZA}, title = {Microbial functional genes associated with coral health and disease.}, journal = {Diseases of aquatic organisms}, volume = {107}, number = {2}, pages = {161-171}, doi = {10.3354/dao02664}, pmid = {24334358}, issn = {0177-5103}, mesh = {Animals ; Anthozoa/*genetics ; Ecosystem ; Gene Expression Regulation/*physiology ; Genetic Variation ; Nitrogen/metabolism ; }, abstract = {Both the incidence and prevalence of coral disease are rapidly increasing, and as a consequence, many studies involving coral microbial associates have been conducted. However, very few of these have considered microbial functional genes. This is an underutilized approach for studying coral disease etiology which is capable of revealing the molecular processes of the coral microbial community. This review presents a summary of the known microbial functional genes that have been linked to coral health and disease. Overall functional gene diversity tended to be lower in healthy corals than diseased or bleached corals, and respiration and photosynthesis functional genes appeared to be crucial to coral health. Genes associated with the nitrogen cycle were the most studied, were highly represented within the coral holobiont, and their expression often shifted in diseased or stressed individuals. Carbon metabolism, such as fatty acid and amino acid catabolism, also tended to shift in unhealthy corals. Genes associated with sulfite respiration as well as dimethylsulfoniopropionate degradation have been detected, although they have yet to be directly associated with coral disease. In addition, genes associated with xenobiotic degradation, antibiotic resistance, virulence, and oxidative stress may all be involved in maintaining coral health. However, the links between these functional genes and their roles in interacting with the coral host are not clear. Continuing identification of coral-associated microbial functional genes within the coral holobiont should facilitate advances in the field of coral health and disease.}, }
@article {pmid24286558, year = {2014}, author = {Desriac, F and Le Chevalier, P and Brillet, B and Leguerinel, I and Thuillier, B and Paillard, C and Fleury, Y}, title = {Exploring the hologenome concept in marine bivalvia: haemolymph microbiota as a pertinent source of probiotics for aquaculture.}, journal = {FEMS microbiology letters}, volume = {350}, number = {1}, pages = {107-116}, doi = {10.1111/1574-6968.12308}, pmid = {24286558}, issn = {1574-6968}, mesh = {Animals ; Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Aquaculture ; Bivalvia/*microbiology ; Cell Survival ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Dose-Response Relationship, Drug ; France ; Gram-Negative Bacteria/drug effects ; Gram-Positive Bacteria/drug effects ; Hemocytes/drug effects ; Hemolymph/*microbiology ; Microbial Sensitivity Tests ; Microbiota ; Phylogeny ; Probiotics/*isolation &amp; purification ; Pseudoalteromonas/*chemistry/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Haemolymph-associated microbiota of marine bivalves was explored for antibacterial activity against important aquaculture pathogens. A collection of 843 strains were cultured from the haemolymph of four bivalve species (Crassostrea gigas, Mytilus edulis, Pecten maximus and Tapes rhomboides) collected by deep-sea diving in the Glenan Archipelago (France). Cell-free culture supernatants were investigated for antibacterial activity using the well-diffusion assay. About 3% of haemolymph-associated cultivable bacteria displayed antibacterial activity toward Gram-negative pathogens. Among the active bacteria, Pseudoalteromonas strains exhibited the highest antibacterial activity. The cell-free culture supernatant of one of them, named hCg-51, was able to inhibit the growth of bacterial pathogens even after drastic dilution (1 : 1024). Hemocyte survival was not significantly altered in the presence of the haemolymph-associated strains assayed. Moreover, a dose-dependent beneficial effect on hemocyte survival rates was observed with the hCg-51 strain. These results suggest that haemolymph microbiota may participate in bivalve protection and therefore confer a health benefit on the host. As a result, the results highlight bivalve haemolymph microbiota as a promising novel source for aquaculture probiotics. This work also gives a first insight into the contribution of the haemolymph-associated microbiota as part of the bivalve 'hologenome'.}, }
@article {pmid24286462, year = {2014}, author = {Stilling, RM and Dinan, TG and Cryan, JF}, title = {Microbial genes, brain &amp; behaviour - epigenetic regulation of the gut-brain axis.}, journal = {Genes, brain, and behavior}, volume = {13}, number = {1}, pages = {69-86}, doi = {10.1111/gbb.12109}, pmid = {24286462}, issn = {1601-183X}, mesh = {Animals ; Brain/*metabolism/physiopathology ; *Chromatin Assembly and Disassembly ; *Epigenesis, Genetic ; Gene-Environment Interaction ; *Genes, Bacterial ; Host-Pathogen Interactions ; Humans ; Intestines/*microbiology ; *Microbiota ; Stress, Psychological/genetics/*microbiology ; }, abstract = {To date, there is rapidly increasing evidence for host-microbe interaction at virtually all levels of complexity, ranging from direct cell-to-cell communication to extensive systemic signalling, and involving various organs and organ systems, including the central nervous system. As such, the discovery that differential microbial composition is associated with alterations in behaviour and cognition has significantly contributed to establishing the microbiota-gut-brain axis as an extension of the well-accepted gut-brain axis concept. Many efforts have been focused on delineating a role for this axis in health and disease, ranging from stress-related disorders such as depression, anxiety and irritable bowel syndrome to neurodevelopmental disorders such as autism. There is also a growing appreciation of the role of epigenetic mechanisms in shaping brain and behaviour. However, the role of epigenetics in informing host-microbe interactions has received little attention to date. This is despite the fact that there are many plausible routes of interaction between epigenetic mechanisms and the host-microbiota dialogue. From this new perspective we put forward novel, yet testable, hypotheses. Firstly, we suggest that gut-microbial products can affect chromatin plasticity within their host's brain that in turn leads to changes in neuronal transcription and eventually alters host behaviour. Secondly, we argue that the microbiota is an important mediator of gene-environment interactions. Finally, we reason that the microbiota itself may be viewed as an epigenetic entity. In conclusion, the fields of (neuro)epigenetics and microbiology are converging at many levels and more interdisciplinary studies are necessary to unravel the full range of this interaction.}, }
@article {pmid24278392, year = {2013}, author = {Hughes, AD and Grottoli, AG}, title = {Heterotrophic compensation: a possible mechanism for resilience of coral reefs to global warming or a sign of prolonged stress?.}, journal = {PloS one}, volume = {8}, number = {11}, pages = {e81172}, pmid = {24278392}, issn = {1932-6203}, mesh = {Autotrophic Processes ; Carbon/metabolism ; *Coral Reefs ; Ecosystem ; *Global Warming ; *Heterotrophic Processes ; Phototrophic Processes ; Seasons ; Temperature ; }, abstract = {Thermally induced bleaching has caused a global decline in corals and the frequency of such bleaching events will increase. Thermal bleaching severely disrupts the trophic behaviour of the coral holobiont, reducing the photosynthetically derived energy available to the coral host. In the short term this reduction in energy transfer from endosymbiotic algae results in an energy deficit for the coral host. If the bleaching event is short-lived then the coral may survive this energy deficit by depleting its lipid reserves, or by increasing heterotrophic energy acquisition. We show for the first time that the coral animal is capable of increasing the amount of heterotrophic carbon incorporated into its tissues for almost a year following bleaching. This prolonged heterotrophic compensation could be a sign of resilience or prolonged stress. If the heterotrophic compensation is in fact an acclimatization response, then this physiological response could act as a buffer from future bleaching by providing sufficient heterotrophic energy to compensate for photoautotrophic energy losses during bleaching, and potentially minimizing the effect of subsequent elevated temperature stresses. However, if the elevated incorporation of zooplankton is a sign that the effects of bleaching continue to be stressful on the holobiont, even after 11 months of recovery, then this physiological response would indicate that complete coral recovery requires more than 11 months to achieve. If coral bleaching becomes an annual global phenomenon by mid-century, then present temporal refugia will not be sufficient to allow coral colonies to recover between bleaching events and coral reefs will become increasingly less resilient to future climate change. If, however, increasing their sequestration of zooplankton-derived nutrition into their tissues over prolonged periods of time is a compensating mechanism, the impacts of annual bleaching may be reduced. Thus, some coral species may be better equipped to face repeated bleaching stress than previously thought.}, }
@article {pmid24098768, year = {2013}, author = {Slapeta, J and Linares, MC}, title = {Combined amplicon pyrosequencing assays reveal presence of the apicomplexan "type-N" (cf. Gemmocystis cylindrus) and Chromera velia on the Great Barrier Reef, Australia.}, journal = {PloS one}, volume = {8}, number = {9}, pages = {e76095}, pmid = {24098768}, issn = {1932-6203}, mesh = {Alveolata/*genetics ; Animals ; Anthozoa/genetics/*parasitology ; Apicomplexa/*genetics/physiology ; Australia ; Base Sequence ; *Coral Reefs ; Likelihood Functions ; Models, Genetic ; Molecular Sequence Data ; Pacific Ocean ; *Phylogeny ; RNA, Ribosomal/genetics ; Sequence Alignment ; Sequence Analysis, RNA ; }, abstract = {BACKGROUND: The coral is predominantly composed of the metabolically dependent coral host and the photosynthetic dinoflagellate Symbiodinium sp. The system as a whole interacts with symbiotic eukaryotes, bacteria and viruses. Gemmocystiscylindrus (cf. "type-N" symbiont) belonging to the obligatory parasitic phylum Apicomplexa (Alveolata) is ubiquitous in the Caribbean coral, but its presence in the Great Barrier Reef coral has yet to be documented. Approaches allowing identification of the healthy community from the pathogenic or saprobic organisms are needed for sustainable coral reef monitoring.<br><br>We investigated the diversity of eukaryotes associated with a common reef-building corals from the southern Great Barrier Reef. We used three tag encoded 454 amplicon pyrosequencing assays targeting eukaryote small-subunit rRNA gene to demonstrate the presence of the apicomplexan type-N and a photosynthetic sister species to Apicomplexa-Chromeravelia. Amplicon pyrosequencing revealed presence of the small-subunit rRNA genes of known eukaryotic pathogens (Cryptosporidium and Cryptococcus). We therefore conducted bacterial tag encoded amplicon pyrosequencing assay for small-subunit rRNA gene to support effluent exposure of the coral. Bacteria of faecal origin (Enterobacteriales) formed 41% of total sequences in contrast to 0-2% of the coral-associated bacterial communities with and without C. velia, respectively.<br><br>SIGNIFICANCE: This is the first time apicomplexan type-N has been detected in the Great Barrier Reef. Eukaryote tag encoded amplicon pyrosequencing assays demonstrate presence of apicomplexan type-N and C. Velia in total coral DNA. The data highlight the need for combined approaches for eukaryotic diversity studies coupled with bacterial community assessment to achieve a more realistic goals of defining the holobiont community and assessing coral disease. With increasing evidence of Apicomplexa in coral reef environments, it is important not only to understand the evolution of these organisms but also identify their potential as pathogens.}, }
@article {pmid24039199, year = {2013}, author = {Tholey, A and Treitz, C and Kussmann, M and Bendixen, E and Schrimpf, SP and Hengartner, MO}, title = {Model organisms proteomics--from holobionts to human nutrition.}, journal = {Proteomics}, volume = {13}, number = {17}, pages = {2537-2541}, doi = {10.1002/pmic.201370144}, pmid = {24039199}, issn = {1615-9861}, mesh = {Animals ; Bacteria/genetics/immunology ; Humans ; Insecta/genetics/immunology ; Microbiota/genetics ; *Models, Animal ; *Models, Biological ; Nutritional Physiological Phenomena ; Plants/genetics ; Proteome/analysis/genetics/metabolism ; Proteomics/*methods ; }, abstract = {Model organisms are an important tool for the development and validation of analytical approaches for proteomics and for the study of basic mechanisms of biological processes. The Initiative on Model Organism Proteomics (iMOP) organized a session during the 11th HUPO World Congress in Boston in 2012, highlighting the potential of proteomics studies in model organism for the elucidation of important mechanisms regulating the interaction of humans with its environment. Major subjects were the use of model organisms for the study of molecular events triggering the interaction of host organisms with the surrounding microbiota and the elucidation of the complex influence of nutrition on the health of human beings.}, }
@article {pmid24035647, year = {2013}, author = {Brucker, RM and Bordenstein, SR}, title = {The capacious hologenome.}, journal = {Zoology (Jena, Germany)}, volume = {116}, number = {5}, pages = {260-261}, doi = {10.1016/j.zool.2013.08.003}, pmid = {24035647}, issn = {1873-2720}, mesh = {Animals ; *Genome ; *Microbiota ; *Symbiosis ; }, abstract = {Blending disciplines can be transformative in science, yet interdisciplinary mergers should not escape healthy skepticism. Indeed, the history of biology shows us that debates about the relative importance of nuclear genetics vs. microbial symbiosis in eukaryotic biology are among the most engaging. Today's technology may help resolve this century old debate as it illuminates the interwoven genomics and functions of symbionts with their host genome. Thus, we can now assert that all subdisciplines of zoology require microbiology. Although controversial to some, the evidence from studies of host-associated microbial communities indicates that metazoans are hologenomes - interconnected compositions of animal and microbes.}, }
@article {pmid24023627, year = {2013}, author = {Denis, V and Guillaume, MM and Goutx, M and de Palmas, S and Debreuil, J and Baker, AC and Boonstra, RK and Bruggemann, JH}, title = {Fast growth may impair regeneration capacity in the branching coral Acropora muricata.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e72618}, pmid = {24023627}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*growth &amp; development/*physiology ; Calcification, Physiologic ; *Coral Reefs ; Regeneration/*physiology ; Reunion ; }, abstract = {Regeneration of artificially induced lesions was monitored in nubbins of the branching coral Acropora muricata at two reef-flat sites representing contrasting environments at Réunion Island (21°07'S, 55°32'E). Growth of these injured nubbins was examined in parallel, and compared to controls. Biochemical compositions of the holobiont and the zooxanthellae density were determined at the onset of the experiment, and the photosynthetic efficiency (Fv/Fm) of zooxanthellae was monitored during the experiment. Acropora muricata rapidly regenerated small lesions, but regeneration rates significantly differed between sites. At the sheltered site characterized by high temperatures, temperature variations, and irradiance levels, regeneration took 192 days on average. At the exposed site, characterized by steadier temperatures and lower irradiation, nubbins demonstrated fast lesion repair (81 days), slower growth, lower zooxanthellae density, chlorophyll a concentration and lipid content than at the former site. A trade-off between growth and regeneration rates was evident here. High growth rates seem to impair regeneration capacity. We show that environmental conditions conducive to high zooxanthellae densities in corals are related to fast skeletal growth but also to reduced lesion regeneration rates. We hypothesize that a lowered regenerative capacity may be related to limited availability of energetic and cellular resources, consequences of coral holobionts operating at high levels of photosynthesis and associated growth.}, }
@article {pmid24003149, year = {2013}, author = {Franzenburg, S and Walter, J and Künzel, S and Wang, J and Baines, JF and Bosch, TC and Fraune, S}, title = {Distinct antimicrobial peptide expression determines host species-specific bacterial associations.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {110}, number = {39}, pages = {E3730-8}, pmid = {24003149}, issn = {1091-6490}, mesh = {Animals ; Antimicrobial Cationic Peptides/*metabolism ; Bacteria/growth &amp; development/*immunology ; Coculture Techniques ; Colony Count, Microbial ; Gene Knockdown Techniques ; Gene Silencing ; *Host Specificity ; Hydra/growth &amp; development/*metabolism/*microbiology ; Microbiota ; Molecular Sequence Data ; Phylogeny ; }, abstract = {Animals are colonized by coevolved bacterial communities, which contribute to the host's health. This commensal microbiota is often highly specific to its host-species, inferring strong selective pressures on the associated microbes. Several factors, including diet, mucus composition, and the immune system have been proposed as putative determinants of host-associated bacterial communities. Here we report that species-specific antimicrobial peptides account for different bacterial communities associated with closely related species of the cnidarian Hydra. Gene family extensions for potent antimicrobial peptides, the arminins, were detected in four Hydra species, with each species possessing a unique composition and expression profile of arminins. For functional analysis, we inoculated arminin-deficient and control polyps with bacterial consortia characteristic for different Hydra species and compared their selective preferences by 454 pyrosequencing of the bacterial microbiota. In contrast to control polyps, arminin-deficient polyps displayed decreased potential to select for bacterial communities resembling their native microbiota. This finding indicates that species-specific antimicrobial peptides shape species-specific bacterial associations.}, }
@article {pmid23997654, year = {2012}, author = {Shearer, T and Rasher, D and Snell, T and Hay, M}, title = {Gene expression patterns of the coral Acropora millepora in response to contact with macroalgae.}, journal = {Coral reefs (Online)}, volume = {31}, number = {4}, pages = {1177-1192}, pmid = {23997654}, issn = {1432-0975}, support = {G12 RR003034/RR/NCRR NIH HHS/United States ; S21 MD000101/MD/NIMHD NIH HHS/United States ; U01 TW007401/TW/FIC NIH HHS/United States ; U19 TW007401/TW/FIC NIH HHS/United States ; }, abstract = {Contact with macroalgae often causes coral mortality, but the roles of abrasion versus shading versus allelopathy in these interactions are rarely clear and effects on gene expression are unknown. Identification of gene expression changes within corals in response to contact with macroalgae can provide insight into the mode of action of allelochemicals, as well as reveal transcriptional strategies of the coral that mitigate damage from this competitive interaction, enabling the coral to survive. Gene expression responses of the coral Acropora millepora after long-term (20 d) direct contact with macroalgae (Chlorodesmis fastigiata, Dictyota bartayresiana, Galaxaura filamentosa and Turbinaria conoides) and short-term (1 h and 24 h) exposure to C. fastigiata thalli and their hydrophobic extract were assessed. After 20 d of exposure, T. conoides thalli elicited no significant change in visual bleaching or zooxanthellae PSII quantum yield within A. millepora nubbins, but stimulated the greatest alteration in gene expression of all treatments. Chlorodesmis fastigiata, D. bartayresiana and G. filamentosa caused significant visual bleaching of coral nubbins and reduced the PSII quantum yield of associated zooxanthellae after 20 d, but elicited fewer changes in gene expression relative to T. conoides at day 20. To evaluate initial molecular processes leading to reduction of zooxanthella PSII quantum yield, visual bleaching, and coral death, short-term exposures to C. fastigiata thalli and hydrophobic extracts were conducted; these interactions revealed protein degradation and significant changes in catalytic and metabolic activity within 24 h of contact. These molecular responses are consistent with the hypothesis that allelopathic interactions lead to alteration of signal transduction and an imbalance between reactive oxidant species production and antioxidant capabilities within the coral holobiont. This oxidative imbalance results in rapid protein degradation and eventually to apoptosis and/or necrosis when compensatory transcriptional action by the coral holobiont insufficiently mitigates damage by the allelochemicals of C. fastigiata.}, }
@article {pmid23985749, year = {2014}, author = {Cavalcanti, GS and Gregoracci, GB and dos Santos, EO and Silveira, CB and Meirelles, PM and Longo, L and Gotoh, K and Nakamura, S and Iida, T and Sawabe, T and Rezende, CE and Francini-Filho, RB and Moura, RL and Amado-Filho, GM and Thompson, FL}, title = {Physiologic and metagenomic attributes of the rhodoliths forming the largest CaCO3 bed in the South Atlantic Ocean.}, journal = {The ISME journal}, volume = {8}, number = {1}, pages = {52-62}, pmid = {23985749}, issn = {1751-7370}, mesh = {Animals ; Archaea/classification/genetics/metabolism/*physiology ; Atlantic Ocean ; Bacteria/classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; *Biodiversity ; Brazil ; Calcium Carbonate/*metabolism ; Carbon/metabolism ; *Ecosystem ; Invertebrates/physiology ; Metagenome/*genetics ; Photosynthesis/genetics ; Rhodophyta/*microbiology ; }, abstract = {Rhodoliths are free-living coralline algae (Rhodophyta, Corallinales) that are ecologically important for the functioning of marine environments. They form extensive beds distributed worldwide, providing a habitat and nursery for benthic organisms and space for fisheries, and are an important source of calcium carbonate. The Abrolhos Bank, off eastern Brazil, harbors the world's largest continuous rhodolith bed (of ∼21,000 km(2)) and has one of the largest marine CaCO3 deposits (producing 25 megatons of CaCO3 per year). Nevertheless, there is a lack of information about the microbial diversity, photosynthetic potential and ecological interactions within the rhodolith holobiont. Herein, we performed an ecophysiologic and metagenomic analysis of the Abrolhos rhodoliths to understand their microbial composition and functional components. Rhodoliths contained a specific microbiome that displayed a significant enrichment in aerobic ammonia-oxidizing betaproteobacteria and dissimilative sulfate-reducing deltaproteobacteria. We also observed a significant contribution of bacterial guilds (that is, photolithoautotrophs, anaerobic heterotrophs, sulfide oxidizers, anoxygenic phototrophs and methanogens) in the rhodolith metagenome, suggested to have important roles in biomineralization. The increased hits in aromatic compounds, fatty acid and secondary metabolism subsystems hint at an important chemically mediated interaction in which a functional job partition among eukaryal, archaeal and bacterial groups allows the rhodolith holobiont to thrive in the global ocean. High rates of photosynthesis were measured for Abrolhos rhodoliths (52.16 μmol carbon m(-2)s(-1)), allowing the entire Abrolhos rhodolith bed to produce 5.65 × 10(5) tons C per day. This estimate illustrates the great importance of the Abrolhos rhodolith beds for dissolved carbon production in the South Atlantic Ocean.}, }
@article {pmid23963908, year = {2013}, author = {Gordon, BR and Leggat, W and Motti, CA}, title = {Extraction protocol for nontargeted NMR and LC-MS metabolomics-based analysis of hard coral and their algal symbionts.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1055}, number = {}, pages = {129-147}, doi = {10.1007/978-1-62703-577-4_10}, pmid = {23963908}, issn = {1940-6029}, mesh = {Animals ; Anthozoa/*chemistry/*metabolism ; Chlorophyta/chemistry/metabolism/physiology ; Chromatography, Liquid/*methods ; Magnetic Resonance Spectroscopy/*methods ; Mass Spectrometry/*methods ; Metabolomics/*methods ; Symbiosis ; }, abstract = {Metabolomics and in particular, nontargeted metabolomics, has become a popular technique for the study of biological samples as it provides considerable amounts of information on extractable metabolites and is ideal for studying the metabolic response of an organism to stressors in its environment. One such organism, the symbiotic hard coral, presents its own complexity when considering a metabolomics approach in that it forms intricate associations with an array of symbiotic macro- and microbiota. While not discounting the importance of these many associations to the function of the coral holobiont, the coral-Symbiodinium relationship has been the most studied to date and as such, is the primary focus of this extraction protocol. This protocol provides details for the sample collection, extraction, and measurement of hard coral holobiont metabolites using both (1)H nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography coupled with mass spectrometry (LC-MS). Using this nontargeted metabolomics approach, the holobiont metabolism can be investigated for perturbations resulting from either (1) natural or anthropogenic environmental challenges, (2) the controlled application of stressors, and (3) differences between phenotypes or species. Consequently, this protocol will benefit both environmental and natural products based research of hard coral and their algal symbionts. Every effort has been made to provide the reader with all the details required to perform this protocol, including many of the costly and time consuming "pitfalls" or "traps" that were discovered during its development. As a result, this protocol can be confidently accomplished by those with less experience in the extraction and analysis of symbiotic hard coral, requiring minimal user input whilst ensuring reproducible and reliable results using readily available lab ware and reagents.}, }
@article {pmid23940737, year = {2013}, author = {Li, J and Chen, Q and Zhang, S and Huang, H and Yang, J and Tian, XP and Long, LJ}, title = {Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.}, journal = {PloS one}, volume = {8}, number = {8}, pages = {e71301}, pmid = {23940737}, issn = {1932-6203}, mesh = {Alphaproteobacteria/genetics ; Animals ; Anthozoa/*microbiology ; Betaproteobacteria/genetics ; China ; *Coral Reefs ; Flavobacteriaceae/genetics ; Gammaproteobacteria/genetics ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Molecular Typing ; Oceans and Seas ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics ; Sequence Analysis, DNA ; }, abstract = {Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.}, }
@article {pmid23906315, year = {2013}, author = {Kenkel, CD and Goodbody-Gringley, G and Caillaud, D and Davies, SW and Bartels, E and Matz, MV}, title = {Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4335-4348}, doi = {10.1111/mec.12391}, pmid = {23906315}, issn = {1365-294X}, mesh = {Acclimatization/genetics/physiology ; Animals ; Anthozoa/genetics/*physiology ; Climate Change ; Coral Reefs ; Dinoflagellida/genetics/*physiology ; Florida ; *Hot Temperature ; *Population Dynamics ; *Symbiosis ; }, abstract = {Studying the mechanisms that enable coral populations to inhabit spatially varying thermal environments can help evaluate how they will respond in time to the effects of global climate change and elucidate the evolutionary forces that enable or constrain adaptation. Inshore reefs in the Florida Keys experience higher temperatures than offshore reefs for prolonged periods during the summer. We conducted a common garden experiment with heat stress as our selective agent to test for local thermal adaptation in corals from inshore and offshore reefs. We show that inshore corals are more tolerant of a 6-week temperature stress than offshore corals. Compared with inshore corals, offshore corals in the 31 °C treatment showed significantly elevated bleaching levels concomitant with a tendency towards reduced growth. In addition, dinoflagellate symbionts (Symbiodinium sp.) of offshore corals exhibited reduced photosynthetic efficiency. We did not detect differences in the frequencies of major (>5%) haplotypes comprising Symbiodinium communities hosted by inshore and offshore corals, nor did we observe frequency shifts ('shuffling') in response to thermal stress. Instead, coral host populations showed significant genetic divergence between inshore and offshore reefs, suggesting that in Porites astreoides, the coral host might play a prominent role in holobiont thermotolerance. Our results demonstrate that coral populations inhabiting reefs <10-km apart can exhibit substantial differences in their physiological response to thermal stress, which could impact their population dynamics under climate change.}, }
@article {pmid23899402, year = {2013}, author = {Kenkel, CD and Meyer, E and Matz, MV}, title = {Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4322-4334}, doi = {10.1111/mec.12390}, pmid = {23899402}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/genetics/*metabolism/physiology ; Climate Change ; Ecosystem ; *Gene Expression Profiling ; Gene Expression Regulation ; Heat-Shock Response/*genetics/physiology ; *Hot Temperature ; Transcriptome ; }, abstract = {Recent evidence suggests that corals can acclimatize or adapt to local stress factors through differential regulation of their gene expression. Profiling gene expression in corals from diverse environments can elucidate the physiological processes that may be responsible for maximizing coral fitness in their natural habitat and lead to a better understanding of the coral's capacity to survive the effects of global climate change. In an accompanying paper, we show that Porites astreoides from thermally different reef habitats exhibit distinct physiological responses when exposed to 6 weeks of chronic temperature stress in a common garden experiment. Here, we describe expression profiles obtained from the same corals for a panel of 9 previously reported and 10 novel candidate stress response genes identified in a pilot RNA-Seq experiment. The strongest expression change was observed in a novel candidate gene potentially involved in calcification, SLC26, a member of the solute carrier family 26 anion exchangers, which was down-regulated by 92-fold in bleached corals relative to controls. The most notable signature of divergence between coral populations was constitutive up-regulation of metabolic genes in corals from the warmer inshore location, including the gluconeogenesis enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase and the lipid beta-oxidation enzyme acyl-CoA dehydrogenase. Our observations highlight several molecular pathways that were not previously implicated in the coral stress response and suggest that host management of energy budgets might play an adaptive role in holobiont thermotolerance.}, }
@article {pmid23889801, year = {2013}, author = {Dunlap, WC and Starcevic, A and Baranasic, D and Diminic, J and Zucko, J and Gacesa, R and van Oppen, MJ and Hranueli, D and Cullum, J and Long, PF}, title = {KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome.}, journal = {BMC genomics}, volume = {14}, number = {}, pages = {509}, pmid = {23889801}, issn = {1471-2164}, support = {BB/H010009/2//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Access to Information ; Animals ; Anthozoa/*genetics ; Conservation of Natural Resources ; Coral Reefs ; *Data Mining ; *Databases, Genetic ; Internet ; Molecular Sequence Annotation/*methods ; Proteomics/*methods ; *Sequence Homology, Nucleic Acid ; }, abstract = {BACKGROUND: Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics.<br><br>DESCRIPTION: Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics.<br><br>CONCLUSIONS: We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives.}, }
@article {pmid23868918, year = {2013}, author = {Brucker, RM and Bordenstein, SR}, title = {The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia.}, journal = {Science (New York, N.Y.)}, volume = {341}, number = {6146}, pages = {667-669}, doi = {10.1126/science.1240659}, pmid = {23868918}, issn = {1095-9203}, mesh = {Animals ; Bacteria/*classification/genetics ; Chimera/microbiology/physiology ; Gastrointestinal Tract/*microbiology ; Germ-Free Life/genetics/*physiology ; Hymenoptera/genetics/*microbiology/*physiology ; Metagenome ; Phylogeny ; Species Specificity ; *Symbiosis ; }, abstract = {Although the gut microbiome influences numerous aspects of organismal fitness, its role in animal evolution and the origin of new species is largely unknown. Here we present evidence that beneficial bacterial communities in the guts of closely related species of the genus Nasonia form species-specific phylosymbiotic assemblages that cause lethality in interspecific hybrids. Bacterial constituents and abundance are irregular in hybrids relative to parental controls, and antibiotic curing of the gut bacteria significantly rescues hybrid survival. Moreover, feeding bacteria to germ-free hybrids reinstates lethality and recapitulates the expression of innate immune genes observed in conventionally reared hybrids. We conclude that in this animal complex, the gut microbiome and host genome represent a coadapted "hologenome" that breaks down during hybridization, promoting hybrid lethality and assisting speciation.}, }
@article {pmid23865748, year = {2013}, author = {Rodriguez-Lanetty, M and Granados-Cifuentes, C and Barberan, A and Bellantuono, AJ and Bastidas, C}, title = {Ecological Inferences from a deep screening of the Complex Bacterial Consortia associated with the coral, Porites astreoides.}, journal = {Molecular ecology}, volume = {22}, number = {16}, pages = {4349-4362}, doi = {10.1111/mec.12392}, pmid = {23865748}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Caribbean Region ; Coral Reefs ; Gammaproteobacteria/classification/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Molecular Sequence Data ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The functional role of the bacterial organisms in the reef ecosystem and their contribution to the coral well-being remain largely unclear. The first step in addressing this gap of knowledge relies on in-depth characterization of the coral microbial community and its changes in diversity across coral species, space and time. In this study, we focused on the exploration of microbial community assemblages associated with an ecologically important Caribbean scleractinian coral, Porites astreoides, using Illumina high-throughput sequencing of the V5 fragment of 16S rRNA gene. We collected data from a large set of biological replicates, allowing us to detect patterns of geographical structure and resolve co-occurrence patterns using network analyses. The taxonomic analysis of the resolved diversity showed consistent and dominant presence of two OTUs affiliated with the order Oceanospirillales, which corroborates a specific pattern of bacterial association emerging for this coral species and for many other corals within the genus Porites. We argue that this specific association might indicate a symbiotic association with the adult coral partner. Furthermore, we identified a highly diverse rare bacterial 'biosphere' (725 OTUs) also living along with the dominant bacterial symbionts, but the assemblage of this biosphere is significantly structured along the geographical scale. We further discuss that some of these rare bacterial members show significant association with other members of the community reflecting the complexity of the networked consortia within the coral holobiont.}, }
@article {pmid23858648, year = {2013}, author = {Howells, EJ and Berkelmans, R and van Oppen, MJ and Willis, BL and Bay, LK}, title = {Historical thermal regimes define limits to coral acclimatization.}, journal = {Ecology}, volume = {94}, number = {5}, pages = {1078-1088}, doi = {10.1890/12-1257.1}, pmid = {23858648}, issn = {0012-9658}, mesh = {*Acclimatization ; Animals ; Anthozoa/*physiology ; *Coral Reefs ; *Hot Temperature ; Time Factors ; }, abstract = {Knowledge of the degree to which corals undergo physiological acclimatization or genetic adaptation in response to changes in their thermal environment is crucial to the success of coral reef conservation strategies. The potential of corals to acclimatize to temperatures exceeding historical thermal regimes was investigated by reciprocal transplantation of Acropora millepora colonies between the warm central and cool southern regions of the Great Barrier Reef (GBR) for a duration of 14 months. Colony fragments retained at native sites remained healthy, whereas transplanted fragments, although healthy over initial months when temperatures remained within native thermal regimes, subsequently bleached and suffered mortality during seasonal temperature extremes. Corals hosting Symbiodinium D transplanted to the southern GBR bleached in winter and the majority suffered whole (40%; n=20 colonies) or partial (50%) mortality at temperatures 1.1 degrees C below their 15-year native minimum. In contrast, corals hosting Symbiodinium C2 transplanted to the central GBR bleached in summer and suffered whole (50%; n=10 colonies) or partial (42%) mortality at temperatures 2.5 degrees C above their 15-year native maximum. During summer bleaching, the dominant Symbiodinium type changed from C2 to D within corals transplanted to the central GBR. Corals transplanted to the cooler, southern GBR grew 74-80% slower than corals at their native site, and only 50% of surviving colonies reproduced, at least partially because of cold water bleaching of transplants. Despite the absence of any visual signs of stress, corals transplanted to the warmer, central GBR grew 52-59% more slowly than corals at their native site before the summer bleaching (i.e., from autumn to spring). Allocation of energy to initial acclimatization or reproduction may explain this pattern, as the majority (65%) of transplants reproduced one month earlier than portions of the same colonies retained at the southern native site. All parameters investigated (bleaching, mortality, Symbiodinium type fidelity, reproductive timing) demonstrated strong interactions between genotype and environment, indicating that the acclimatization potential of A. millepora populations may be limited by adaptation of the holobiont to native thermal regimes.}, }
@article {pmid23846183, year = {2013}, author = {Six, DL}, title = {The bark beetle holobiont: why microbes matter.}, journal = {Journal of chemical ecology}, volume = {39}, number = {7}, pages = {989-1002}, pmid = {23846183}, issn = {1573-1561}, mesh = {Animals ; Climate Change ; Coleoptera/*microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {All higher organisms are involved in symbioses with microbes. The importance of these partnerships has led to the concept of the holobiont, defined as the animal or plant with all its associated microbes. Indeed, the interactions between insects and symbionts form much of the basis for the success and diversity of this group of arthropods. Insects rely on microbes to perform basic life functions and to exploit resources and habitats. By "partnering" with microbes, insects access new genomic variation instantaneously allowing the exploitation of new adaptive zones, influencing not only outcomes in ecological time, but the degree of innovation and change that occurs over evolutionary time. In this review, I present a brief overview of the importance of insect-microbe holobionts to illustrate how critical an understanding of the holobiont is to understanding the insect host and it interactions with its environment. I then review what is known about the most influential insect holobionts in many forest ecosystems-bark beetles and their microbes-and how new approaches and technologies are allowing us to illuminate how these symbioses function. Finally, I discuss why it will be critical to study bark beetles as a holobiont to understand the ramifications and extent of anthropogenic change in forest ecosystems.}, }
@article {pmid23844217, year = {2013}, author = {Tonk, L and Sampayo, EM and Weeks, S and Magno-Canto, M and Hoegh-Guldberg, O}, title = {Host-specific interactions with environmental factors shape the distribution of symbiodinium across the Great Barrier Reef.}, journal = {PloS one}, volume = {8}, number = {7}, pages = {e68533}, pmid = {23844217}, issn = {1932-6203}, mesh = {Animals ; Biodiversity ; *Coral Reefs ; Dinoflagellida/*physiology ; Ecosystem ; *Environment ; Host Specificity ; Oceanography ; *Symbiosis ; }, abstract = {BACKGROUND: The endosymbiotic dinoflagellates (genus Symbiodinium) within coral reef invertebrates are critical to the survival of the holobiont. The genetic variability of Symbiodinium may contribute to the tolerance of the symbiotic association to elevated sea surface temperatures (SST). To assess the importance of factors such as the local environment, host identity and biogeography in driving Symbiodinium distributions on reef-wide scales, data from studies on reef invertebrate-Symbiodinium associations from the Great Barrier Reef (GBR) were compiled.<br><br>The resulting database consisted of 3717 entries from 26 studies. It was used to explore ecological patterns such as host-specificity and environmental drivers structuring community complexity using a multi-scalar approach. The data was analyzed in several ways: (i) frequently sampled host species were analyzed independently to investigate the influence of the environment on symbiont distributions, thereby excluding the influence of host specificity, (ii) host species distributions across sites were added as an environmental variable to determine the contribution of host identity on symbiont distribution, and (iii) data were pooled based on clade (broad genetic groups dividing the genus Symbiodinium) to investigate factors driving Symbiodinium distributions using lower taxonomic resolution. The results indicated that host species identity plays a dominant role in determining the distribution of Symbiodinium and environmental variables shape distributions on a host species-specific level. SST derived variables (especially SSTstdev) most often contributed to the selection of the best model. Clade level comparisons decreased the power of the predictive model indicating that it fails to incorporate the main drivers behind Symbiodinium distributions.<br><br>CONCLUSIONS/SIGNIFICANCE: Including the influence of different host species on Symbiodinium distributional patterns improves our understanding of the drivers behind the complexity of Symbiodinium-invertebrate symbioses. This will increase our ability to generate realistic models estimating the risk reefs are exposed to and their resilience in response to a changing climate.}, }
@article {pmid23840768, year = {2013}, author = {Vezzulli, L and Pezzati, E and Huete-Stauffer, C and Pruzzo, C and Cerrano, C}, title = {16SrDNA Pyrosequencing of the Mediterranean Gorgonian Paramuricea clavata Reveals a Link among Alterations in Bacterial Holobiont Members, Anthropogenic Influence and Disease Outbreaks.}, journal = {PloS one}, volume = {8}, number = {6}, pages = {e67745}, pmid = {23840768}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Bacterial Infections/*epidemiology/genetics/microbiology ; DNA, Bacterial/*genetics ; DNA, Ribosomal/*genetics ; *Disease Outbreaks ; Mediterranean Sea ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Mass mortality events of benthic invertebrates in the Mediterranean Sea are becoming an increasing concern with catastrophic effects on the coastal marine environment. Sea surface temperature anomalies leading to physiological stress, starvation and microbial infections were identified as major factors triggering animal mortality. However the highest occurrence of mortality episodes in particular geographic areas and occasionally in low temperature deep environments suggest that other factors play a role as well. We conducted a comparative analysis of bacterial communities associated with the purple gorgonian Paramuricea clavata, one of the most affected species, collected at different geographic locations and depth, showing contrasting levels of anthropogenic disturbance and health status. Using massive parallel 16SrDNA gene pyrosequencing we showed that the bacterial community associated with healthy P. clavata in pristine locations was dominated by a single genus Endozoicomonas within the order Oceanospirillales which represented ∼90% of the overall bacterial community. P. clavata samples collected in human impacted areas and during disease events had higher bacterial diversity and abundance of disease-related bacteria, such as vibrios, than samples collected in pristine locations whilst showed a reduced dominance of Endozoicomonas spp. In contrast, bacterial symbionts exhibited remarkable stability in P. clavata collected both at euphotic and mesophotic depths in pristine locations suggesting that fluctuations in environmental parameters such as temperature have limited effect in structuring the bacterial holobiont. Interestingly the coral pathogen Vibrio coralliilyticus was not found on diseased corals collected during a deep mortality episode suggesting that neither temperature anomalies nor recognized microbial pathogens are solely sufficient to explain for the events. Overall our data suggest that anthropogenic influence may play a significant role in determining the coral health status by affecting the composition of the associated microbial community. Environmental stressful events and microbial infections may thus be superimposed to compromise immunity and trigger mortality outbreaks.}, }
@article {pmid23836873, year = {2013}, author = {Snyder, AK and Rio, RV}, title = {Interwoven biology of the tsetse holobiont.}, journal = {Journal of bacteriology}, volume = {195}, number = {19}, pages = {4322-4330}, pmid = {23836873}, issn = {1098-5530}, mesh = {Animals ; Bacteria/*classification/genetics ; Biological Evolution ; Symbiosis ; Tsetse Flies/genetics/*microbiology ; }, abstract = {Microbial symbionts can be instrumental to the evolutionary success of their hosts. Here, we discuss medically significant tsetse flies (Diptera: Glossinidae), a group comprised of over 30 species, and their use as a valuable model system to study the evolution of the holobiont (i.e., the host and associated microbes). We first describe the tsetse microbiota, which, despite its simplicity, harbors a diverse range of associations. The maternally transmitted microbes consistently include two Gammaproteobacteria, the obligate mutualists Wigglesworthia spp. and the commensal Sodalis glossinidius, along with the parasitic Alphaproteobacteria Wolbachia. These associations differ in their establishment times, making them unique and distinct from previously characterized symbioses, where multiple microbial partners have associated with their host for a significant portion of its evolution. We then expand into discussing the functional roles and intracommunity dynamics within this holobiont, which enhances our understanding of tsetse biology to encompass the vital functions and interactions of the microbial community. Potential disturbances influencing the tsetse microbiome, including salivary gland hypertrophy virus and trypanosome infections, are highlighted. While previous studies have described evolutionary consequences of host association for symbionts, the initial steps facilitating their incorporation into a holobiont and integration of partner biology have only begun to be explored. Research on the tsetse holobiont will contribute to the understanding of how microbial metabolic integration and interdependency initially may develop within hosts, elucidating mechanisms driving adaptations leading to cooperation and coresidence within the microbial community. Lastly, increased knowledge of the tsetse holobiont may also contribute to generating novel African trypanosomiasis disease control strategies.}, }
@article {pmid23750924, year = {2013}, author = {Kimes, NE and Johnson, WR and Torralba, M and Nelson, KE and Weil, E and Morris, PJ}, title = {The Montastraea faveolata microbiome: ecological and temporal influences on a Caribbean reef-building coral in decline.}, journal = {Environmental microbiology}, volume = {15}, number = {7}, pages = {2082-2094}, doi = {10.1111/1462-2920.12130}, pmid = {23750924}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Caribbean Region ; *Coral Reefs ; *Ecosystem ; Eukaryota/genetics ; Genes, rRNA/genetics ; Microbiota/*physiology ; Molecular Sequence Data ; Seasons ; }, abstract = {Coral-associated microbial communities, including protists, bacteria, archaea and viruses, are important components of the coral holobiont that influence the health of corals and coral reef ecosystems. Evidence suggests that the composition of these microbial communities is affected by numerous parameters; however, little is known about the confluence of these ecological and temporal effects. In this study, we used ribosomal RNA gene sequencing to identify the zooxanthellae, bacteria and archaea associated with healthy and yellow band diseased (YBD) colonies in the Media Luna reef of La Parguera, Puerto Rico, in order to examine the influence of YBD on the Montastraea faveolata microbiome. In addition, we evaluated the influence of season on the differences between healthy and YBD M. faveolata microbiomes by sampling from the same tagged colonies in both March and September of 2007. To the best of our knowledge, this is the first coral microbiome study to examine sequences from the zooxanthellar, bacterial and archaeal communities simultaneously from individual coral samples. Our results confirm differences in the M. faveolata zooxanthellar, bacterial and archaeal communities between healthy and YBD colonies in March; however, the September communities do not exhibit the same differences. Moreover, we provide evidence that the differences in the M. faveolata microbiomes between March and September are more significant than those observed between healthy and YBD. This data suggest that the entire coral microbiome, not just the bacterial community, is a dynamic environment where both disease and season play important roles.}, }
@article {pmid23730715, year = {2013}, author = {Howells, EJ and Willis, BL and Bay, LK and van Oppen, MJ}, title = {Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the Great Barrier Reef.}, journal = {Molecular ecology}, volume = {22}, number = {14}, pages = {3693-3708}, doi = {10.1111/mec.12342}, pmid = {23730715}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/genetics/*physiology ; Coral Reefs ; DNA, Ribosomal/genetics ; Dinoflagellida/genetics/*physiology ; Microsatellite Repeats/genetics ; *Population Dynamics ; Symbiosis/*genetics ; }, abstract = {The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume-induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70-86% of the total genetic variation. An additional 9-27% of variation was explained by significant differentiation of populations among sites separated by 0.4-13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6-7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.}, }
@article {pmid23694677, year = {2013}, author = {Singh, Y and Ahmad, J and Musarrat, J and Ehtesham, NZ and Hasnain, SE}, title = {Emerging importance of holobionts in evolution and in probiotics.}, journal = {Gut pathogens}, volume = {5}, number = {1}, pages = {12}, pmid = {23694677}, issn = {1757-4749}, abstract = {The existence of microbe free animals or plants in nature is virtually impossible as they and plants have a certain degree of symbiotic association with microbes. This symbiotic association leads to the formation of holobiont (host and its symbionts). This mutual coexistence is not merely at the physical or chemical level but also at the genetic level leading to the emergence of the concept of hologenome (gene pool of host and its associated symbionts). The abundance of symbionts with the associated gene diversity contributes to the fitness of the holobiont under varying environmental conditions. The hologenome theory of evolution considers the dynamic holobiont as a single unit for natural selection and provides a more accommodating view of evolution blending Darwinism and Lamarkism. Additionally, holobionts are providing scientific basis to our understanding of the growing importance of probiotics in human health and in disease management.}, }
@article {pmid23688194, year = {2013}, author = {Minard, G and Mavingui, P and Moro, CV}, title = {Diversity and function of bacterial microbiota in the mosquito holobiont.}, journal = {Parasites &amp; vectors}, volume = {6}, number = {}, pages = {146}, pmid = {23688194}, issn = {1756-3305}, mesh = {Animals ; Bacteria/*classification/*genetics ; Bacterial Physiological Phenomena ; *Biodiversity ; Culicidae/*microbiology ; Female ; Male ; *Metagenome ; Mosquito Control/methods ; Symbiosis ; }, abstract = {Mosquitoes (Diptera: Culicidae) have been shown to host diverse bacterial communities that vary depending on the sex of the mosquito, the developmental stage, and ecological factors. Some studies have suggested a potential role of microbiota in the nutritional, developmental and reproductive biology of mosquitoes. Here, we present a review of the diversity and functions of mosquito-associated bacteria across multiple variation factors, emphasizing recent findings. Mosquito microbiota is considered in the context of possible extended phenotypes conferred on the insect hosts that allow niche diversification and rapid adaptive evolution in other insects. These kinds of observations have prompted the recent development of new mosquito control methods based on the use of symbiotically-modified mosquitoes to interfere with pathogen transmission or reduce the host life span and reproduction. New opportunities for exploiting bacterial function for vector control are highlighted.}, }
@article {pmid23658817, year = {2013}, author = {Levas, SJ and Grottoli, AG and Hughes, A and Osburn, CL and Matsui, Y}, title = {Physiological and biogeochemical traits of bleaching and recovery in the mounding species of coral Porites lobata: implications for resilience in mounding corals.}, journal = {PloS one}, volume = {8}, number = {5}, pages = {e63267}, pmid = {23658817}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/metabolism/*physiology ; Conservation of Natural Resources ; *Geology ; *Pigmentation ; }, abstract = {Mounding corals survive bleaching events in greater numbers than branching corals. However, no study to date has determined the underlying physiological and biogeochemical trait(s) that are responsible for mounding coral holobiont resilience to bleaching. Furthermore, the potential of dissolved organic carbon (DOC) as a source of fixed carbon to bleached corals has never been determined. Here, Porites lobata corals were experimentally bleached for 23 days and then allowed to recover for 0, 1, 5, and 11 months. At each recovery interval a suite of analyses were performed to assess their recovery (photosynthesis, respiration, chlorophyll a, energy reserves, tissue biomass, calcification, δ(13)C of the skeletal, δ(13)C, and δ(15)N of the animal host and endosymbiont fractions). Furthermore, at 0 months of recovery, the assimilation of photosynthetically acquired and zooplankton-feeding acquired carbon into the animal host, endosymbiont, skeleton, and coral-mediated DOC were measured via (13)C-pulse-chase labeling. During the first month of recovery, energy reserves and tissue biomass in bleached corals were maintained despite reductions in chlorophyll a, photosynthesis, and the assimilation of photosynthetically fixed carbon. At the same time, P. lobata corals catabolized carbon acquired from zooplankton and seemed to take up DOC as a source of fixed carbon. All variables that were negatively affected by bleaching recovered within 5 to 11 months. Thus, bleaching resilience in the mounding coral P. lobata is driven by its ability to actively catabolize zooplankton-acquired carbon and seemingly utilize DOC as a significant fixed carbon source, facilitating the maintenance of energy reserves and tissue biomass. With the frequency and intensity of bleaching events expected to increase over the next century, coral diversity on future reefs may favor not only mounding morphologies but species like P. lobata, which have the ability to utilize heterotrophic sources of fixed carbon that minimize the impact of bleaching and promote fast recovery.}, }
@article {pmid23649754, year = {2013}, author = {Domaschke, S and Vivas, M and Sancho, LG and Printzen, C}, title = {Ecophysiology and genetic structure of polar versus temperate populations of the lichen Cetraria aculeata.}, journal = {Oecologia}, volume = {173}, number = {3}, pages = {699-709}, pmid = {23649754}, issn = {1432-1939}, mesh = {Adaptation, Biological/genetics/*physiology ; Analysis of Variance ; Antarctic Regions ; Base Sequence ; Carbon Dioxide/metabolism ; Chlorophyll/analysis ; *Climate ; Germany ; Lichens/*genetics/*physiology ; Light ; Molecular Sequence Data ; Photosynthesis/physiology ; Sequence Analysis, DNA ; Spain ; Svalbard ; Temperature ; }, abstract = {We studied polar and temperate samples of the lichen Cetraria aculeata to investigate whether genetical differences between photobionts are correlated with physiological properties of the lichen holobiont. Net photosynthesis and dark respiration (DR) at different temperatures (from 0 to 30 °C) and photon flux densities (from 0 to 1,200 μmol m(-2) s(-1)) were studied for four populations of Cetraria aculeata. Samples were collected from maritime Antarctica, Svalbard, Germany and Spain, representing different climatic situations. Sequencing of the photobiont showed that the investigated samples fall in the polar and temperate clade described in Fernández-Mendoza et al. (Mol Ecol 20:1208-1232, 2011). Lichens with photobionts from these clades differ in their temperature optimum for photosynthesis, maximal net photosynthesis, maximal DR and chlorophyll content. Maximal net photosynthesis was much lower in Antarctica and Svalbard than in Germany and Spain. The difference was smaller when rates were expressed by chlorophyll content. The same is true for the temperature optima of polar (11 °C) and temperate (15 and 17 °C) lichens. Our results indicate that lichen mycobionts may adapt or acclimate to local environmental conditions either by selecting algae from regional pools or by regulating algal cell numbers (chlorophyll content) within the thallus.}, }
@article {pmid23645316, year = {2013}, author = {Walter, J and Martínez, I and Rose, DJ}, title = {Holobiont nutrition: considering the role of the gastrointestinal microbiota in the health benefits of whole grains.}, journal = {Gut microbes}, volume = {4}, number = {4}, pages = {340-346}, pmid = {23645316}, issn = {1949-0984}, mesh = {*Diet ; *Edible Grain ; Female ; Gastrointestinal Tract/*microbiology ; Humans ; Male ; *Metagenome ; }, abstract = {Intake of whole grains and other food products high in dietary fiber have long been linked to the prevention of chronic diseases associated with inflammation. A contribution of the gastrointestinal microbiota to these effects has been suggested, but little is known on how whole grains interact with gut bacteria. We have recently published the first human trial that made use of next-generation sequencing to determine the effect of whole grains (whole grain barley, brown rice or a mixture of the two) on fecal microbiota structure and tested for associations between the gut microbiota and blood markers of inflammation, glucose and lipid metabolism. Our study revealed that whole grains impacted gut microbial ecology by increasing microbial diversity and inducing compositional alterations, some of which are considered to have beneficial effects on the host. Interestingly, whole grains, and in particular the combination of whole grain barley and brown rice, caused a reduction in plasma interleukin-6 (IL-6), which was linked to compositional features of the gut microbiota. Therefore, the study provided evidence that a short-term increased intake of whole grains led to compositional alterations of the gut microbiota that coincided with improvements in systemic inflammation. In this addendum, we summarize the findings of the study and provide a perspective on the importance of regarding humans as holobionts when considering the health effects of dietary strategies.}, }
@article {pmid23630625, year = {2013}, author = {Jessen, C and Villa Lizcano, JF and Bayer, T and Roder, C and Aranda, M and Wild, C and Voolstra, CR}, title = {In-situ effects of eutrophication and overfishing on physiology and bacterial diversity of the red sea coral Acropora hemprichii.}, journal = {PloS one}, volume = {8}, number = {4}, pages = {e62091}, pmid = {23630625}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; Anthozoa/microbiology/*physiology ; Bacteria/genetics ; Biodiversity ; Conservation of Natural Resources ; *Eutrophication ; *Fisheries ; Gammaproteobacteria/classification/*genetics ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Molecular Typing ; Nitrogen Fixation ; Phylogeny ; Principal Component Analysis ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; }, abstract = {Coral reefs of the Central Red Sea display a high degree of endemism, and are increasingly threatened by anthropogenic effects due to intense local coastal development measures. Overfishing and eutrophication are among the most significant local pressures on these reefs, but there is no information available about their potential effects on the associated microbial community. Therefore, we compared holobiont physiology and 16S-based bacterial communities of tissue and mucus of the hard coral Acropora hemprichii after 1 and 16 weeks of in-situ inorganic nutrient enrichment (via fertilizer diffusion) and/or herbivore exclusion (via caging) in an offshore reef of the Central Red Sea. Simulated eutrophication and/or overfishing treatments did not affect coral physiology with respect to coral respiration rates, chlorophyll a content, zooxanthellae abundance, or δ (15)N isotopic signatures. The bacterial community of A. hemprichii was rich and uneven, and diversity increased over time in all treatments. While distinct bacterial species were identified as a consequence of eutrophication, overfishing, or both, two bacterial species that could be classified to the genus Endozoicomonas were consistently abundant and constituted two thirds of bacteria in the coral. Several nitrogen-fixing and denitrifying bacteria were found in the coral specimens that were exposed to experimentally increased nutrients. However, no particular bacterial species was consistently associated with the coral under a given treatment and the single effects of manipulated eutrophication and overfishing could not predict the combined effect. Our data underlines the importance of conducting field studies in a holobiont framework, taking both, physiological and molecular measures into account.}, }
@article {pmid23564007, year = {2013}, author = {Yang, S and Sun, W and Zhang, F and Li, Z}, title = {Phylogenetically diverse denitrifying and ammonia-oxidizing bacteria in corals Alcyonium gracillimum and Tubastraea coccinea.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {15}, number = {5}, pages = {540-551}, pmid = {23564007}, issn = {1436-2236}, mesh = {Ammonia/metabolism ; Animals ; Anthozoa/*microbiology ; Bacteria/*genetics/*metabolism ; Base Sequence ; China ; Cluster Analysis ; Computational Biology ; DNA Primers/genetics ; Denitrification/genetics/physiology ; Gene Library ; Genetic Markers/genetics ; Microbiota/*genetics ; Molecular Sequence Data ; Nitrite Reductases/genetics ; Oceans and Seas ; Oxidation-Reduction ; Oxidoreductases/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {To date, the association of coral-bacteria and the ecological roles of bacterial symbionts in corals remain largely unknown. In particular, little is known about the community components of bacterial symbionts of corals involved in the process of denitrification and ammonia oxidation. In this study, the nitrite reductase (nirS and nirK) and ammonia monooxygenase subunit A (amoA) genes were used as functional markers. Diverse bacteria with the potential to be active as denitrifiers and ammonia-oxidizing bacteria (AOB) were found in two East China Sea corals: stony coral Alcyonium gracillimum and soft coral Tubastraea coccinea. The 16S rRNA gene library analysis demonstrated different communities of bacterial symbionts in these two corals of the same location. Nitrite reductase nirK gene was found only in T. coccinea, while both nirK and nirS genes were detected in A. gracillimum, which might be the result of the presence of different bacterial symbionts in these two corals. AOB rather than ammonia-oxidizing archaea were detected in both corals, suggesting that AOB might play an important role in the ammonia oxidation process of the corals. This study indicates that the coral bacterial symbionts with the potential for nitrite reduction and ammonia oxidation might have multiple ecological roles in the coral holobiont, which promotes our understanding of bacteria-mediated nitrogen cycling in corals. To our knowledge, this study is the first assessment of the community structure and phylogenetic diversity of denitrifying bacteria and AOB in corals based on nirK, nirS, and amoA gene library analysis.}, }
@article {pmid23553821, year = {2013}, author = {Bell, JJ and Davy, SK and Jones, T and Taylor, MW and Webster, NS}, title = {Could some coral reefs become sponge reefs as our climate changes?.}, journal = {Global change biology}, volume = {19}, number = {9}, pages = {2613-2624}, doi = {10.1111/gcb.12212}, pmid = {23553821}, issn = {1354-1013}, mesh = {Animals ; *Climate Change ; *Coral Reefs ; *Porifera ; }, abstract = {Coral reefs across the world have been seriously degraded and have a bleak future in response to predicted global warming and ocean acidification (OA). However, this is not the first time that biocalcifying organisms, including corals, have faced the threat of extinction. The end-Triassic mass extinction (200 million years ago) was the most severe biotic crisis experienced by modern marine invertebrates, which selected against biocalcifiers; this was followed by the proliferation of another invertebrate group, sponges. The duration of this sponge-dominated period far surpasses that of alternative stable-ecosystem or phase-shift states reported on modern day coral reefs and, as such, a shift to sponge-dominated reefs warrants serious consideration as one future trajectory of coral reefs. We hypothesise that some coral reefs of today may become sponge reefs in the future, as sponges and corals respond differently to changing ocean chemistry and environmental conditions. To support this hypothesis, we discuss: (i) the presence of sponge reefs in the geological record; (ii) reported shifts from coral- to sponge-dominated systems; and (iii) direct and indirect responses of the sponge holobiont and its constituent parts (host and symbionts) to changes in temperature and pH. Based on this evidence, we propose that sponges may be one group to benefit from projected climate change and ocean acidification scenarios, and that increased sponge abundance represents a possible future trajectory for some coral reefs, which would have important implications for overall reef functioning.}, }
@article {pmid23545857, year = {2013}, author = {Wanick, RC and de Sousa Barbosa, H and Frazão, LR and Santelli, RE and Arruda, MA and Coutinho, CC}, title = {Evaluation of differential protein expression in Haliclona aquarius and sponge-associated microorganisms under cadmium stress.}, journal = {Analytical and bioanalytical chemistry}, volume = {405}, number = {24}, pages = {7661-7670}, doi = {10.1007/s00216-013-6898-x}, pmid = {23545857}, issn = {1618-2650}, mesh = {Animals ; Cadmium/*toxicity ; Electrophoresis, Gel, Two-Dimensional ; Gene Expression Regulation/*drug effects ; Haliclona/*genetics/metabolism/*microbiology ; Proteins/chemistry/*genetics ; Proteomics ; Spectrometry, Mass, Electrospray Ionization ; Water Pollutants, Chemical/*toxicity ; }, abstract = {A comparative proteomic approach was used to assess differentially expressed proteins in marine sponges after 36 h of exposure to cadmium (Cd). After separation performed by 2-D polyacrylamide gel electrophoresis, 46 protein spots indicated differential expression, and 17 of these proteins were identified by electrospray ionization quadrupole time-of-flight mass spectrometry. From the proteins identified, 76% were attributed to sponge-associated microorganisms (fungi and bacteria), and 24% were attributed to Haliclona aquarius. Some of the proteins that were identified may be related to cell proliferation and differentiation or processes of oxidative stress repair and energy procurement. An integrated evaluation based on spot expression levels and the postulated functions of these proteins allowed a more accurate evaluation of the stress caused to the sponge holobiont system by cadmium exposure. This study could provide new insights into the use of a proteomic approach in the marine sponge to assess the effects of Cd pollution in a marine environment.}, }
@article {pmid23531826, year = {2013}, author = {Béraud, E and Gevaert, F and Rottier, C and Ferrier-Pagès, C}, title = {The response of the scleractinian coral Turbinaria reniformis to thermal stress depends on the nitrogen status of the coral holobiont.}, journal = {The Journal of experimental biology}, volume = {216}, number = {Pt 14}, pages = {2665-2674}, doi = {10.1242/jeb.085183}, pmid = {23531826}, issn = {1477-9145}, mesh = {Ammonium Compounds/pharmacology ; Analysis of Variance ; Animals ; Anthozoa/metabolism/*physiology ; Calcification, Physiologic/drug effects ; Carotenoids ; Chlorophyll/metabolism ; Chlorophyll A ; Dinoflagellida/*drug effects/metabolism ; Fluorescence ; *Hot Temperature ; Indian Ocean ; Nitrogen/*metabolism/pharmacology ; Photosynthesis/drug effects/physiology ; Stress, Physiological/*physiology ; *Symbiosis ; Xanthophylls/metabolism ; beta Carotene/metabolism ; }, abstract = {The physiological response of the scleractinian coral Turbinaria reniformis to ammonium enrichment (3 μmol l(-1)) was examined at 26°C as well as during a 7 day increase in temperature to 31°C (thermal stress). At 26°C, ammonium supplementation had little effect on the coral physiology. It induced a decrease in symbiont density, compensated by an increase in chlorophyll content per symbiont cell. Organic carbon release was reduced, likely because of a better utilization of the photosynthesized carbon (i.e. incorporation into proteins, kept in the coral tissue). The δ(15)N signatures of the ammonium-enriched symbionts and host tissue were also significantly decreased, by 4 and 2‰, respectively, compared with the non-enriched conditions, suggesting a significant uptake of inorganic nitrogen by the holobiont. Under thermal stress, coral colonies that were not nitrogen enriched experienced a drastic decrease in photosynthetic and photoprotective pigments (chlorophyll a, β-carotene, diadinoxanthin, diatoxanthin and peridinin), followed by a decrease in the rates of photosynthesis and calcification. Organic carbon release was not affected by this thermal stress. Conversely, nitrogen-enriched corals showed an increase in their pigment concentrations, and maintained rates of photosynthesis and calcification at ca. 60% and 100% of those measured under control conditions, respectively. However, these corals lost more organic carbon into the environment. Overall, these results indicate that inorganic nitrogen availability can be important to determining the resilience of some scleractinian coral species to thermal stress, and can have a function equivalent to that of heterotrophic feeding concerning the maintenance of coral metabolism under stress conditions.}, }
@article {pmid23437379, year = {2013}, author = {La Rivière, M and Roumagnac, M and Garrabou, J and Bally, M}, title = {Transient shifts in bacterial communities associated with the temperate gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e57385}, pmid = {23437379}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Biodiversity ; *Coral Reefs ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Gene Library ; Mediterranean Sea ; Microbial Consortia/*genetics ; Phylogeny ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S/classification/*genetics/isolation &amp; purification ; Ribotyping ; Sequence Analysis, DNA ; Symbiosis/physiology ; }, abstract = {BACKGROUND: Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont.<br><br>The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed.<br><br>CONCLUSION/SIGNIFICANCE: This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals. However, a transient imbalance in bacterial associations can be tolerated by the holobiont without apparent symptoms of disease. The subsequent restoration of the Hahellaceae-dominated community is indicative of the specificity and resilience of the bacteria associated with the gorgonian host.}, }
@article {pmid23407311, year = {2013}, author = {Baker, DM and Andras, JP and Jordán-Garza, AG and Fogel, ML}, title = {Nitrate competition in a coral symbiosis varies with temperature among Symbiodinium clades.}, journal = {The ISME journal}, volume = {7}, number = {6}, pages = {1248-1251}, pmid = {23407311}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/classification/growth &amp; development/*physiology ; Carbon/metabolism ; *Coral Reefs ; Dinoflagellida/genetics/*physiology ; Nitrates/metabolism ; Oceans and Seas ; Photosynthesis ; Symbiosis ; Temperature ; }, abstract = {Many reef-building corals form symbioses with dinoflagellates from the diverse genus Symbiodinium. There is increasing evidence of functional significance to Symbiodinium diversity, which affects the coral holobiont's response to changing environmental conditions. For example, corals hosting Symbiodinium from the clade D taxon exhibit greater resistance to heat-induced coral bleaching than conspecifics hosting the more common clade C. Yet, the relatively low prevalence of clade D suggests that this trait is not advantageous in non-stressful environments. Thus, clade D may only be able to out-compete other Symbiodinium types within the host habitat when conditions are chronically stressful. Previous studies have observed enhanced photosynthesis and fitness by clade C holobionts at non-stressful temperatures, relative to clade D. Yet, carbon-centered metrics cannot account for enhanced growth rates and patterns of symbiont succession to other genetic types when nitrogen often limits reef productivity. To investigate the metabolic costs of hosting thermally tolerant symbionts, we examined the assimilation and translocation of inorganic (15)N and (13)C in the coral Acropora tenuis experimentally infected with either clade C (sub-type C1) or D Symbiodinium at 28 and 30 °C. We show that at 28 °C, C1 holobionts acquired 22% more (15)N than clade D. However, at 30 °C, C1 symbionts acquired equivalent nitrogen and 16% less carbon than D. We hypothesize that C1 competitively excludes clade D in hospite via enhanced nitrogen acquisition and thus dominates coral populations despite warming oceans.}, }
@article {pmid23405104, year = {2013}, author = {Sammarco, PW and Strychar, KB}, title = {Responses to high seawater temperatures in zooxanthellate octocorals.}, journal = {PloS one}, volume = {8}, number = {2}, pages = {e54989}, pmid = {23405104}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*physiology ; Apoptosis/physiology ; Australia ; Hot Temperature ; Necrosis/physiopathology ; Seawater ; Symbiosis/physiology ; Temperature ; }, abstract = {Increases in Sea Surface Temperatures (SSTs) as a result of global warming have caused reef-building scleractinian corals to bleach worldwide, a result of the loss of obligate endosymbiotic zooxanthellae. Since the 1980's, bleaching severity and frequency has increased, in some cases causing mass mortality of corals. Earlier experiments have demonstrated that zooxanthellae in scleractinian corals from three families from the Great Barrier Reef, Australia (Faviidae, Poritidae, and Acroporidae) are more sensitive to heat stress than their hosts, exhibiting differential symptoms of programmed cell death - apoptosis and necrosis. Most zooxanthellar phylotypes are dying during expulsion upon release from the host. The host corals appear to be adapted or exapted to the heat increases. We attempt to determine whether this adaptation/exaptation occurs in octocorals by examining the heat-sensitivities of zooxanthellae and their host octocoral alcyonacean soft corals - Sarcophyton ehrenbergi (Alcyoniidae), Sinularia lochmodes (Alcyoniidae), and Xenia elongata (Xeniidae), species from two different families. The soft coral holobionts were subjected to experimental seawater temperatures of 28, 30, 32, 34, and 36°C for 48 hrs. Host and zooxanthellar cells were examined for viability, apoptosis, and necrosis (in hospite and expelled) using transmission electron microscopy (TEM), fluorescent microscopy (FM), and flow cytometry (FC). As experimental temperatures increased, zooxanthellae generally exhibited apoptotic and necrotic symptoms at lower temperatures than host cells and were expelled. Responses varied species-specifically. Soft coral hosts were adapted/exapted to higher seawater temperatures than their zooxanthellae. As with the scleractinians, the zooxanthellae appear to be the limiting factor for survival of the holobiont in the groups tested, in this region. These limits have now been shown to operate in six species within five families and two orders of the Cnidaria in the western Pacific. We hypothesize that this relationship may have taxonomic implications for other obligate zooxanthellate cnidarians subject to bleaching.}, }
@article {pmid23397797, year = {2012}, author = {Gilbert, SF and Sapp, J and Tauber, AI}, title = {A symbiotic view of life: we have never been individuals.}, journal = {The Quarterly review of biology}, volume = {87}, number = {4}, pages = {325-341}, doi = {10.1086/668166}, pmid = {23397797}, issn = {0033-5770}, mesh = {Animals ; Humans ; *Symbiosis ; }, abstract = {The notion of the "biological individual" is crucial to studies of genetics, immunology, evolution, development, anatomy, and physiology. Each of these biological subdisciplines has a specific conception of individuality, which has historically provided conceptual contexts for integrating newly acquired data. During the past decade, nucleic acid analysis, especially genomic sequencing and high-throughput RNA techniques, has challenged each of these disciplinary definitions by finding significant interactions of animals and plants with symbiotic microorganisms that disrupt the boundaries that heretofore had characterized the biological individual. Animals cannot be considered individuals by anatomical or physiological criteria because a diversity of symbionts are both present and functional in completing metabolic pathways and serving other physiological functions. Similarly, these new studies have shown that animal development is incomplete without symbionts. Symbionts also constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. The immune system also develops, in part, in dialogue with symbionts and thereby functions as a mechanism for integrating microbes into the animal-cell community. Recognizing the "holobiont"--the multicellular eukaryote plus its colonies of persistent symbionts--as a critically important unit of anatomy, development, physiology, immunology, and evolution opens up new investigative avenues and conceptually challenges the ways in which the biological subdisciplines have heretofore characterized living entities.}, }
@article {pmid23346080, year = {2012}, author = {Webster, NS and Luter, HM and Soo, RM and Botté, ES and Simister, RL and Abdo, D and Whalan, S}, title = {Same, same but different: symbiotic bacterial associations in GBR sponges.}, journal = {Frontiers in microbiology}, volume = {3}, number = {}, pages = {444}, pmid = {23346080}, issn = {1664-302X}, abstract = {Symbioses in marine sponges involve diverse consortia of microorganisms that contribute to the health and ecology of their hosts. The microbial communities of 13 taxonomically diverse Great Barrier Reef (GBR) sponge species were assessed by DGGE and 16S rRNA gene sequencing to determine intra and inter species variation in bacterial symbiont composition. Microbial profiling revealed communities that were largely conserved within different individuals of each species with intra species similarity ranging from 65-100%. 16S rRNA gene sequencing revealed that the communities were dominated by Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Nitrospira, and Cyanobacteria. Sponge-associated microbes were also highly host-specific with no operational taxonomic units (OTUs) common to all species and the most ubiquitous OTU found in only 5 of the 13 sponge species. In total, 91% of the OTUs were restricted to a single sponge species. However, GBR sponge microbes were more closely related to other sponge-derived bacteria than they were to environmental communities with sequences falling within 50 of the 173 previously defined sponge-(or sponge-coral) specific sequence clusters (SC). These SC spanned the Acidobacteria, Actinobacteria, Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Gemmatimonadetes, Nitrospira, and the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. The number of sequences assigned to these sponge-specific clusters across all species ranged from 0 to 92%. No relationship between host phylogeny and symbiont communities were observed across the different sponge orders, although the highest level of similarity was detected in two closely related Xestospongia species. This study identifies the core microbial inhabitants in a range of GBR sponges thereby providing the basis for future studies on sponge symbiotic function and research aiming to predict how sponge holobionts will respond to environmental perturbation.}, }
@article {pmid23303372, year = {2013}, author = {Bourne, DG and Dennis, PG and Uthicke, S and Soo, RM and Tyson, GW and Webster, N}, title = {Coral reef invertebrate microbiomes correlate with the presence of photosymbionts.}, journal = {The ISME journal}, volume = {7}, number = {7}, pages = {1452-1458}, pmid = {23303372}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/genetics/*microbiology/physiology ; Australia ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Coral Reefs ; Dinoflagellida/genetics/*physiology ; Invertebrates/*microbiology ; Microbiota/genetics/*physiology ; Photosynthesis/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Homology, Nucleic Acid ; *Symbiosis ; }, abstract = {Coral reefs provide habitat for an array of marine invertebrates that host symbiotic microbiomes. Photosynthetic symbionts including Symbiodinium dinoflagellates and diatoms potentially influence the diversity of their host-associated microbiomes by releasing carbon-containing photosynthates and other organic compounds that fuel microbial metabolism. Here we used 16S ribosomal RNA (rRNA) gene amplicon pyrosequencing to characterise the microbiomes of 11 common Great Barrier Reef marine invertebrate species that host photosynthetic symbionts and five taxa in which they are absent. The presence of photosynthetic symbionts influenced the composition but not the species richness, evenness and phylogenetic diversity of invertebrate-associated microbiomes. Invertebrates without photosynthetic symbionts were dominated by Alphaproteobacteria, whereas those hosting photosynthetic symbionts were dominated by Gammaproteobacteria. Interestingly, many microbial species from photosymbiont-bearing invertebrates, including Oceanospirillales spp., Alteromonas spp., Pseudomonas spp., Halomonas spp., are implicated in the metabolism of dimethylsulfoniopropionate (DMSP). DMSP is produced in high concentrations by photosynthetic dinoflagellates and is involved in climate regulation by facilitating cloud formation. Microbiomes correlated with host taxa and replicate individuals from most sampled species grouped in distance-based redundancy analysis of retrieved 16S rRNA gene sequences. This study highlights the complex nature of invertebrate holobionts and confirms the importance of photosynthetic symbionts in structuring marine invertebrate bacterial communities.}, }
@article {pmid23303369, year = {2013}, author = {Nelson, CE and Goldberg, SJ and Wegley Kelly, L and Haas, AF and Smith, JE and Rohwer, F and Carlson, CA}, title = {Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {962-979}, pmid = {23303369}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/chemistry/metabolism/*microbiology ; Bacteria/*classification/growth &amp; development/isolation &amp; purification/metabolism ; Carbohydrate Metabolism ; Carbon/metabolism ; Chlorophyta/chemistry/microbiology ; Coral Reefs ; Hydrogen-Ion Concentration ; Plankton/classification/growth &amp; development/isolation &amp; purification/metabolism ; Polynesia ; RNA, Ribosomal, 16S ; Rhodophyta/chemistry/microbiology ; Seawater/*chemistry/*microbiology ; Seaweed/chemistry/*microbiology ; }, abstract = {Increasing algal cover on tropical reefs worldwide may be maintained through feedbacks whereby algae outcompete coral by altering microbial activity. We hypothesized that algae and coral release compositionally distinct exudates that differentially alter bacterioplankton growth and community structure. We collected exudates from the dominant hermatypic coral holobiont Porites spp. and three dominant macroalgae (one each Ochrophyta, Rhodophyta and Chlorophyta) from reefs of Mo'orea, French Polynesia. We characterized exudates by measuring dissolved organic carbon (DOC) and fractional dissolved combined neutral sugars (DCNSs) and subsequently tracked bacterioplankton responses to each exudate over 48 h, assessing cellular growth, DOC/DCNS utilization and changes in taxonomic composition (via 16S rRNA amplicon pyrosequencing). Fleshy macroalgal exudates were enriched in the DCNS components fucose (Ochrophyta) and galactose (Rhodophyta); coral and calcareous algal exudates were enriched in total DCNS but in the same component proportions as ambient seawater. Rates of bacterioplankton growth and DOC utilization were significantly higher in algal exudate treatments than in coral exudate and control incubations with each community selectively removing different DCNS components. Coral exudates engendered the smallest shift in overall bacterioplankton community structure, maintained high diversity and enriched taxa from Alphaproteobacteria lineages containing cultured representatives with relatively few virulence factors (VFs) (Hyphomonadaceae and Erythrobacteraceae). In contrast, macroalgal exudates selected for less diverse communities heavily enriched in copiotrophic Gammaproteobacteria lineages containing cultured pathogens with increased VFs (Vibrionaceae and Pseudoalteromonadaceae). Our results demonstrate that algal exudates are enriched in DCNS components, foster rapid growth of bacterioplankton and select for bacterial populations with more potential VFs than coral exudates.}, }
@article {pmid23291051, year = {2013}, author = {Edge, SE and Shearer, TL and Morgan, MB and Snell, TW}, title = {Sub-lethal coral stress: detecting molecular responses of coral populations to environmental conditions over space and time.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {128-129}, number = {}, pages = {135-146}, doi = {10.1016/j.aquatox.2012.11.014}, pmid = {23291051}, issn = {1879-1514}, mesh = {Alveolata/physiology ; Analysis of Variance ; Animals ; Anthozoa/*genetics/*metabolism ; *Ecosystem ; Environmental Monitoring ; Gene Expression Profiling ; *Gene Expression Regulation ; *Stress, Physiological ; Time Factors ; }, abstract = {In order for sessile organisms to survive environmental fluctuations and exposures to pollutants, molecular mechanisms (i.e. stress responses) are elicited. Previously, detrimental effects of natural and anthropogenic stressors on coral health could not be ascertained until significant physiological responses resulted in visible signs of stress (e.g. tissue necrosis, bleaching). In this study, a focused anthozoan holobiont microarray was used to detect early and sub-lethal effects of spatial and temporal environmental changes on gene expression patterns in the scleractinian coral, Montastraea cavernosa, on south Florida reefs. Although all colonies appeared healthy (i.e. no visible tissue necrosis or bleaching), corals were differentially physiologically compensating for exposure to stressors that varied over time. Corals near the Port of Miami inlet experienced significant changes in expression of stress responsive and symbiont (zooxanthella)-specific genes after periods of heavy precipitation. In contrast, coral populations did not demonstrate stress responses during periods of increased water temperature (up to 29°C). Specific acute and long-term localized responses to other stressors were also evident. A correlation between stress response genes and symbiont-specific genes was also observed, possibly indicating early processes involved in the maintenance or disruption of the coral-zooxanthella symbiosis. This is the first study to reveal spatially- and temporally-related variation in gene expression in response to different stressors of in situ coral populations, and demonstrates that microarray technology can be used to detect specific sub-lethal physiological responses to specific environmental conditions that are not visually detectable.}, }
@article {pmid23283017, year = {2013}, author = {Fan, L and Liu, M and Simister, R and Webster, NS and Thomas, T}, title = {Marine microbial symbiosis heats up: the phylogenetic and functional response of a sponge holobiont to thermal stress.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {991-1002}, pmid = {23283017}, issn = {1751-7370}, mesh = {Animals ; Bacteria/classification/*growth &amp; development/*metabolism ; *Climate Change ; Coral Reefs ; Ecosystem ; *Microbiota ; Phylogeny ; Porifera/*microbiology/physiology ; Seawater ; Symbiosis ; }, abstract = {Large-scale mortality of marine invertebrates is a major global concern for ocean ecosystems and many sessile, reef-building animals, such as sponges and corals, are experiencing significant declines through temperature-induced disease and bleaching. The health and survival of marine invertebrates is often dependent on intimate symbiotic associations with complex microbial communities, yet we have a very limited understanding of the detailed biology and ecology of both the host and the symbiont community in response to environmental stressors, such as elevated seawater temperatures. Here, we use the ecologically important sponge Rhopaloeides odorabile as a model to explore the changes in symbiosis during the development of temperature-induced necrosis. Expression profiling of the sponge host was examined in conjunction with the phylogenetic and functional structure and the expression profile of the symbiont community. Elevated temperature causes an immediate stress response in both the host and symbiont community, including reduced expression of functions that mediate their partnership. Disruption to nutritional interdependence and molecular interactions during early heat stress further destabilizes the holobiont, ultimately leading to the loss of archetypal sponge symbionts and the introduction of new microorganisms that have functional and expression profiles consistent with a scavenging lifestyle, a lack virulence functions and a high growth rate. Previous models have postulated various mechanisms of mortality and disease in marine invertebrates. Our study suggests that interruption of symbiotic interactions is a major determinant for mortality in marine sessile invertebrates. High symbiont specialization and low functional redundancy, thus make these holobionts extremely vulnerable to environmental perturbations, including climate change.}, }
@article {pmid23264045, year = {2013}, author = {Seemann, J and Sawall, Y and Auel, H and Richter, C}, title = {The use of lipids and fatty acids to measure the trophic plasticity of the coral Stylophora subseriata.}, journal = {Lipids}, volume = {48}, number = {3}, pages = {275-286}, pmid = {23264045}, issn = {1558-9307}, mesh = {Acclimatization ; Animals ; Anthozoa/*physiology ; Autotrophic Processes ; Chlorophyll/metabolism ; Chlorophyll A ; Fatty Acids/*metabolism ; Heterotrophic Processes ; *Lipid Metabolism ; Plankton/physiology ; Symbiosis ; }, abstract = {Following up on previous investigations on the stress resistance of corals, this study assessed the trophic plasticity of the coral Stylophora subseriata in the Spermonde Archipelago (Indonesia) along an eutrophication gradient. Trophic plasticity was assessed in terms of lipid content and fatty acid composition in the holobiont relative to its plankton (50-300 μm) food as well as the zooxanthellae density, lipid, FA and chlorophyll a content. A cross-transplantation experiment was carried out for 1.5 months in order to assess the trophic potential of corals. Corals, which live in the eutrophied nearshore area showed higher zooxanthellae and chlorophyll a values and higher amounts of the dinoflagellate biomarker FA 18:4n-3. Their lipid contents were maintained at similar to levels from specimens further away from the anthropogenic impact source going up to 14.9 ± 0.9 %. A similarity percentage analysis of the groups holobiont, zooxanthellae and plankton >55 μm found that differences between the FA composition of the holobiont and zooxanthellae symbionts were more distinct in the site closer to the shore, thus heterotrophic feeding became more important. Transplanted corals attained very similar zooxanthellae, chlorophyll a and lipid values at all sites as the specimens originating from those sites, which indicates a high potential for trophic plasticity in the case of a change in food sources, which makes this species competitive and resistant to eutrophication.}, }
@article {pmid23254513, year = {2013}, author = {Krediet, CJ and Ritchie, KB and Alagely, A and Teplitski, M}, title = {Members of native coral microbiota inhibit glycosidases and thwart colonization of coral mucus by an opportunistic pathogen.}, journal = {The ISME journal}, volume = {7}, number = {5}, pages = {980-990}, pmid = {23254513}, issn = {1751-7370}, mesh = {Acetylglucosaminidase/metabolism ; Animals ; Anthozoa/*microbiology/physiology ; *Antibiosis ; Bacillales/growth &amp; development/*metabolism ; Glycoside Hydrolases/metabolism ; Sea Anemones/microbiology ; Serratia marcescens/genetics/*growth &amp; development/metabolism/pathogenicity ; Symbiosis ; Virulence ; }, abstract = {The outcome of the interactions between native commensal microorganisms and opportunistic pathogens is crucial to the health of the coral holobiont. During the establishment within the coral surface mucus layer, opportunistic pathogens, including a white pox pathogen Serratia marcescens PDL100, compete with native bacteria for available nutrients. Both commensals and pathogens employ glycosidases and N-acetyl-glucosaminidase to utilize components of coral mucus. This study tested the hypothesis that specific glycosidases were critical for the growth of S. marcescens on mucus and that their inhibition by native coral microbiota reduces fitness of the pathogen. Consistent with this hypothesis, a S. marcescens transposon mutant with reduced glycosidase and N-acetyl-glucosaminidase activities was unable to compete with the wild type on the mucus of the host coral Acropora palmata, although it was at least as competitive as the wild type on a minimal medium with glycerol and casamino acids. Virulence of the mutant was modestly reduced in the Aiptasia model. A survey revealed that ∼8% of culturable coral commensal bacteria have the ability to inhibit glycosidases in the pathogen. A small molecular weight, ethanol-soluble substance(s) produced by the coral commensal Exiguobacterium sp. was capable of the inhibition of the induction of catabolic enzymes in S. marcescens. This inhibition was in part responsible for the 10-100-fold reduction in the ability of the pathogen to grow on coral mucus. These results provide insight into potential mechanisms of commensal interference with early colonization and infection behaviors in opportunistic pathogens and highlight an important function for the native microbiota in coral health.}, }
@article {pmid23174086, year = {2013}, author = {Cima, F and Ferrari, G and Ferreira, NG and Rocha, RJ and Serôdio, J and Loureiro, S and Calado, R}, title = {Preliminary evaluation of the toxic effects of the antifouling biocide Sea-Nine 211™ in the soft coral Sarcophyton cf. glaucum (Octocorallia, Alcyonacea) based on PAM fluorometry and biomarkers.}, journal = {Marine environmental research}, volume = {83}, number = {}, pages = {16-22}, doi = {10.1016/j.marenvres.2012.10.004}, pmid = {23174086}, issn = {1879-0291}, mesh = {Animals ; Anthozoa/*drug effects/metabolism ; Biomarkers/*analysis ; Disinfectants/*toxicity ; Enzyme Activation/drug effects ; *Fluorometry ; Microalgae/drug effects ; Photosynthesis/drug effects ; Thiazoles/*toxicity ; Toxicity Tests/standards ; }, abstract = {Sea-Nine 211™ is a new biocide specifically formulated for antifouling paints and being considered to have a low environmental impact. Even with a short environmental half-life, this compound can cause toxic effects on marine organisms. This study used PAM fluorometry and biomarkers of oxidative stress (GST, CAT and LPO) to monitor potential toxic effects of Sea-Nine 211™ on fragments of the soft coral Sarcophyton cf. glaucum. After exposure to concentrations of 1-100 μg l(-1) for 72 h, CAT activity was inhibited under the two highest concentrations, being in accordance with the activity of GST. LPO activity (as TBARS) and photosynthetic efficiency of endosymbiotic zooxanthellae were not significantly affected. These results show that PAM fluorometry alone cannot detect the full effects of Sea-Nine 211™ on Sarcophyton cf. glaucum and should be used together with other biomarkers. This holobiont driven approach to evaluate chemical toxicity in photosynthetic corals is therefore recommended for biocides which are not photosystem II inhibitors.}, }
@article {pmid23170223, year = {2012}, author = {Oliver, KR and Greene, WK}, title = {Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis.}, journal = {Ecology and evolution}, volume = {2}, number = {11}, pages = {2912-2933}, pmid = {23170223}, issn = {2045-7758}, abstract = {In addition to the strong divergent evolution and significant and episodic evolutionary transitions and speciation we previously attributed to TE-Thrust, we have expanded the hypothesis to more fully account for the contribution of viruses to TE-Thrust and evolution. The concept of symbiosis and holobiontic genomes is acknowledged, with particular emphasis placed on the creativity potential of the union of retroviral genomes with vertebrate genomes. Further expansions of the TE-Thrust hypothesis are proposed regarding a fuller account of horizontal transfer of TEs, the life cycle of TEs, and also, in the case of a mammalian innovation, the contributions of retroviruses to the functions of the placenta. The possibility of drift by TE families within isolated demes or disjunct populations, is acknowledged, and in addition, we suggest the possibility of horizontal transposon transfer into such subpopulations. "Adaptive potential" and "evolutionary potential" are proposed as the extremes of a continuum of "intra-genomic potential" due to TE-Thrust. Specific data is given, indicating "adaptive potential" being realized with regard to insecticide resistance, and other insect adaptations. In this regard, there is agreement between TE-Thrust and the concept of adaptation by a change in allele frequencies. Evidence on the realization of "evolutionary potential" is also presented, which is compatible with the known differential survivals, and radiations of lineages. Collectively, these data further suggest the possibility, or likelihood, of punctuated episodes of speciation events and evolutionary transitions, coinciding with, and heavily underpinned by, intermittent bursts of TE activity.}, }
@article {pmid23157386, year = {2013}, author = {Egan, S and Harder, T and Burke, C and Steinberg, P and Kjelleberg, S and Thomas, T}, title = {The seaweed holobiont: understanding seaweed-bacteria interactions.}, journal = {FEMS microbiology reviews}, volume = {37}, number = {3}, pages = {462-476}, doi = {10.1111/1574-6976.12011}, pmid = {23157386}, issn = {1574-6976}, mesh = {Bacteria/metabolism/pathogenicity ; *Bacterial Physiological Phenomena ; *Biodiversity ; *Host-Pathogen Interactions ; *Metagenome ; Seaweed/*microbiology ; *Symbiosis ; }, abstract = {Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich diversity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept.}, }
@article {pmid23145489, year = {2012}, author = {Ladner, JT and Barshis, DJ and Palumbi, SR}, title = {Protein evolution in two co-occurring types of Symbiodinium: an exploration into the genetic basis of thermal tolerance in Symbiodinium clade D.}, journal = {BMC evolutionary biology}, volume = {12}, number = {}, pages = {217}, pmid = {23145489}, issn = {1471-2148}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/*microbiology ; Biological Evolution ; Climate Change ; Coral Reefs ; Dinoflagellida/*genetics ; *Hot Temperature ; *Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: The symbiosis between reef-building corals and photosynthetic dinoflagellates (Symbiodinium) is an integral part of the coral reef ecosystem, as corals are dependent on Symbiodinium for the majority of their energy needs. However, this partnership is increasingly at risk due to changing climatic conditions. It is thought that functional diversity within Symbiodinium may allow some corals to rapidly adapt to different environments by changing the type of Symbiodinium with which they partner; however, very little is known about the molecular basis of the functional differences among symbiont groups. One group of Symbiodinium that is hypothesized to be important for the future of reefs is clade D, which, in general, seems to provide the coral holobiont (i.e., coral host and associated symbiont community) with elevated thermal tolerance. Using high-throughput sequencing data from field-collected corals we assembled, de novo, draft transcriptomes for Symbiodinium clades C and D. We then explore the functional basis of thermal tolerance in clade D by comparing rates of coding sequence evolution among the four clades of Symbiodinium most commonly found in reef-building corals (A-D).<br><br>RESULTS: We are able to highlight a number of genes and functional categories as candidates for involvement in the increased thermal tolerance of clade D. These include a fatty acid desaturase, molecular chaperones and proteins involved in photosynthesis and the thylakoid membrane. We also demonstrate that clades C and D co-occur within most of the sampled colonies of Acropora hyacinthus, suggesting widespread potential for this coral species to acclimatize to changing thermal conditions via 'shuffling' the proportions of these two clades from within their current symbiont communities.<br><br>CONCLUSIONS: Transcriptome-wide analysis confirms that the four main Symbiodinium clades found within corals exhibit extensive evolutionary divergence (18.5-27.3% avg. pairwise nucleotide difference). Despite these evolutionary distinctions, many corals appear to host multiple clades simultaneously, which may allow for rapid acclimatization to changing environmental conditions. This study provides a first step toward understanding the molecular basis of functional differences between Symbiodinium clades by highlighting a number of genes with signatures consistent with positive selection along the thermally tolerant clade D lineage.}, }
@article {pmid23133637, year = {2012}, author = {Cardoso, AM and Cavalcante, JJ and Cantão, ME and Thompson, CE and Flatschart, RB and Glogauer, A and Scapin, SM and Sade, YB and Beltrão, PJ and Gerber, AL and Martins, OB and Garcia, ES and de Souza, W and Vasconcelos, AT}, title = {Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes.}, journal = {PloS one}, volume = {7}, number = {11}, pages = {e48505}, pmid = {23133637}, issn = {1932-6203}, mesh = {Animals ; Biofuels ; Biomass ; Biotechnology/methods ; Carbohydrates/chemistry ; Carbon Dioxide/chemistry ; Computational Biology/methods ; Ethanol/chemistry ; Glycoside Hydrolases/chemistry ; Lignin/chemistry ; Metagenome ; *Metagenomics ; Oligosaccharides/chemistry ; Petroleum/metabolism ; Phylogeny ; Protein Binding ; Sequence Analysis, DNA/methods ; Snails ; }, abstract = {The shortage of petroleum reserves and the increase in CO(2) emissions have raised global concerns and highlighted the importance of adopting sustainable energy sources. Second-generation ethanol made from lignocellulosic materials is considered to be one of the most promising fuels for vehicles. The giant snail Achatina fulica is an agricultural pest whose biotechnological potential has been largely untested. Here, the composition of the microbial population within the crop of this invasive land snail, as well as key genes involved in various biochemical pathways, have been explored for the first time. In a high-throughput approach, 318 Mbp of 454-Titanium shotgun metagenomic sequencing data were obtained. The predominant bacterial phylum found was Proteobacteria, followed by Bacteroidetes and Firmicutes. Viruses, Fungi, and Archaea were present to lesser extents. The functional analysis reveals a variety of microbial genes that could assist the host in the degradation of recalcitrant lignocellulose, detoxification of xenobiotics, and synthesis of essential amino acids and vitamins, contributing to the adaptability and wide-ranging diet of this snail. More than 2,700 genes encoding glycoside hydrolase (GH) domains and carbohydrate-binding modules were detected. When we compared GH profiles, we found an abundance of sequences coding for oligosaccharide-degrading enzymes (36%), very similar to those from wallabies and giant pandas, as well as many novel cellulase and hemicellulase coding sequences, which points to this model as a remarkable potential source of enzymes for the biofuel industry. Furthermore, this work is a major step toward the understanding of the unique genetic profile of the land snail holobiont.}, }
@article {pmid23091033, year = {2012}, author = {Beinart, RA and Sanders, JG and Faure, B and Sylva, SP and Lee, RW and Becker, EL and Gartman, A and Luther, GW and Seewald, JS and Fisher, CR and Girguis, PR}, title = {Evidence for the role of endosymbionts in regional-scale habitat partitioning by hydrothermal vent symbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, number = {47}, pages = {E3241-50}, pmid = {23091033}, issn = {1091-6490}, mesh = {Animals ; Bayes Theorem ; Carbon Isotopes ; *Ecosystem ; Electrochemical Techniques ; Electron Transport Complex IV/genetics ; Epsilonproteobacteria/*genetics ; Gammaproteobacteria/*genetics ; Gastropoda/*genetics/*microbiology ; Geography ; Haplotypes/genetics ; Hydrothermal Vents/*microbiology ; Isotope Labeling ; Mitochondria/genetics ; Molecular Sequence Data ; Pacific Ocean ; Phylogeny ; Protein Subunits/genetics ; RNA, Ribosomal, 16S/genetics ; Symbiosis/*genetics ; Temperature ; }, abstract = {Deep-sea hydrothermal vents are populated by dense communities of animals that form symbiotic associations with chemolithoautotrophic bacteria. To date, our understanding of which factors govern the distribution of host/symbiont associations (or holobionts) in nature is limited, although host physiology often is invoked. In general, the role that symbionts play in habitat utilization by vent holobionts has not been thoroughly addressed. Here we present evidence for symbiont-influenced, regional-scale niche partitioning among symbiotic gastropods (genus Alviniconcha) in the Lau Basin. We extensively surveyed Alviniconcha holobionts from four vent fields using quantitative molecular approaches, coupled to characterization of high-temperature and diffuse vent-fluid composition using gastight samplers and in situ electrochemical analyses, respectively. Phylogenetic analyses exposed cryptic host and symbiont diversity, revealing three distinct host types and three different symbiont phylotypes (one ε-proteobacteria and two γ-proteobacteria) that formed specific associations with one another. Strikingly, we observed that holobionts with ε-proteobacterial symbionts were dominant at the northern fields, whereas holobionts with γ-proteobacterial symbionts were dominant in the southern fields. This pattern of distribution corresponds to differences in the vent geochemistry that result from deep subsurface geological and geothermal processes. We posit that the symbionts, likely through differences in chemolithoautotrophic metabolism, influence niche utilization among these holobionts. The data presented here represent evidence linking symbiont type to habitat partitioning among the chemosynthetic symbioses at hydrothermal vents and illustrate the coupling between subsurface geothermal processes and niche availability.}, }
@article {pmid23014479, year = {2013}, author = {Al-Dahash, LM and Mahmoud, HM}, title = {Harboring oil-degrading bacteria: a potential mechanism of adaptation and survival in corals inhabiting oil-contaminated reefs.}, journal = {Marine pollution bulletin}, volume = {72}, number = {2}, pages = {364-374}, doi = {10.1016/j.marpolbul.2012.08.029}, pmid = {23014479}, issn = {1879-3363}, mesh = {*Adaptation, Physiological ; Animals ; Anthozoa/*physiology ; Bacteria/classification/genetics/*metabolism ; Biodegradation, Environmental ; Biodiversity ; *Coral Reefs ; Petroleum/*metabolism ; Petroleum Pollution/statistics &amp; numerical data ; Phylogeny ; Symbiosis ; Water Pollutants, Chemical/*metabolism ; }, abstract = {Certain coral reef systems north of the Arabian Gulf are characterized by corals with a unique ability to thrive and flourish despite the presence of crude oil continuously seeping from natural cracks in the seabed. Harboring oil-degrading bacteria as a part of the holobiont has been investigated as a potential mechanism of adaptation and survival for corals in such systems. The use of conventional and molecular techniques verified a predominance of bacteria affiliated with Gammaproteobacteria, Actinobacteria and Firmicutes in the mucus and tissues of Acropora clathrata and Porites compressa. These bacteria were capable of degrading a wide range of aliphatic (C9-C28) aromatic hydrocarbons (Phenanthrene, Biphenyl, Naphthalene) and crude oil. In addition, microcosms supplied with coral samples and various concentrations of crude oil shifted their bacterial population toward the more advantageous types of oil degraders as oil concentrations increased.}, }
@article {pmid23011286, year = {2013}, author = {Meron, D and Buia, MC and Fine, M and Banin, E}, title = {Changes in microbial communities associated with the sea anemone Anemonia viridis in a natural pH gradient.}, journal = {Microbial ecology}, volume = {65}, number = {2}, pages = {269-276}, pmid = {23011286}, issn = {1432-184X}, mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; *Biota ; Carbon Dioxide/analysis ; Chlorophyll/analysis ; DNA, Bacterial/genetics ; Dinoflagellida/isolation &amp; purification ; *Hydrogen-Ion Concentration ; Italy ; Mediterranean Sea ; Proton-Motive Force ; Sea Anemones/*microbiology ; Seawater/chemistry ; }, abstract = {Ocean acidification, resulting from rising atmospheric carbon dioxide concentrations, is a pervasive stressor that can affect many marine organisms and their symbionts. Studies which examine the host physiology and microbial communities have shown a variety of responses to the ocean acidification process. Recently, several studies were conducted based on field experiments, which take place in natural CO(2) vents, exposing the host to natural environmental conditions of varying pH. This study examines the sea anemone Anemonia viridis which is found naturally along the pH gradient in Ischia, Italy, with an aim to characterize whether exposure to pH impacts the holobiont. The physiological parameters of A. viridis (Symbiodinium density, protein, and chlorophyll a+c concentration) and its microbial community were monitored. Although reduction in pH was seen to have had an impact on composition and diversity of associated microbial communities, no significant changes were observed in A. viridis physiology, and no microbial stress indicators (i.e., pathogens, antibacterial activity, etc.) were detected. In light of these results, it appears that elevated CO(2) does not have a negative influence on A. viridis that live naturally in the site. This suggests that natural long-term exposure and dynamic diverse microbial communities may contribute to the acclimation process of the host in a changing pH environment.}, }
@article {pmid22985125, year = {2012}, author = {de Oliveira, LS and Gregoracci, GB and Silva, GG and Salgado, LT and Filho, GA and Alves-Ferreira, M and Pereira, RC and Thompson, FL}, title = {Transcriptomic analysis of the red seaweed Laurencia dendroidea (Florideophyceae, Rhodophyta) and its microbiome.}, journal = {BMC genomics}, volume = {13}, number = {}, pages = {487}, pmid = {22985125}, issn = {1471-2164}, mesh = {Cyanobacteria/*genetics/metabolism ; DNA, Complementary/biosynthesis ; Expressed Sequence Tags ; Laurencia/*genetics/metabolism/microbiology ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Photosynthesis ; Proteobacteria/*genetics/metabolism ; Seaweed/*genetics/metabolism/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Terpenes/metabolism ; *Transcriptome ; }, abstract = {BACKGROUND: Seaweeds of the Laurencia genus have a broad geographic distribution and are largely recognized as important sources of secondary metabolites, mainly halogenated compounds exhibiting diverse potential pharmacological activities and relevant ecological role as anti-epibiosis. Host-microbe interaction is a driving force for co-evolution in the marine environment, but molecular studies of seaweed-associated microbial communities are still rare. Despite the large amount of research describing the chemical compositions of Laurencia species, the genetic knowledge regarding this genus is currently restricted to taxonomic markers and general genome features. In this work we analyze the transcriptomic profile of L. dendroidea J. Agardh, unveil the genes involved on the biosynthesis of terpenoid compounds in this seaweed and explore the interactions between this host and its associated microbiome.<br><br>RESULTS: A total of 6 transcriptomes were obtained from specimens of L. dendroidea sampled in three different coastal locations of the Rio de Janeiro state. Functional annotations revealed predominantly basic cellular metabolic pathways. Bacteria was the dominant active group in the microbiome of L. dendroidea, standing out nitrogen fixing Cyanobacteria and aerobic heterotrophic Proteobacteria. The analysis of the relative contribution of each domain highlighted bacterial features related to glycolysis, lipid and polysaccharide breakdown, and also recognition of seaweed surface and establishment of biofilm. Eukaryotic transcripts, on the other hand, were associated with photosynthesis, synthesis of carbohydrate reserves, and defense mechanisms, including the biosynthesis of terpenoids through the mevalonate-independent pathway.<br><br>CONCLUSIONS: This work describes the first transcriptomic profile of the red seaweed L. dendroidea, increasing the knowledge about ESTs from the Florideophyceae algal class. Our data suggest an important role for L. dendroidea in the primary production of the holobiont and the role of Bacteria as consumers of organic matter and possibly also as nitrogen source. Furthermore, this seaweed expressed sequences related to terpene biosynthesis, including the complete mevalonate-independent pathway, which offers new possibilities for biotechnological applications using secondary metabolites from L. dendroidea.}, }
@article {pmid22983034, year = {2012}, author = {Bosch, TC}, title = {What hydra has to say about the role and origin of symbiotic interactions.}, journal = {The Biological bulletin}, volume = {223}, number = {1}, pages = {78-84}, doi = {10.1086/BBLv223n1p78}, pmid = {22983034}, issn = {1939-8697}, mesh = {Animals ; Bacteria/growth &amp; development ; *Bacterial Physiological Phenomena ; Chlorella/growth &amp; development/*physiology ; Genomics/methods ; Hydra/*microbiology/*physiology ; Metabolomics/methods ; Proteomics/methods ; *Symbiosis ; Toll-Like Receptors/metabolism ; }, abstract = {The Hydra holobiont involves at least three types of organisms that all share a long coevolutionary history and appear to depend on each other. Here I review how symbiotic algae and stably associated bacteria interact with the Hydra host and where in the tissue they are located. In particular I discuss the role of Toll-like receptor (TLR) signaling in maintaining Hydra's species-specific microbiota. I also discuss studies in Hydra viridis and its symbiotic Chlorella algae which indicate that the symbiotic algae are critically involved in the control of sexual differentiation in green Hydra. Finally, I review the state of "omics" in this tripartite association and the fact that the functioning of this holobiont is also a tale of several genomes.}, }
@article {pmid22944243, year = {2012}, author = {Barott, KL and Rohwer, FL}, title = {Unseen players shape benthic competition on coral reefs.}, journal = {Trends in microbiology}, volume = {20}, number = {12}, pages = {621-628}, doi = {10.1016/j.tim.2012.08.004}, pmid = {22944243}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*microbiology/virology ; Bacteria/growth &amp; development ; *Biota ; *Coral Reefs ; *Microbial Interactions ; Organic Chemicals/metabolism ; Population Dynamics ; Seawater/microbiology/virology ; Seaweed/growth &amp; development/metabolism ; Viruses/growth &amp; development ; }, abstract = {Recent work has shown that hydrophilic and hydrophobic organic matter (OM) from algae disrupts the function of the coral holobiont and promotes the invasion of opportunistic pathogens, leading to coral morbidity and mortality. Here we refer to these dynamics as the (3)DAM [dissolved organic matter (DOM), direct contact, disease, algae and microbes] model. There is considerable complexity in coral-algae interactions; turf algae and macroalgae promote heterotrophic microbial overgrowth of coral, macroalgae also directly harm the corals via hydrophobic OM, whereas crustose coralline algae generally encourage benign microbial communities. In addition, complex flow patterns transport OM and pathogens from algae to downstream corals, and direct algal contact enhances their delivery. These invisible players (microbes, viruses, and OM) are important drivers of coral reefs because they have non-linear responses to disturbances and are the first to change in response to perturbations, providing near real-time trajectories for a coral reef, a vital metric for conservation and restoration.}, }
@article {pmid22933373, year = {2012}, author = {Putnam, HM and Stat, M and Pochon, X and Gates, RD}, title = {Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1746}, pages = {4352-4361}, pmid = {22933373}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/*parasitology/*physiology ; Climate Change ; Dinoflagellida/classification/*genetics/physiology ; Ecosystem ; Environment ; Molecular Sequence Data ; Phylogeny ; Polynesia ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {Flexibility in biological systems is seen as an important driver of macro-ecosystem function and stability. Spatially constrained endosymbiotic settings, however, are less studied, although environmental thresholds of symbiotic corals are linked to the function of their endosymbiotic dinoflagellate communities. Symbiotic flexibility is a hypothesized mechanism that corals may exploit to adapt to climate change. This study explores the flexibility of the coral-Symbiodinium symbiosis through quantification of Symbiodinium ITS2 sequence assemblages in a range of coral species and genera. Sequence assemblages are expressed as an index of flexibility incorporating phylogenetic divergence and relative abundance of Symbiodinium sequences recovered from the host. This comparative analysis reveals profound differences in the flexibility of corals for Symbiodinium, thereby classifying corals as generalists or specifists. Generalists such as Acropora and Pocillopora exhibit high intra- and inter-species flexibility in their Symbiodinium assemblages and are some of the most environmentally sensitive corals. Conversely, specifists such as massive Porites colonies exhibit low flexibility, harbour taxonomically narrow Symbiodinium assemblages, and are environmentally resistant corals. Collectively, these findings challenge the paradigm that symbiotic flexibility enhances holobiont resilience. This underscores the need for a deeper examination of the extent and duration of the functional benefits associated with endosymbiotic diversity and flexibility under environmental stress.}, }
@article {pmid22919645, year = {2012}, author = {Salvucci, E}, title = {Selfishness, warfare, and economics; or integration, cooperation, and biology.}, journal = {Frontiers in cellular and infection microbiology}, volume = {2}, number = {}, pages = {54}, pmid = {22919645}, issn = {2235-2988}, mesh = {Biology/*trends ; *Evolution, Molecular ; Humans ; }, abstract = {The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an "infective" way and become an essential part of multicellular organisms. They have content with "biological sense" i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a "superorganism") along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.}, }
@article {pmid22906221, year = {2013}, author = {del Campo, EM and Catalá, S and Gimeno, J and del Hoyo, A and Martínez-Alberola, F and Casano, LM and Grube, M and Barreno, E}, title = {The genetic structure of the cosmopolitan three-partner lichen Ramalina farinacea evidences the concerted diversification of symbionts.}, journal = {FEMS microbiology ecology}, volume = {83}, number = {2}, pages = {310-323}, doi = {10.1111/j.1574-6941.2012.01474.x}, pmid = {22906221}, issn = {1574-6941}, mesh = {Ascomycota/classification/*genetics/isolation &amp; purification ; Chlorophyta/classification/*genetics ; Europe ; Genetic Variation ; Genotype ; Lichens/classification/*genetics/isolation &amp; purification ; Nucleic Acid Conformation ; Phylogeny ; RNA, Ribosomal/chemistry ; Spain ; Symbiosis/*genetics ; }, abstract = {The epiphytic lichen Ramalina farinacea is distributed throughout the northern hemisphere in which the same two algal Trebouxia species (provisionally named TR1 and TR9) coexist in every thallus. Ramalina farinacea symbionts were characterized based on the two fungal nuclear loci (nrITS and rpb2) along with the primary and secondary structures of nrITS from each Trebouxia species in the Iberian Peninsula and Canary Islands. The results indicated a noticeable genetic differentiation between mycobionts from these two geographic areas and also suggested concerted changes in the three partners of a lichen symbiosis toward two clearly distinguishable 'holobiont' lineages. Modeling of ITS2 RNA secondary structures suggested their temperature sensitivity in TR1 but not in TR9, which was consistent with the observed superior physiological performance of TR9 phycobionts under relatively high temperatures. Both TR1 and TR9 phycobionts have been also found in a variety of taxonomically distinct lichens with a preferably Mediterranean distribution, being TR1 much more widespread than TR9. Our observations support a model in which ecological diversification and speciation of lichen symbionts in different habitats could include a transient phase consisting of associations with more than one photobiont in individual thalli. Such diversification is likely to be promoted by different physiological backgrounds.}, }
@article {pmid22895828, year = {2013}, author = {Ceh, J and van Keulen, M and Bourne, DG}, title = {Intergenerational transfer of specific bacteria in corals and possible implications for offspring fitness.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {227-231}, pmid = {22895828}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; DNA, Bacterial/genetics ; Germ Cells/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; }, abstract = {Diverse and abundant bacterial populations play important functional roles in the multi-partite association of the coral holobiont. The specificity of coral-associated assemblages remains unclear, and little is known about the inheritance of specific bacteria from the parent colony to their offspring. This study investigated if broadcast spawning and brooding corals release specific and potentially beneficial bacteria with their offspring to secure maintenance across generations. Two coral species, Acropora tenuis and Pocillopora damicornis, were maintained in 0.2 μm filtered seawater during the release of their gametes and planulae, respectively. Water samples, excluding gametes and planulae, were subsequently collected, and bacterial diversity was assessed through a pyrosequencing approach amplifying a 470-bp region of the 16S rRNA gene including the variable regions 1-3. Compared to the high bacterial diversity harboured by corals, only a few taxa of bacteria were released by adult corals. Both A. tenuis and P. damicornis released similar bacteria, and the genera Alteromonas and Roseobacter were abundant in large proportions in the seawater of both species after reproduction. This study suggests that adult corals may release bacteria with their offspring to benefit the fitness in early coral life stages.}, }
@article {pmid22877610, year = {2012}, author = {Stat, M and Baker, AC and Bourne, DG and Correa, AM and Forsman, Z and Huggett, MJ and Pochon, X and Skillings, D and Toonen, RJ and van Oppen, MJ and Gates, RD}, title = {Molecular delineation of species in the coral holobiont.}, journal = {Advances in marine biology}, volume = {63}, number = {}, pages = {1-65}, doi = {10.1016/B978-0-12-394282-1.00001-6}, pmid = {22877610}, issn = {0065-2881}, mesh = {Animals ; Anthozoa/*classification/genetics/*physiology ; *Biodiversity ; Climate Change ; *Coral Reefs ; *Genetic Speciation ; }, abstract = {The coral holobiont is a complex assemblage of organisms spanning a diverse taxonomic range including a cnidarian host, as well as various dinoflagellate, prokaryotic and acellular symbionts. With the accumulating information on the molecular diversity of these groups, binomial species classification and a reassessment of species boundaries for the partners in the coral holobiont is a logical extension of this work and will help enhance the capacity for comparative research among studies. To aid in this endeavour, we review the current literature on species diversity for the three best studied partners of the coral holobiont (coral, Symbiodinium, prokaryotes) and provide suggestions for future work on systematics within these taxa. We advocate for an integrative approach to the delineation of species using both molecular genetics in combination with phenetic characters. We also suggest that an a priori set of criteria be developed for each taxonomic group as no one species concept or accompanying set of guidelines is appropriate for delineating all members of the coral holobiont.}, }
@article {pmid22864853, year = {2013}, author = {Lins-de-Barros, MM and Cardoso, AM and Silveira, CB and Lima, JL and Clementino, MM and Martins, OB and Albano, RM and Vieira, RP}, title = {Microbial community compositional shifts in bleached colonies of the Brazilian reef-building coral Siderastrea stellata.}, journal = {Microbial ecology}, volume = {65}, number = {1}, pages = {205-213}, pmid = {22864853}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Brazil ; Chlorophyta/classification/*genetics ; DNA Barcoding, Taxonomic ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; Diatoms/classification/genetics ; Ecosystem ; Gene Library ; Phylogeny ; Plastids/genetics ; RNA, Ribosomal, 16S/genetics ; Rhodophyta/*classification/genetics ; Symbiosis ; }, abstract = {The association of metazoan, protist, and microbial communities with Scleractinian corals forms the basis of the coral holobiont. Coral bleaching events have been occurring around the world, introducing changes in the delicate balance of the holobiont symbiotic interactions. In this study, Archaea, bacteria, and eukaryotic phototrophic plastids of bleached colonies of the Brazilian coral Siderastrea stellata were analyzed for the first time, using 16S rRNA gene libraries. Prokaryotic communities were slightly more diverse in healthy than in bleached corals. However, the eukaryotic phototrophic plastids community was more diverse in bleached corals. Archaea phylogenetic analyses revealed a high percentage of Crenarchaeota sequences, mainly related to Nitrosopumilus maritimus and Cenarchaeum symbiosum. Dramatic changes in bacterial community composition were observed in this bleaching episode. The dominant bacterial group was Alphaproteobacteria followed by Gammaproteobacteria in bleached and Betaproteobacteria in healthy samples. Plastid operational taxonomic units (OTUs) from both coral samples were mainly related to red algae chloroplasts (Florideophycea), but we also observed some OTUs related to green algae chloroplasts (Chlorophyta). There seems to be a strong relationship between the Bacillariophyta phylum and our bleached coral samples as clones related to members of the diatom genera Amphora and Nitzschia were detected. The present study reveals information from a poorly investigated coral species and improves the knowledge of coral microbial community shifts that could occur during bleaching episodes.}, }
@article {pmid22822369, year = {2012}, author = {Hunt, LR and Smith, SM and Downum, KR and Mydlarz, LD}, title = {Microbial regulation in gorgonian corals.}, journal = {Marine drugs}, volume = {10}, number = {6}, pages = {1225-1243}, pmid = {22822369}, issn = {1660-3397}, mesh = {Animals ; Anthozoa/*chemistry/*microbiology ; Anti-Bacterial Agents/*chemistry/*pharmacology ; Bacteria/*drug effects ; Cell Communication/drug effects ; Florida ; Puerto Rico ; Quorum Sensing/*drug effects ; }, abstract = {Gorgonian corals possess many novel natural products that could potentially mediate coral-bacterial interactions. Since many bacteria use quorum sensing (QS) signals to facilitate colonization of host organisms, regulation of prokaryotic cell-to-cell communication may represent an important bacterial control mechanism. In the present study, we examined extracts of twelve species of Caribbean gorgonian corals, for mechanisms that regulate microbial colonization, such as antibacterial activity and QS regulatory activity. Ethanol extracts of gorgonians collected from Puerto Rico and the Florida Keys showed a range of both antibacterial and QS activities using a specific Pseudomonas aeruginosa QS reporter, sensitive to long chain AHLs and a short chain N-acylhomoserine lactones (AHL) biosensor, Chromobacterium violaceium. Overall, the gorgonian corals had higher antimicrobial activity against non-marine strains when compared to marine strains. Pseudopterogorgia americana, Pseusopterogorgia acerosa, and Pseudoplexuara flexuosa had the highest QS inhibitory effect. Interestingly, Pseudoplexuara porosa extracts stimulated QS activity with a striking 17-fold increase in signal. The stimulation of QS by P. porosa or other elements of the holobiont may encourage colonization or recruitment of specific microbial species. Overall, these results suggest the presence of novel stimulatory QS, inhibitory QS and bactericidal compounds in gorgonian corals. A better understanding of these compounds may reveal insight into coral-microbial ecology and whether a therapeutic potential exists.}, }
@article {pmid22809041, year = {2012}, author = {Keshavmurthy, S and Hsu, CM and Kuo, CY and Meng, PJ and Wang, JT and Chen, CA}, title = {Symbiont communities and host genetic structure of the brain coral Platygyra verweyi, at the outlet of a nuclear power plant and adjacent areas.}, journal = {Molecular ecology}, volume = {21}, number = {17}, pages = {4393-4407}, doi = {10.1111/j.1365-294X.2012.05704.x}, pmid = {22809041}, issn = {1365-294X}, mesh = {Acclimatization/genetics ; Animals ; Anthozoa/*genetics/microbiology ; DNA, Protozoan/genetics ; DNA, Ribosomal Spacer/genetics ; Dinoflagellida/genetics/*physiology ; *Genetics, Population ; *Nuclear Power Plants ; *Symbiosis ; Taiwan ; Temperature ; }, abstract = {In the context of rising seawater temperatures associated with climate change, the issue of whether coral holobionts deal with this challenge by shuffling their associations with stress- and/or heat-tolerant Symbiodinium, by generating heat-resistant host genotypes, or both is important for coral survival. In this study, the composition of communities of the endosymbiont Symbiodinium and the population genetics of the coral host Platygyra verweyi were examined in a reef impacted by hot-water discharged from the outlet of a nuclear power plant in operation in Kenting, Southern Taiwan since 1984. The water at this site is 2.0-3.0 °C warmer than adjacent reefs in summer, which have an average seawater temperature of 29.0 °C. The data were compared with those for the same species at other sites within 12 km of the outlet site. Platygyra verwyei was associated with one or both of Symbiodinium types C3 (heat sensitive) and D1a (heat tolerant) at all sites with the latter being the dominant at the nuclear power plant outlet. The proportion of C3 in populations increased gradually with increasing distance from the hot-water discharge. Genetic analysis of the Platygyra verweyi host using mitochondrial and nuclear markers showed no genetic differentiation among sites. Changes in the composition of Symbiodinium types associated with P. verweyi among closely located sites in Kenting suggested that this coral might have acclimatized to the constant thermal stress by selective association with heat-tolerant Symbiodinium types, whereas the role of the host in adaptation was inconclusive.}, }
@article {pmid22773636, year = {2012}, author = {Morrow, KM and Moss, AG and Chadwick, NE and Liles, MR}, title = {Bacterial associates of two Caribbean coral species reveal species-specific distribution and geographic variability.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {18}, pages = {6438-6449}, pmid = {22773636}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*isolation &amp; purification ; *Biota ; Caribbean Region ; DNA Barcoding, Taxonomic ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; Host-Parasite Interactions ; *Phylogeography ; Ribotyping ; }, abstract = {Scleractinian corals harbor microorganisms that form dynamic associations with the coral host and exhibit substantial genetic and ecological diversity. Microbial associates may provide defense against pathogens and serve as bioindicators of changing environmental conditions. Here we describe the bacterial assemblages associated with two of the most common and phylogenetically divergent reef-building corals in the Caribbean, Montastraea faveolata and Porites astreoides. Contrasting life history strategies and disease susceptibilities indicate potential differences in their microbiota and immune function that may in part drive changes in the composition of coral reef communities. The ribotype structure and diversity of coral-associated bacteria within the surface mucosal layer (SML) of healthy corals were assessed using denaturing gradient gel electrophoresis (DGGE) fingerprinting and 454 bar-coded pyrosequencing. Corals were sampled at disparate Caribbean locations representing various levels of anthropogenic impact. We demonstrate here that M. faveolata and P. astreoides harbor distinct, host-specific bacteria but that specificity varies by species and site. P. astreoides generally hosts a bacterial assemblage of low diversity that is largely dominated by one bacterial genus, Endozoicomonas, within the order Oceanospirillales. The bacterial assemblages associated with M. faveolata are significantly more diverse and exhibit higher specificity at the family level than P. astreoides assemblages. Both corals have more bacterial diversity and higher abundances of disease-related bacteria at sites closer to the mainland than at those furthest away. The most diverse bacterial taxa and highest relative abundance of disease-associated bacteria were seen for corals near St. Thomas, U.S. Virgin Islands (USVI) (2.5 km from shore), and the least diverse taxa and lowest relative abundance were seen for corals near our most pristine site in Belize (20 km from shore). We conclude that the two coral species studied harbor distinct bacterial assemblages within the SML, but the degree to which each species maintains specific microbial associations varies both within each site and across large spatial scales. The taxonomic scale (i.e., phylum versus genus) at which scientists examine coral-microbe associations, in addition to host-elicited factors and environmental fluctuations, must be considered carefully in future studies of the coral holobiont.}, }
@article {pmid22767125, year = {2012}, author = {Shnit-Orland, M and Sivan, A and Kushmaro, A}, title = {Antibacterial activity of Pseudoalteromonas in the coral holobiont.}, journal = {Microbial ecology}, volume = {64}, number = {4}, pages = {851-859}, pmid = {22767125}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; DNA, Bacterial/analysis/genetics ; *Ecosystem ; Gram-Negative Bacteria/genetics/growth &amp; development/isolation &amp; purification ; Gram-Positive Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; Indian Ocean ; Israel ; Microbial Sensitivity Tests/methods ; Microbial Viability ; Phylogeny ; Pseudoalteromonas/classification/genetics/growth &amp; development/*isolation &amp; purification ; Sequence Analysis, DNA ; Staphylococcus aureus/genetics/growth &amp; development ; Symbiosis ; }, abstract = {Corals harbor diverse and abundant prokaryotic populations. Bacterial communities residing in the coral mucus layer may be either pathogenic or symbiotic. Some species may produce antibiotics as a method of controlling populations of competing microbial species. The present study characterizes cultivable Pseudoalteromonas sp. isolated from the mucus layer of different coral species from the northern Gulf of Eilat, Red Sea, Israel. Six mucus-associated Pseudoalteromonas spp. obtained from different coral species were screened for antibacterial activity against 23 tester strains. Five of the six Pseudoalteromonas strains demonstrated extracellular antibacterial activity against Gram-positive-but not Gram-negative-tester strains. Active substances secreted into the cell-free supernatant are heat-tolerant and inhibit growth of Bacillus cereus, Staphylococcus aureus, and of ten endogenous Gram-positive marine bacteria isolated from corals. The Pseudoalteromonas spp. isolated from Red sea corals aligned in a phylogenetic tree with previously isolated Pseudoalteromonas spp. of marine origin that demonstrated antimicrobial activity. These results suggest that coral mucus-associated Pseudoalteromonas may play a protective role in the coral holobiont's defense against potential Gram-positive coral pathogens.}, }
@article {pmid22701613, year = {2012}, author = {White, JR and Patel, J and Ottesen, A and Arce, G and Blackwelder, P and Lopez, JV}, title = {Pyrosequencing of bacterial symbionts within Axinella corrugata sponges: diversity and seasonal variability.}, journal = {PloS one}, volume = {7}, number = {6}, pages = {e38204}, pmid = {22701613}, issn = {1932-6203}, mesh = {Animals ; Bacteria/*genetics ; Base Sequence ; *Biodiversity ; Cluster Analysis ; Computational Biology ; Florida ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; Porifera/*microbiology/ultrastructure ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; *Seasons ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; }, abstract = {BACKGROUND: Marine sponge species are of significant interest to many scientific fields including marine ecology, conservation biology, genetics, host-microbe symbiosis and pharmacology. One of the most intriguing aspects of the sponge "holobiont" system is the unique physiology, interaction with microbes from the marine environment and the development of a complex commensal microbial community. However, intraspecific variability and temporal stability of sponge-associated bacterial symbionts remain relatively unknown.<br><br>We have characterized the bacterial symbiont community biodiversity of seven different individuals of the Caribbean reef sponge Axinella corrugata, from two different Florida reef locations during variable seasons using multiplex 454 pyrosequencing of 16 S rRNA amplicons. Over 265,512 high-quality 16 S rRNA sequences were generated and analyzed. Utilizing versatile bioinformatics methods and analytical software such as the QIIME and CloVR packages, we have identified 9,444 distinct bacterial operational taxonomic units (OTUs). Approximately 65,550 rRNA sequences (24%) could not be matched to bacteria at the class level, and may therefore represent novel taxa. Differentially abundant classes between seasonal Axinella communities included Gammaproteobacteria, Flavobacteria, Alphaproteobacteria, Cyanobacteria, Acidobacter and Nitrospira. Comparisons with a proximal outgroup sponge species (Amphimedon compressa), and the growing sponge symbiont literature, indicate that this study has identified approximately 330 A. corrugata-specific symbiotic OTUs, many of which are related to the sulfur-oxidizing Ectothiorhodospiraceae. This family appeared exclusively within A. corrugata, comprising >34.5% of all sequenced amplicons. Other A. corrugata symbionts such as Deltaproteobacteria, Bdellovibrio, and Thiocystis among many others are described.<br><br>CONCLUSIONS/SIGNIFICANCE: Slight shifts in several bacterial taxa were observed between communities sampled during spring and fall seasons. New 16 S rDNA sequences and concomitant identifications greatly expand the microbial community profile for this model reef sponge, and will likely be useful as a baseline for any future comparisons regarding sponge microbial community dynamics.}, }
@article {pmid22688725, year = {2012}, author = {Bosch, TC}, title = {Understanding complex host-microbe interactions in Hydra.}, journal = {Gut microbes}, volume = {3}, number = {4}, pages = {345-351}, pmid = {22688725}, issn = {1949-0984}, mesh = {Animals ; Bacteria/*pathogenicity ; *Host-Pathogen Interactions ; Hydra/*microbiology ; Models, Animal ; }, abstract = {Any multicellular organism may be considered a metaorganism or holobiont-comprised of the macroscopic host and synergistic interdependence with bacteria, archaea, fungi, viruses, and numerous other microbial and eukaryotic species including algal symbionts. Defining the individual microbe-host conversations in these consortia is a challenging but necessary step on the path to understanding the function of the associations as a whole. Dissecting the fundamental principles that underlie all host-microbe interactions requires simple animal models with only a few specific bacterial species. Here I present Hydra as such a model with one of the simplest epithelia in the animal kingdom, with the availability of a fully sequenced genome and numerous genomic tools, and with few associated bacterial species.}, }
@article {pmid22675185, year = {2012}, author = {Dimond, JL and Holzman, BJ and Bingham, BL}, title = {Thicker host tissues moderate light stress in a cnidarian endosymbiont.}, journal = {The Journal of experimental biology}, volume = {215}, number = {Pt 13}, pages = {2247-2254}, doi = {10.1242/jeb.067991}, pmid = {22675185}, issn = {1477-9145}, mesh = {*Acclimatization ; Animals ; Chlorophyll/analysis/metabolism ; Chlorophyta/*physiology ; Cnidaria/*anatomy &amp; histology/chemistry/*physiology ; Epidermis/anatomy &amp; histology/chemistry ; Light ; *Photosynthesis ; *Symbiosis ; }, abstract = {The susceptibility of algal-cnidarian holobionts to environmental stress is dependent on attributes of both host and symbiont, but the role of the host is often unclear. We examined the influence of the host on symbiont light stress, comparing the photophysiology of the chlorophyte symbiont Elliptochloris marina in two species of sea anemones in the genus Anthopleura. After 3 months of acclimation in outdoor tanks, polyp photoprotective contraction behavior was similar between the two host species, but photochemical efficiency was 1.5 times higher in A. xanthogrammica than in A. elegantissima. Maximum relative electron transport rates, derived from rapid light curves, were 1.5 times higher in A. xanthogrammica than in A. elegantissima when symbionts were inside intact tissues, but were not significantly different between host species upon removal of outer (epidermis and mesoglea) tissue layers from symbiont-containing gastrodermal cells. Tissues of A. xanthogrammica were 1.8 times thicker than those of A. elegantissima, with outer tissue layers attenuating 1.6 times more light. We found no significant differences in light absorption properties per unit volume of tissue, confirming the direct effect of tissue thickness on light attenuation. The thicker tissues of A. xanthogrammica thus provide a favorable environment for E. marina - a relatively stress-susceptible symbiont - and may explain its higher prevalence and expanded range in A. xanthogrammica along the Pacific coast of North America. Our findings also support a photoprotective role for thicker host tissues in reef corals that has long been thought to influence variability in bleaching susceptibility among coral taxa.}, }
@article {pmid22648507, year = {2012}, author = {Hartmann, A and Schikora, A}, title = {Quorum sensing of bacteria and trans-kingdom interactions of N-acyl homoserine lactones with eukaryotes.}, journal = {Journal of chemical ecology}, volume = {38}, number = {6}, pages = {704-713}, pmid = {22648507}, issn = {1573-1561}, mesh = {Acyl-Butyrolactones/immunology/*metabolism ; Animals ; *Bacterial Physiological Phenomena ; Fungi/physiology ; Host-Pathogen Interactions ; Humans ; Plant Immunity ; Plant Physiological Phenomena ; Plants/immunology/microbiology ; *Quorum Sensing ; }, abstract = {Many environmental and interactive important traits of bacteria, such as antibiotic, siderophore or exoenzyme (like cellulose, pectinase) production, virulence factors of pathogens, as well as symbiotic interactions, are regulated in a population density-dependent manner by using small signaling molecules. This phenomenon, called quorum sensing (QS), is widespread among bacteria. Many different bacterial species are communicating or "speaking" through diffusible small molecules. The production often is sophisticatedly regulated via an autoinducing mechanism. A good example is the production of N-acyl homoserine lactones (AHL), which occur in many variations of molecular structure in a wide variety of Gram-negative bacteria. In Gram-positive bacteria, other compounds, such as peptides, regulate cellular activity and behavior by sensing the cell density. The degradation of the signaling molecule--called quorum quenching--is probably another important integral part in the complex quorum sensing circuit. Most interestingly, bacterial quorum sensing molecules also are recognized by eukaryotes that are colonized by QS-active bacteria. In this case, the cross-kingdom interaction can lead to specific adjustment and physiological adaptations in the colonized eukaryote. The responses are manifold, such as modifications of the defense system, modulation of the immune response, or changes in the hormonal status and growth responses. Thus, the interaction with the quorum sensing signaling molecules of bacteria can profoundly change the physiology of higher organisms too. Higher organisms are obligatorily associated with microbial communities, and these truly multi-organismic consortia, which are also called holobionts, can actually be steered via multiple interlinked signaling substances that originate not only from the host but also from the associated bacteria.}, }
@article {pmid22552233, year = {2012}, author = {Seveso, D and Montano, S and Strona, G and Orlandi, I and Vai, M and Galli, P}, title = {Up-regulation of Hsp60 in response to skeleton eroding band disease but not by algal overgrowth in the scleractinian coral Acropora muricata.}, journal = {Marine environmental research}, volume = {78}, number = {}, pages = {34-39}, doi = {10.1016/j.marenvres.2012.03.008}, pmid = {22552233}, issn = {1879-0291}, mesh = {Animals ; Anthozoa/*metabolism ; Biomarkers/metabolism ; Chaperonin 60/*biosynthesis ; Plant Development ; Protozoan Infections, Animal/*metabolism ; Stress, Physiological/*physiology ; Up-Regulation ; }, abstract = {Heat shock proteins are biomarkers commonly used to determine the effects of abiotic stresses on the physiology of reef building corals. In this study the effectiveness of the Hsp60 as indicator of biotic stresses in the scleractinian coral Acropora muricata was analyzed, considering the whole holobiont. We focused on two biological interactions recognized to be important contributors to coral reef degradation such as a coral disease, the Skeleton eroding band (SEB) caused by the protozoan Halofolliculina corallasia and the algal overgrowth. In the lagoon of Magoodhoo Island (Maldives) fragments of living tissue of A. muricata exposed to these biotic factors were sampled and proteins subjected to Western analysis. The two different biological interactions trigger diverse responses on Hsp60 level. No detectable effect on Hsp60 modulation appeared in colonies subjected to algal overgrowth. On the contrary, corals displayed a robust up-regulation of Hsp60 in the fragments sampled just above the SEB dark band, where the level of Hsp60 was almost twice compared to the control colonies, indicating that the aggressive behavior of the protozoan causes cellular damage also in coral portions neighboring and along the advancing front of the infection. Portions of coral sampled distant to the SEB band showed a Hsp60 level comparable to that observed in healthy colonies. We propose Hsp60 expression as a promising tool to evaluate physiological stress caused by SEB disease in reef corals.}, }
@article {pmid22527059, year = {2012}, author = {Harder, T and Campbell, AH and Egan, S and Steinberg, PD}, title = {Chemical mediation of ternary interactions between marine holobionts and their environment as exemplified by the red alga Delisea pulchra.}, journal = {Journal of chemical ecology}, volume = {38}, number = {5}, pages = {442-450}, pmid = {22527059}, issn = {1573-1561}, mesh = {Bacterial Physiological Phenomena ; *Ecosystem ; Furans/metabolism ; Herbivory ; Rhodophyta/metabolism/*physiology ; }, abstract = {The need for animals and plants to control microbial colonization is important in the marine environment with its high densities of microscopic propagules and seawater that provides an ideal medium for their dispersal. In contrast to the traditional emphasis on antagonistic interactions of marine organisms with microbes, emerging studies lend support to the notion that health and performance of many marine organisms are functionally regulated and assisted by associated microbes, an ecological concept defined as a holobiont. While antimicrobial activities of marine secondary metabolites have been studied in great depth ex-situ, we are beginning to understand how some of these compounds function in an ecological context to maintain the performance of marine holobionts. The present article reviews two decades of our research on the red seaweed Delisea pulchra by addressing: the defense chemistry of this seaweed; chemically-mediated interactions between the seaweed and its natural enemies; and the negative influence of elevated seawater temperature on these interactions. Our understanding of these defense compounds and the functional roles they play for D. pulchra extends from molecular interactions with bacterial cell signaling molecules, to ecosystem-scale consequences of chemically-controlled disease and herbivory. Delisea pulchra produces halogenated furanones that antagonize the same receptor as acylated homoserine lactones (AHL)-a group of widespread intercellular communication signals among bacteria. Halogenated furanones compete with and inhibit bacterial cell-to-cell communication, and thus interfere with important bacterial communication-regulated processes, such as biofilm formation. In a predictable pattern that occurs at the ecological level of entire populations, environmental stress interferes with the production of halogenated furanones, causing downstream processes that ultimately result in disease of the algal holobiont.}, }
@article {pmid22438932, year = {2012}, author = {Cardoso, AM and Cavalcante, JJ and Vieira, RP and Lima, JL and Grieco, MA and Clementino, MM and Vasconcelos, AT and Garcia, ES and de Souza, W and Albano, RM and Martins, OB}, title = {Gut bacterial communities in the giant land snail Achatina fulica and their modification by sugarcane-based diet.}, journal = {PloS one}, volume = {7}, number = {3}, pages = {e33440}, pmid = {22438932}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Base Sequence ; DNA Primers/genetics ; DNA, Bacterial/genetics ; Diet ; Digestive System/microbiology ; Ecosystem ; Humans ; *Metagenome ; Phylogeny ; Saccharum ; Snails/*microbiology/pathogenicity ; }, abstract = {The invasive land snail Achatina fulica is one of the most damaging agricultural pests worldwide representing a potentially serious threat to natural ecosystems and human health. This species is known to carry parasites and harbors a dense and metabolically active microbial community; however, little is known about its diversity and composition. Here, we assessed for the first time the complexity of bacterial communities occurring in the digestive tracts of field-collected snails (FC) by using culture-independent molecular analysis. Crop and intestinal bacteria in FC were then compared to those from groups of snails that were reared in the laboratory (RL) on a sugarcane-based diet. Most of the sequences recovered were novel and related to those reported for herbivorous gut. Changes in the relative abundance of Bacteroidetes and Firmicutes were observed when the snails were fed a high-sugar diet, suggesting that the snail gut microbiota can influence the energy balance equation. Furthermore, this study represents a first step in gaining a better understanding of land snail gut microbiota and shows that this is a complex holobiont system containing diverse, abundant and active microbial communities.}, }
@article {pmid22437157, year = {2012}, author = {Meron, D and Rodolfo-Metalpa, R and Cunning, R and Baker, AC and Fine, M and Banin, E}, title = {Changes in coral microbial communities in response to a natural pH gradient.}, journal = {The ISME journal}, volume = {6}, number = {9}, pages = {1775-1785}, pmid = {22437157}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; Hydrogen-Ion Concentration ; Metagenome/genetics/*physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*chemistry ; }, abstract = {Surface seawater pH is currently 0.1 units lower than pre-industrial values and is projected to decrease by up to 0.4 units by the end of the century. This acidification has the potential to cause significant perturbations to the physiology of ocean organisms, particularly those such as corals that build their skeletons/shells from calcium carbonate. Reduced ocean pH could also have an impact on the coral microbial community, and thus may affect coral physiology and health. Most of the studies to date have examined the impact of ocean acidification on corals and/or associated microbiota under controlled laboratory conditions. Here we report the first study that examines the changes in coral microbial communities in response to a natural pH gradient (mean pH(T) 7.3-8.1) caused by volcanic CO(2) vents off Ischia, Gulf of Naples, Italy. Two Mediterranean coral species, Balanophyllia europaea and Cladocora caespitosa, were examined. The microbial community diversity and the physiological parameters of the endosymbiotic dinoflagellates (Symbiodinium spp.) were monitored. We found that pH did not have a significant impact on the composition of associated microbial communities in both coral species. In contrast to some earlier studies, we found that corals present at the lower pH sites exhibited only minor physiological changes and no microbial pathogens were detected. Together, these results provide new insights into the impact of ocean acidification on the coral holobiont.}, }
@article {pmid22344646, year = {2012}, author = {Lema, KA and Willis, BL and Bourne, DG}, title = {Corals form characteristic associations with symbiotic nitrogen-fixing bacteria.}, journal = {Applied and environmental microbiology}, volume = {78}, number = {9}, pages = {3136-3144}, pmid = {22344646}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Australia ; Bacteria/*classification/genetics/*isolation &amp; purification/metabolism ; Bacterial Physiological Phenomena ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; Molecular Sequence Data ; *Nitrogen Fixation ; Oxidoreductases/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {The complex symbiotic relationship between corals and their dinoflagellate partner Symbiodinium is believed to be sustained through close associations with mutualistic bacterial communities, though little is known about coral associations with bacterial groups able to fix nitrogen (diazotrophs). In this study, we investigated the diversity of diazotrophic bacterial communities associated with three common coral species (Acropora millepora, Acropora muricata, and Pocillopora damicormis) from three midshelf locations of the Great Barrier Reef (GBR) by profiling the conserved subunit of the nifH gene, which encodes the dinitrogenase iron protein. Comparisons of diazotrophic community diversity among coral tissue and mucus microenvironments and the surrounding seawater revealed that corals harbor diverse nifH phylotypes that differ between tissue and mucus microhabitats. Coral mucus nifH sequences displayed high heterogeneity, and many bacterial groups overlapped with those found in seawater. Moreover, coral mucus diazotrophs were specific neither to coral species nor to reef location, reflecting the ephemeral nature of coral mucus. In contrast, the dominant diazotrophic bacteria in tissue samples differed among coral species, with differences remaining consistent at all three reefs, indicating that coral-diazotroph associations are species specific. Notably, dominant diazotrophs for all coral species were closely related to the bacterial group rhizobia, which represented 71% of the total sequences retrieved from tissue samples. The species specificity of coral-diazotroph associations further supports the coral holobiont model that bacterial groups associated with corals are conserved. Our results suggest that, as in terrestrial plants, rhizobia have developed a mutualistic relationship with corals and may contribute fixed nitrogen to Symbiodinium.}, }
@article {pmid22335606, year = {2012}, author = {Ribes, M and Jiménez, E and Yahel, G and López-Sendino, P and Diez, B and Massana, R and Sharp, JH and Coma, R}, title = {Functional convergence of microbes associated with temperate marine sponges.}, journal = {Environmental microbiology}, volume = {14}, number = {5}, pages = {1224-1239}, doi = {10.1111/j.1462-2920.2012.02701.x}, pmid = {22335606}, issn = {1462-2920}, mesh = {Animals ; Bacteria/*classification/genetics/metabolism ; *Bacterial Physiological Phenomena ; Carbon/metabolism ; Mediterranean Sea ; Microbial Consortia/*physiology ; Molecular Sequence Data ; Nitrogen/metabolism ; *Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Most marine sponges establish a persistent association with a wide array of phylogenetically and physiologically diverse microbes. To date, the role of these symbiotic microbial communities in the metabolism and nutrient cycles of the sponge-microbe consortium remains largely unknown. We identified and quantified the microbial communities associated with three common Mediterranean sponge species, Dysidea avara, Agelas oroides and Chondrosia reniformis (Demospongiae) that cohabitate coralligenous community. For each sponge we quantified the uptake and release of dissolved organic carbon (DOC) and nitrogen (DON), inorganic nitrogen and phosphate. Low microbial abundance and no evidence for DOC uptake or nitrification were found for D. avara. In contrast A. oroides and C. reniformis showed high microbial abundance (30% and 70% of their tissue occupied by microbes respectively) and both species exhibited high nitrification and high DOC and NH(4) (+) uptake. Surprisingly, these unique metabolic pathways were mediated in each sponge species by a different, and host specific, microbial community. The functional convergence of microbial consortia found in these two sympatric sponge species, suggest that these metabolic processes may be of special relevance to the success of the holobiont.}, }
@article {pmid22286497, year = {2012}, author = {Siboni, N and Ben-Dov, E and Sivan, A and Kushmaro, A}, title = {Geographic specific coral-associated ammonia-oxidizing archaea in the northern Gulf of Eilat (Red Sea).}, journal = {Microbial ecology}, volume = {64}, number = {1}, pages = {18-24}, pmid = {22286497}, issn = {1432-184X}, mesh = {Ammonia/*metabolism ; Animals ; Anthozoa/*microbiology ; Archaea/classification/genetics/*isolation &amp; purification/*metabolism ; Archaeal Proteins/genetics ; Biodiversity ; Geography ; Indian Ocean ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases/genetics ; Phylogeny ; }, abstract = {Coral holobionts are densely populated with microorganisms that are essential for their well-being. Here we compared the diversity of the archaeal ammonia monooxygenase alpha subunit (amoA) gene from three coral genera, Acanthastrea sp., Favia sp., and Fungia granulosa, from the Gulf of Eilat, Red Sea. At 99% similarity, archaeal amoA from the three coral genera shared 71% of their cloned sequences, while the Favia and Acanthastrea presented a few genus-specific clones. In addition, the sequences retrieved in our samples displayed lower similarity to amoA sequences previously found in association with other coral species from different geographic regions. This finding suggests that the populations of ammonia-oxidizing archaea are less host-specific and more geographically dependent.}, }
@article {pmid22226071, year = {2012}, author = {Patowary, A and Chauhan, RK and Singh, M and Kv, S and Periwal, V and Kp, K and Sapkal, GN and Bondre, VP and Gore, MM and Sivasubbu, S and Scaria, V}, title = {De novo identification of viral pathogens from cell culture hologenomes.}, journal = {BMC research notes}, volume = {5}, number = {}, pages = {11}, pmid = {22226071}, issn = {1756-0500}, abstract = {BACKGROUND: Fast, specific identification and surveillance of pathogens is the cornerstone of any outbreak response system, especially in the case of emerging infectious diseases and viral epidemics. This process is generally tedious and time-consuming thus making it ineffective in traditional settings. The added complexity in these situations is the non-availability of pure isolates of pathogens as they are present as mixed genomes or hologenomes. Next-generation sequencing approaches offer an attractive solution in this scenario as it provides adequate depth of sequencing at fast and affordable costs, apart from making it possible to decipher complex interactions between genomes at a scale that was not possible before. The widespread application of next-generation sequencing in this field has been limited by the non-availability of an efficient computational pipeline to systematically analyze data to delineate pathogen genomes from mixed population of genomes or hologenomes.<br><br>FINDINGS: We applied next-generation sequencing on a sample containing mixed population of genomes from an epidemic with appropriate processing and enrichment. The data was analyzed using an extensive computational pipeline involving mapping to reference genome sets and de-novo assembly. In depth analysis of the data generated revealed the presence of sequences corresponding to Japanese encephalitis virus. The genome of the virus was also independently de-novo assembled. The presence of the virus was in addition, verified using standard molecular biology techniques.<br><br>CONCLUSIONS: Our approach can accurately identify causative pathogens from cell culture hologenome samples containing mixed population of genomes and in principle can be applied to patient hologenome samples without any background information. This methodology could be widely applied to identify and isolate pathogen genomes and understand their genomic variability during outbreaks.}, }
@article {pmid23761367, year = {2011}, author = {Webster, NS and Botté, ES and Soo, RM and Whalan, S}, title = {The larval sponge holobiont exhibits high thermal tolerance.}, journal = {Environmental microbiology reports}, volume = {3}, number = {6}, pages = {756-762}, doi = {10.1111/j.1758-2229.2011.00296.x}, pmid = {23761367}, issn = {1758-2229}, abstract = {Marine sponges are critical components of benthic environments; however, their sessile habit, requirement to filter large volumes of water and complex symbiotic partnerships make them particularly vulnerable to the effects of global climate change. We assessed the effect of elevated seawater temperature on bacterial communities in larvae of the Great Barrier Reef sponge, Rhopaloeides odorabile. In contrast to the strict thermal threshold of 32°C previously identified in adult R. odorabile, larvae exhibit a markedly higher thermal tolerance, with no adverse health effects detected at temperatures below 36°C. Similarly, larval microbial communities were conserved at temperatures up to 34°C with a highly significant shift occurring after 24 h at 36°C. This shift involved the loss of previously described symbionts (in particular the Nitrospira, Chloroflexi and a Roseobacter lineage) and the appearance of new Gammaproteobacteria not detected at lower temperatures. Here, we demonstrated that sponge larvae maintain highly stable symbioses at seawater temperatures exceeding those that are predicted under current climate change scenarios. In addition, by revealing that the shift in microbial composition occurs in conjunction with necrosis and mortality of larvae at 36°C we have provided additional evidence of the strong link between host health and the stability of symbiont communities.}, }
@article {pmid23761353, year = {2011}, author = {Littman, R and Willis, BL and Bourne, DG}, title = {Metagenomic analysis of the coral holobiont during a natural bleaching event on the Great Barrier Reef.}, journal = {Environmental microbiology reports}, volume = {3}, number = {6}, pages = {651-660}, doi = {10.1111/j.1758-2229.2010.00234.x}, pmid = {23761353}, issn = {1758-2229}, abstract = {Understanding the effects of elevated seawater temperatures on each member of the coral holobiont (the complex comprised of coral polyps and associated symbiotic microorganisms, including Bacteria, viruses, Fungi, Archaea and endolithic algae) is becoming increasingly important as evidence accumulates that microbial members contribute to overall coral health, particularly during thermal stress. Here we use a metagenomic approach to identify metabolic and taxonomic shifts in microbial communities associated with the hard coral Acropora millepora throughout a natural thermal bleaching event at Magnetic Island (Great Barrier Reef). A direct comparison of metagenomic data sets from healthy versus bleached corals indicated major shifts in microbial associates during heat stress, including Bacteria, Archaea, viruses, Fungi and micro-algae. Overall, metabolism of the microbial community shifted from autotrophy to heterotrophy, including increases in genes associated with the metabolism of fatty acids, proteins, simple carbohydrates, phosphorus and sulfur. In addition, the proportion of virulence genes was higher in the bleached library, indicating an increase in microorganisms capable of pathogenesis following bleaching. These results demonstrate that thermal stress results in shifts in coral-associated microbial communities that may lead to deteriorating coral health.}, }
@article {pmid22127887, year = {2012}, author = {Augustin, R and Fraune, S and Franzenburg, S and Bosch, TC}, title = {Where simplicity meets complexity: hydra, a model for host-microbe interactions.}, journal = {Advances in experimental medicine and biology}, volume = {710}, number = {}, pages = {71-81}, doi = {10.1007/978-1-4419-5638-5_8}, pmid = {22127887}, issn = {0065-2598}, mesh = {Animals ; Antimicrobial Cationic Peptides/immunology ; *Biological Evolution ; Genome ; *Host-Pathogen Interactions ; Humans ; Hydra/classification/immunology/*microbiology/physiology ; Immunity, Innate/immunology ; Phylogeny ; }, abstract = {For a long time, the main purpose of microbiology and immunology was to study pathogenic bacteria and infectious disease; the potential benefit of commensal bacteria remained unrecognised. Discovering that individuals from Hydra to man are not solitary, homogenous entities but consist of complex communities of many species that likely evolved during a billion years of coexistence (Fraune and Bosch 2010) led to the hologenome theory of evolution (Zilber-Rosenberg and Rosenberg 2008) which considers the holobiont with its hologenome as the unit of selection in evolution. Defining the individual microbe-host conversations in these consortia is a challenging but necessary step on the path to understanding the function of the associations as a whole. Untangling the complex interactions requires simple animal models with only a few specific bacterial species. Such models can function as living test tubes and may be key to dissecting the fundamental principles that underlie all host-microbe interactions. Here we introduce Hydra (Bosch et al. 2009) as such a model with one of the simplest epithelia in the animal kingdom (only two cell layers), with few cell types derived from only three distinct stem cell lineages, and with the availability of a fully sequenced genome and numerous genomic tools including transgenesis. Recognizing the entire system with its inputs, outputs and the interconnections (Fraune and Bosch 2010; Bosch et al. 2009; Fraune and Bosch 2007; Fraune et al. 2009a) we here present observations which may have profound impact on understanding a strictly microbe-dependent life style and its evolutionary consequences.}, }
@article {pmid22092516, year = {2012}, author = {Erwin, PM and López-Legentil, S and González-Pech, R and Turon, X}, title = {A specific mix of generalists: bacterial symbionts in Mediterranean Ircinia spp.}, journal = {FEMS microbiology ecology}, volume = {79}, number = {3}, pages = {619-637}, doi = {10.1111/j.1574-6941.2011.01243.x}, pmid = {22092516}, issn = {1574-6941}, mesh = {Animals ; Bacteria/*classification/genetics/growth &amp; development ; Base Sequence ; Biodiversity ; Genes, rRNA ; Genetic Variation ; Mediterranean Sea ; Molecular Sequence Data ; Phylogeny ; Porifera/classification/genetics/*microbiology/ultrastructure ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Microbial symbionts form abundant and diverse components of marine sponge holobionts, yet the ecological and evolutionary factors that dictate their community structure are unresolved. Here, we characterized the bacterial symbiont communities of three sympatric host species in the genus Ircinia from the NW Mediterranean Sea, using electron microscopy and replicated 16S rRNA gene sequence clone libraries. All Ircinia host species harbored abundant and phylogenetically diverse symbiont consortia, comprised primarily of sequences related to other sponge-derived microorganisms. Community-level analyses of bacterial symbionts revealed host species-specific genetic differentiation and structuring of Ircinia-associated microbiota. Phylogenetic analyses of host sponges showed a close evolutionary relationship between Ircinia fasciculata and Ircinia variabilis, the two host species exhibiting more similar symbiont communities. In addition, several bacterial operational taxonomic units were shared between I. variabilis and Ircinia oros, the two host species inhabiting semi-sciophilous communities in more cryptic benthic habitats, and absent in I. fasciculata, which occurs in exposed, high-irradiance habitats. The generalist nature of individual symbionts and host-specific structure of entire communities suggest that: (1) a 'specific mix of generalists' framework applies to bacterial symbionts in Ircinia hosts and (2) factors specific to each host species contribute to the distinct symbiont mix observed in Ircinia hosts.}, }
@article {pmid22046302, year = {2011}, author = {Mayfield, AB and Wang, LH and Tang, PC and Fan, TY and Hsiao, YY and Tsai, CL and Chen, CS}, title = {Assessing the impacts of experimentally elevated temperature on the biological composition and molecular chaperone gene expression of a reef coral.}, journal = {PloS one}, volume = {6}, number = {10}, pages = {e26529}, pmid = {22046302}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*genetics/physiology ; DNA/isolation &amp; purification ; Gene Expression Regulation/*physiology ; HSP70 Heat-Shock Proteins/analysis/genetics ; *Hot Temperature ; Molecular Chaperones/analysis/*genetics ; Proteins/analysis ; RNA/isolation &amp; purification ; Temperature ; }, abstract = {Due to the potential for increasing ocean temperatures to detrimentally impact reef-building corals, there is an urgent need to better understand not only the coral thermal stress response, but also natural variation in their sub-cellular composition. To address this issue, while simultaneously developing a molecular platform for studying one of the most common Taiwanese reef corals, Seriatopora hystrix, 1,092 cDNA clones were sequenced and characterized. Subsequently, RNA, DNA and protein were extracted sequentially from colonies exposed to elevated (30°C) temperature for 48 hours. From the RNA phase, a heat shock protein-70 (hsp70)-like gene, deemed hsp/c, was identified in the coral host, and expression of this gene was measured with real-time quantitative PCR (qPCR) in both the host anthozoan and endosymbiotic dinoflagellates (genus Symbiodinium). While mRNA levels were not affected by temperature in either member, hsp/c expression was temporally variable in both and co-varied within biopsies. From the DNA phase, host and Symbiodinium hsp/c genome copy proportions (GCPs) were calculated to track changes in the biological composition of the holobiont during the experiment. While there was no temperature effect on either host or Symbiodinium GCP, both demonstrated significant temporal variation. Finally, total soluble protein was responsive to neither temperature nor exposure time, though the protein/DNA ratio varied significantly over time. Collectively, it appears that time, and not temperature, is a more important driver of the variation in these parameters, highlighting the need to consider natural variation in both gene expression and the molecular make-up of coral holobionts when conducting manipulative studies. This represents the first study to survey multiple macromolecules from both compartments of an endosymbiotic organism with methodologies that reflect their dual-compartmental nature, ideally generating a framework for assessing molecular-level changes within corals and other endosymbioses exposed to changes in their environment.}, }
@article {pmid21984347, year = {2012}, author = {Kvennefors, EC and Sampayo, E and Kerr, C and Vieira, G and Roff, G and Barnes, AC}, title = {Regulation of bacterial communities through antimicrobial activity by the coral holobiont.}, journal = {Microbial ecology}, volume = {63}, number = {3}, pages = {605-618}, pmid = {21984347}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/*microbiology/physiology ; Anti-Bacterial Agents/*metabolism ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Biodiversity ; Mucus/chemistry/metabolism ; Phylogeny ; }, abstract = {Interactions between corals and associated bacteria and amongst these bacterial groups are likely to play a key role in coral health. However, the complexity of these interactions is poorly understood. We investigated the functional role of specific coral-associated bacteria in maintaining microbial communities on the coral Acropora millepora (Ehrenberg 1834) and the ability of coral mucus to support or inhibit bacterial growth. Culture-independent techniques were used to assess bacterial community structures whilst bacterial culture was employed to assess intra- and inter-specific antimicrobial activities of bacteria. Members of Pseudoalteromonas and ribotypes closely related to Vibrio coralliilyticus displayed potent antimicrobial activity against a range of other cultured isolates and grew readily on detached coral mucus. Although such bacterial ribotypes would be expected to have a competitive advantage, they were rare or absent on intact and healthy coral colonies growing in situ (analysed using denaturing gradient gel electrophoresis and 16S rRNA gene sequencing). The most abundant bacterial ribotypes found on healthy corals were Gammaproteobacteria, previously defined as type A coral associates. Our results indicate that this group of bacteria and specific members of the Alphaproteobacteria described here as 'type B associates' may be important functional groups for coral health. We suggest that bacterial communities on coral are kept in check by a combination of host-derived and microbial interactions and that the type A associates in particular may play a key role in maintaining stability of microbial communities on healthy coral colonies.}, }
@article {pmid21976690, year = {2012}, author = {Bellantuono, AJ and Hoegh-Guldberg, O and Rodriguez-Lanetty, M}, title = {Resistance to thermal stress in corals without changes in symbiont composition.}, journal = {Proceedings. Biological sciences}, volume = {279}, number = {1731}, pages = {1100-1107}, pmid = {21976690}, issn = {1471-2954}, mesh = {*Acclimatization ; Alveolata/genetics/physiology ; Animals ; Anthozoa/genetics/microbiology/*physiology ; Climate Change ; Coral Reefs ; Genotype ; Oceans and Seas ; *Stress, Physiological ; *Symbiosis ; *Temperature ; }, abstract = {Discovering how corals can adjust their thermal sensitivity in the context of global climate change is important in understanding the long-term persistence of coral reefs. In this study, we showed that short-term preconditioning to higher temperatures, 3°C below the experimentally determined bleaching threshold, for a period of 10 days provides thermal tolerance for the symbiosis stability between the scleractinian coral, Acropora millepora and Symbiodinium. Based on genotypic analysis, our results indicate that the acclimatization of this coral species to thermal stress does not come down to simple changes in Symbiodinium and/or the bacterial communities that associate with reef-building corals. This suggests that the physiological plasticity of the host and/or symbiotic components appears to play an important role in responding to ocean warming. The further study of host and symbiont physiology, both of Symbiodinium and prokaryotes, is of paramount importance in the context of global climate change, as mechanisms for rapid holobiont acclimatization will become increasingly important to the long-standing persistence of coral reefs.}, }
@article {pmid21955993, year = {2012}, author = {Cárdenas, A and Rodriguez-R, LM and Pizarro, V and Cadavid, LF and Arévalo-Ferro, C}, title = {Shifts in bacterial communities of two Caribbean reef-building coral species affected by white plague disease.}, journal = {The ISME journal}, volume = {6}, number = {3}, pages = {502-512}, pmid = {21955993}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Colombia ; Coral Reefs ; DNA, Bacterial/genetics ; DNA, Ribosomal/chemistry ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Coral reefs are deteriorating at an alarming rate mainly as a consequence of the emergence of coral diseases. The white plague disease (WPD) is the most prevalent coral disease in the southwestern Caribbean, affecting dozens of coral species. However, the identification of a single causal agent has proved problematic. This suggests more complex etiological scenarios involving alterations in the dynamic interaction between environmental factors, the coral immune system and the symbiotic microbial communities. Here we compare the microbiome of healthy and WPD-affected corals from the two reef-building species Diploria strigosa and Siderastrea siderea collected at the Tayrona National Park in the Caribbean of Colombia. Microbiomes were analyzed by combining culture-dependent methods and pyrosequencing of 16S ribosomal DNA (rDNA) V5-V6 hypervariable regions. A total of 20,410 classifiable 16S rDNA sequences reads were obtained including all samples. No significant differences in operational taxonomic unit diversity were found between healthy and affected tissues; however, a significant increase of Alphaproteobacteria and a concomitant decrease in the Beta- and Gammaproteobacteria was observed in WPD-affected corals of both species. Significant shifts were also observed in the orders Rhizobiales, Caulobacteriales, Burkholderiales, Rhodobacterales, Aleteromonadales and Xanthomonadales, although they were not consistent between the two coral species. These shifts in the microbiome structure of WPD-affected corals suggest a loss of community-mediated growth control mechanisms on bacterial populations specific for each holobiont system.}, }
@article {pmid21949755, year = {2011}, author = {Riegl, BM and Purkis, SJ and Al-Cibahy, AS and Abdel-Moati, MA and Hoegh-Guldberg, O}, title = {Present limits to heat-adaptability in corals and population-level responses to climate extremes.}, journal = {PloS one}, volume = {6}, number = {9}, pages = {e24802}, pmid = {21949755}, issn = {1932-6203}, mesh = {*Adaptation, Physiological ; Animal Migration ; Animals ; Anthozoa/*physiology ; *Climate Change ; Decision Making ; Environment ; *Hot Temperature ; Indian Ocean ; Models, Biological ; Population Dynamics ; Species Specificity ; Time Factors ; Tropical Climate ; Water ; }, abstract = {Climate change scenarios suggest an increase in tropical ocean temperature by 1-3°C by 2099, potentially killing many coral reefs. But Arabian/Persian Gulf corals already exist in this future thermal environment predicted for most tropical reefs and survived severe bleaching in 2010, one of the hottest years on record. Exposure to 33-35°C was on average twice as long as in non-bleaching years. Gulf corals bleached after exposure to temperatures above 34°C for a total of 8 weeks of which 3 weeks were above 35°C. This is more heat than any other corals can survive, providing an insight into the present limits of holobiont adaptation. We show that average temperatures as well as heat-waves in the Gulf have been increasing, that coral population levels will fluctuate strongly, and reef-building capability will be compromised. This, in combination with ocean acidification and significant local threats posed by rampant coastal development puts even these most heat-adapted corals at risk. WWF considers the Gulf ecoregion as "critically endangered". We argue here that Gulf corals should be considered for assisted migration to the tropical Indo-Pacific. This would have the double benefit of avoiding local extinction of the world's most heat-adapted holobionts while at the same time introducing their genetic information to populations naïve to such extremes, potentially assisting their survival. Thus, the heat-adaptation acquired by Gulf corals over 6 k, could benefit tropical Indo-Pacific corals who have <100 y until they will experience a similarly harsh climate. Population models suggest that the heat-adapted corals could become dominant on tropical reefs within ∼20 years.}, }
@article {pmid21804354, year = {2011}, author = {Sharon, G and Segal, D and Zilber-Rosenberg, I and Rosenberg, E}, title = {Symbiotic bacteria are responsible for diet-induced mating preference in Drosophila melanogaster, providing support for the hologenome concept of evolution.}, journal = {Gut microbes}, volume = {2}, number = {3}, pages = {190-192}, doi = {10.4161/gmic.2.3.16103}, pmid = {21804354}, issn = {1949-0984}, mesh = {Animals ; Bacteria/*genetics/isolation &amp; purification ; *Biological Evolution ; Drosophila melanogaster/genetics/microbiology/*physiology ; Feeding Behavior ; Female ; Gastrointestinal Tract/*microbiology ; Genome ; Humans ; Male ; *Mating Preference, Animal ; *Metagenome ; Models, Animal ; *Symbiosis ; }, abstract = {Diet-induced mating preference in Drosophila melanogaster results from amplification of the commensal bacterium Lactobacillus plantarum, providing a new role for gut microbiota and support for the hologenome concept of evolution. When the flies were treated with antibiotics prior to changing their diet, mating preference did not occur. These data also indicate that other potentially beneficial bacteria could be irreversibly lost by antibiotic treatment and that their replacement could provide a health benefit. We suggest that D. melanogaster can be a useful model organism to study the activities of gut microbiota and their interaction with the immune system.}, }
@article {pmid21553265, year = {2011}, author = {Edmunds, PJ and Putnam, HM and Nisbet, RM and Muller, EB}, title = {Benchmarks in organism performance and their use in comparative analyses.}, journal = {Oecologia}, volume = {167}, number = {2}, pages = {379-390}, pmid = {21553265}, issn = {1432-1939}, mesh = {Animals ; Anthozoa/*physiology ; Coral Reefs ; *Energy Metabolism ; Environment ; Models, Biological ; Species Specificity ; Stress, Physiological ; }, abstract = {Evaluating the response of organisms to stress assumes that functional benchmarks are available against which the response can be gauged, but this expectation remains unfulfilled for many taxa. As a result, attempts to describe the organismic effects of environmental degradation and physiological stress can prove misleading. Functional benchmarks and the effects of stress are particularly germane to coral reefs that globally are exposed to significant environmental challenges, and in this study, we compiled data on scleractinian corals to describe a reference against which stress responses can be gauged. Based on this construct, we tested the veracity of well-established contrasts--involving differences in physiological function among depths and families--to evaluate the capacity of available data to support synthetic analyses. Our analysis used 126 papers describing 37 genera, and at least 73 species, and described 13 traits, first independent of depth, and second, by depth. Data appropriate for these analyses were so sparse that depth- and family-level effects were inconspicuous, although the depth contrast revealed a decline in dark respiration and an increase in calcification (both normalized to area) in deeper water. Our analyses of scleractinian literature revealed limitations of the data available for synthetic analyses, as well for describing functional benchmarks within this taxon. We attribute some of these effects to differences in the physical environment under which measurements were made, and suspect that such problems are commonplace for other taxa. Dynamic Energy Budget (DEB) models provide one means to overcome some of these problems, and they can be used for any taxon to quantitatively summarize data for comparative analyses of stressor responses. The suitability of these models is illustrated for scleractinian corals by predicting from first principles the ratio of Symbiodinium to holobiont carbon and the respiration.}, }
@article {pmid21523464, year = {2011}, author = {Golberg, K and Eltzov, E and Shnit-Orland, M and Marks, RS and Kushmaro, A}, title = {Characterization of quorum sensing signals in coral-associated bacteria.}, journal = {Microbial ecology}, volume = {61}, number = {4}, pages = {783-792}, pmid = {21523464}, issn = {1432-184X}, mesh = {4-Butyrolactone/analogs &amp; derivatives/metabolism ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Molecular Sequence Data ; Phylogeny ; *Quorum Sensing ; Signal Transduction ; }, abstract = {Marine environment habitats, such as the coral mucus layer, are abundant in nutrients and rich with diverse populations of microorganisms. Since interactions among microorganisms found in coral mucus can be either mutualistic or competitive, understanding quorum sensing-based acyl homoserine lactone (AHL) language may shed light on the interaction between coral-associated microbial communities in the native host. More than 100 bacterial isolates obtained from different coral species were screened for their ability to produce AHL. When screening the isolated coral bacteria for AHL induction activity using the reporter strains Escherichia coli K802NR-pSB1075 and Agrobacterium tumefaciens KYC55, we found that approximately 30% of the isolates tested positive. Thin layer chromatography separation of supernatant extracts revealed different AHL profiles, with detection of at least one active compound in the supernatant of those bacterial extracts being able to induce AHL activity in the two different bioreporter strains. The active extract of bacterial isolate 3AT 1-10-4 was subjected to further analysis by preparative thin layer chromatography and liquid chromatography tandem mass spectrometry. One of the compounds was found to correspond with N-(3-hydroxydecanoyl)-L-homoserine lactone. 16S rRNA gene sequencing of the isolates with positive AHL activity affiliated them with the Vibrio genus. Understanding the ecological role of AHL in the coral environment and its regulatory circuits in the coral holobiont-associated microbial community will further expand our knowledge of such interactions.}, }
@article {pmid21509042, year = {2011}, author = {Alagely, A and Krediet, CJ and Ritchie, KB and Teplitski, M}, title = {Signaling-mediated cross-talk modulates swarming and biofilm formation in a coral pathogen Serratia marcescens.}, journal = {The ISME journal}, volume = {5}, number = {10}, pages = {1609-1620}, pmid = {21509042}, issn = {1751-7370}, mesh = {Acyl-Butyrolactones/metabolism ; Animals ; Anthozoa/*microbiology/physiology ; Bacterial Physiological Phenomena ; *Biofilms ; Ecology ; *Quorum Sensing ; Serratia marcescens/*metabolism ; Symbiosis ; }, abstract = {Interactions within microbial communities associated with marine holobionts contribute importantly to the health of these symbiotic organisms formed by invertebrates, dinoflagellates and bacteria. However, mechanisms that control invertebrate-associated microbiota are not yet fully understood. Hydrophobic compounds that were isolated from surfaces of asymptomatic corals inhibited biofilm formation by the white pox pathogen Serratia marcescens PDL100, indicating that signals capable of affecting the associated microbiota are produced in situ. However, neither the origin nor structures of these signals are currently known. A functional survey of bacteria recovered from coral mucus and from cultures of the dinoflagellate Symbiodinium spp. revealed that they could alter swarming and biofilm formation in S. marcescens. As swarming and biofilm formation are inversely regulated, the ability of some native α-proteobacteria to affect both behaviors suggests that the α-proteobacterial signal(s) target a global regulatory switch controlling the behaviors in the pathogen. Isolates of Marinobacter sp. inhibited both biofilm formation and swarming in S. marcescens PDL100, without affecting growth of the coral pathogen, indicative of the production of multiple inhibitors, likely targeting lower level regulatory genes or functions. A multi-species cocktail containing these strains inhibited progression of a disease caused by S. marcescens in a model polyp Aiptasia pallida. An α-proteobacterial isolate 44B9 had a similar effect. Even though ∼4% of native holobiont-associated bacteria produced compounds capable of triggering responses in well-characterized N-acyl homoserine lactone (AHL) biosensors, there was no strong correlation between the production of AHL-like signals and disruption of biofilms or swarming in S. marcescens.}, }
@article {pmid21468227, year = {2010}, author = {Jones, BV}, title = {The human gut mobile metagenome: a metazoan perspective.}, journal = {Gut microbes}, volume = {1}, number = {6}, pages = {415-431}, pmid = {21468227}, issn = {1949-0984}, support = {//Medical Research Council/United Kingdom ; }, mesh = {Bacteria/*genetics ; Gastrointestinal Tract/*microbiology ; Humans ; *Metagenome ; Plasmids/*analysis ; }, abstract = {Using the culture independent TRACA system in conjunction with a comparative metagenomic approach, we have recently explored the pool of plasmids associated with the human gut mobile metagenome. This revealed that some plasmids or plasmid families are present in the gut microbiomes of geographically isolated human hosts with a broad global distribution (America, Japan and Europe), and are potentially unique to the human gut microbiome. Functions encoded by the most widely distributed plasmid (pTRACA22) were found to be enriched in the human gut microbiome when compared to microbial communities from other environments, and of particular interest was the increased prevalence of a putative RelBE toxin-antitoxin (TA) addiction module. Subsequent analysis revealed that this was most closely related to putative TA modules from gut associated bacteria belonging to the Firmicutes, but homologues of the RelE toxin were associated with all major bacterial divisions comprising the human gut microbiota. In this addendum, functions of the gut mobile metagenome are considered from the perspective of the human host, and within the context of the hologenome theory of human evolution. In doing so, our original analysis is also extended to include the gut metagenomes of a further 124 individuals comprising the METAHIT dataset. Differences in the incidence and relative abundance of pTRACA22 and associated TA modules between healthy individuals and those with inflammatory bowel diseases are explored, and potential functions of pTRACA22 type RelBE modules in the human gut microbiome are discussed.}, }
@article {pmid21425442, year = {2011}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Symbiosis and development: the hologenome concept.}, journal = {Birth defects research. Part C, Embryo today : reviews}, volume = {93}, number = {1}, pages = {56-66}, doi = {10.1002/bdrc.20196}, pmid = {21425442}, issn = {1542-9768}, mesh = {Adaptation, Biological ; Animals ; Anthozoa/genetics/*microbiology ; Biological Evolution ; Developmental Biology ; Epigenomics ; Genetic Variation ; Humans ; Insecta/genetics/*microbiology ; *Metagenome ; Mice ; Nitrogen Fixation ; Plants/genetics/*microbiology ; *Symbiosis ; }, abstract = {All animals and plants establish symbiotic relationships with microorganisms; often the combined genetic information of the diverse microbiota exceeds that of the host. How the genetic wealth of the microbiota affects all aspects of the holobiont's (host plus all of its associated microorganisms) fitness (adaptation, survival, development, growth and reproduction) and evolution is reviewed, using selected coral, insect, squid, plant, and human/mouse published experimental results. The data are discussed within the framework of the hologenome theory of evolution, which demonstrates that changes in environmental parameters, for example, diet, can cause rapid changes in the diverse microbiota, which not only can benefit the holobiont in the short term but also can be transmitted to offspring and lead to long lasting cooperations. As acquired characteristics (microbes) are heritable, consideration of the holobiont as a unit of selection in evolution leads to neo-Lamarckian principles within a Darwinian framework. The potential application of these principles can be seen in the growing fields of prebiotics and probiotics.}, }
@article {pmid21272183, year = {2011}, author = {Barott, KL and Rodriguez-Brito, B and Janouškovec, J and Marhaver, KL and Smith, JE and Keeling, P and Rohwer, FL}, title = {Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis.}, journal = {Environmental microbiology}, volume = {13}, number = {5}, pages = {1192-1204}, doi = {10.1111/j.1462-2920.2010.02419.x}, pmid = {21272183}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; Carbon/metabolism ; Caribbean Region ; *Coral Reefs ; Cyanobacteria/classification/*genetics/growth &amp; development ; Gene Library ; Microalgae/*microbiology ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; }, abstract = {The coral reef benthos is primarily colonized by corals and algae, which are often in direct competition with one another for space. Numerous studies have shown that coral-associated Bacteria are different from the surrounding seawater and are at least partially species specific (i.e. the same bacterial species on the same coral species). Here we extend these microbial studies to four of the major ecological functional groups of algae found on coral reefs: upright and encrusting calcifying algae, fleshy algae, and turf algae, and compare the results to the communities found on the reef-building coral Montastraea annularis. It was found using 16S rDNA tag pyrosequencing that the different algal genera harbour characteristic bacterial communities, and these communities were generally more diverse than those found on corals. While the majority of coral-associated Bacteria were related to known heterotrophs, primarily consuming carbon-rich coral mucus, algal-associated communities harboured a high percentage of autotrophs. The majority of algal-associated autotrophic Bacteria were Cyanobacteria and may be important for nitrogen cycling on the algae. There was also a rich diversity of photosynthetic eukaryotes associated with the algae, including protists, diatoms, and other groups of microalgae. Together, these observations support the hypothesis that coral reefs are a vast landscape of distinctive microbial communities and extend the holobiont concept to benthic algae.}, }
@article {pmid21209889, year = {2010}, author = {Turque, AS and Batista, D and Silveira, CB and Cardoso, AM and Vieira, RP and Moraes, FC and Clementino, MM and Albano, RM and Paranhos, R and Martins, OB and Muricy, G}, title = {Environmental shaping of sponge associated archaeal communities.}, journal = {PloS one}, volume = {5}, number = {12}, pages = {e15774}, pmid = {21209889}, issn = {1932-6203}, mesh = {Ammonia/chemistry ; Animals ; Archaea/*metabolism ; Biodiversity ; Brazil ; Ecology ; Environment ; Models, Genetic ; Molecular Sequence Data ; Phylogeny ; Plankton ; Porifera/*metabolism ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; Seawater ; }, abstract = {BACKGROUND: Archaea are ubiquitous symbionts of marine sponges but their ecological roles and the influence of environmental factors on these associations are still poorly understood.<br><br>We compared the diversity and composition of archaea associated with seawater and with the sponges Hymeniacidon heliophila, Paraleucilla magna and Petromica citrina in two distinct environments: Guanabara Bay, a highly impacted estuary in Rio de Janeiro, Brazil, and the nearby Cagarras Archipelago. For this we used metagenomic analyses of 16S rRNA and ammonia monooxygenase (amoA) gene libraries. Hymeniacidon heliophila was more abundant inside the bay, while P. magna was more abundant outside and P. citrina was only recorded at the Cagarras Archipelago. Principal Component Analysis plots (PCA) generated using pairwise unweighted UniFrac distances showed that the archaeal community structure of inner bay seawater and sponges was different from that of coastal Cagarras Archipelago. Rarefaction analyses showed that inner bay archaeaoplankton were more diverse than those from the Cagarras Archipelago. Only members of Crenarchaeota were found in sponge libraries, while in seawater both Crenarchaeota and Euryarchaeota were observed. Although most amoA archaeal genes detected in this study seem to be novel, some clones were affiliated to known ammonia oxidizers such as Nitrosopumilus maritimus and Cenarchaeum symbiosum.<br><br>CONCLUSION/SIGNIFICANCE: The composition and diversity of archaeal communities associated with pollution-tolerant sponge species can change in a range of few kilometers, probably influenced by eutrophication. The presence of archaeal amoA genes in Porifera suggests that Archaea are involved in the nitrogen cycle within the sponge holobiont, possibly increasing its resistance to anthropogenic impacts. The higher diversity of Crenarchaeota in the polluted area suggests that some marine sponges are able to change the composition of their associated archaeal communities, thereby improving their fitness in impacted environments.}, }
@article {pmid21105980, year = {2011}, author = {Mumby, PJ and Elliott, IA and Eakin, CM and Skirving, W and Paris, CB and Edwards, HJ and Enríquez, S and Iglesias-Prieto, R and Cherubin, LM and Stevens, JR}, title = {Reserve design for uncertain responses of coral reefs to climate change.}, journal = {Ecology letters}, volume = {14}, number = {2}, pages = {132-140}, doi = {10.1111/j.1461-0248.2010.01562.x}, pmid = {21105980}, issn = {1461-0248}, mesh = {Acclimatization ; Algorithms ; Animals ; Anthozoa/growth &amp; development/*physiology ; Aquatic Organisms ; Bahamas ; Climate Change ; *Conservation of Natural Resources ; *Coral Reefs ; Hot Temperature ; Larva/growth &amp; development/physiology ; }, abstract = {Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.}, }
@article {pmid21041648, year = {2010}, author = {Sharon, G and Segal, D and Ringo, JM and Hefetz, A and Zilber-Rosenberg, I and Rosenberg, E}, title = {Commensal bacteria play a role in mating preference of Drosophila melanogaster.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {107}, number = {46}, pages = {20051-20056}, pmid = {21041648}, issn = {1091-6490}, mesh = {Animals ; Bacteria/*metabolism ; Diet/veterinary ; Drosophila melanogaster/growth &amp; development/*microbiology/*physiology ; Female ; Hydrocarbons/metabolism ; Integumentary System/microbiology ; Male ; Mating Preference, Animal/*physiology ; }, abstract = {Development of mating preference is considered to be an early event in speciation. In this study, mating preference was achieved by dividing a population of Drosophila melanogaster and rearing one part on a molasses medium and the other on a starch medium. When the isolated populations were mixed, "molasses flies" preferred to mate with other molasses flies and "starch flies" preferred to mate with other starch flies. The mating preference appeared after only one generation and was maintained for at least 37 generations. Antibiotic treatment abolished mating preference, suggesting that the fly microbiota was responsible for the phenomenon. This was confirmed by infection experiments with microbiota obtained from the fly media (before antibiotic treatment) as well as with a mixed culture of Lactobacillus species and a pure culture of Lactobacillus plantarum isolated from starch flies. Analytical data suggest that symbiotic bacteria can influence mating preference by changing the levels of cuticular hydrocarbon sex pheromones. The results are discussed within the framework of the hologenome theory of evolution.}, }
@article {pmid20962876, year = {2011}, author = {Chen, CP and Tseng, CH and Chen, CA and Tang, SL}, title = {The dynamics of microbial partnerships in the coral Isopora palifera.}, journal = {The ISME journal}, volume = {5}, number = {4}, pages = {728-740}, pmid = {20962876}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Biodiversity ; Dinoflagellida/*classification/genetics/isolation &amp; purification ; Host Specificity ; Seasons ; Symbiosis ; }, abstract = {Both bacteria and algal symbionts (genus Symbiodinium), the two major microbial partners in the coral holobiont, respond to fluctuations in the environment, according to current reports; however, little evidence yet indicates that both populations have any direct interaction with each other in seasonal fluctuation. In this study, we present field observations of a compositional change in bacteria and Symbiodinium in the coral Isopora palifera in three separate coral colonies following monthly sampling from February to November in 2008. Using massively parallel pyrosequencing, over 200,000 bacterial V6 sequences were classified to build the bacterial community profile; in addition, the relative composition and quantity of Symbiodinium clades C and D were determined by real-time PCR. The results showed that coral-associated bacterial and Symbiodinium communities were highly dynamic and dissimilar among the tagged coral colonies, suggesting that the effect of host specificity was insignificant. The coral-associated bacterial community was more diverse (Shannon index up to 6.71) than previous estimates in other corals and showed rapid seasonal changes. The population ratios between clade C and D groups of Symbiodinium varied in the tagged coral colonies through the different seasons; clade D dominated in most of the samples. Although significant association between bacteria and symbiont was not detected, this study presents a more detailed picture of changes in these two major microbial associates of the coral at the same time, using the latest molecular approaches.}, }
@article {pmid23766221, year = {2010}, author = {Rosenberg, E and Sharon, G and Atad, I and Zilber-Rosenberg, I}, title = {The evolution of animals and plants via symbiosis with microorganisms.}, journal = {Environmental microbiology reports}, volume = {2}, number = {4}, pages = {500-506}, doi = {10.1111/j.1758-2229.2010.00177.x}, pmid = {23766221}, issn = {1758-2229}, abstract = {Animals and plants evolved from prokaryotes and have remained in close association with them. We suggest that early eukaryotic cells, formed by the fusion of two or more prokaryotes, already contained prokaryotic genetic information for aggregation and the formation of multicellular structures. The hologenome theory of evolution posits that a unit of selection in evolution is the holobiont (host plus symbionts). The hologenome is defined as the genetic information of the host and its microbiota, which function in consortium. Genetic variation of the holobiont, the raw material for evolution, can arise from changes in either the host or the symbiotic microbiota genomes. Changes in the hologenome can occur by two processes that are specific to holobionts: microbial amplification and acquisition of novel strains from the environment. Recent data from culture-independent studies provides considerable support of the hologenome theory: (i) all animals and plants contain abundant and diverse microbiota, (ii) the symbiotic microbiota affects the fitness of their host and (iii) symbiotic microorganisms are transmitted from parent to offspring. Consideration of the dynamic aspects of symbioses of hosts with their diverse microbiota leads to the conclusion that holobionts can evolve not only via Darwinian but also by adaptive Lamarckian principles.}, }
@article {pmid20668489, year = {2011}, author = {Meron, D and Atias, E and Iasur Kruh, L and Elifantz, H and Minz, D and Fine, M and Banin, E}, title = {The impact of reduced pH on the microbial community of the coral Acropora eurystoma.}, journal = {The ISME journal}, volume = {5}, number = {1}, pages = {51-60}, pmid = {20668489}, issn = {1751-7370}, mesh = {Alteromonadaceae/genetics ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biodiversity ; Cluster Analysis ; Hydrogen-Ion Concentration ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry ; Sequence Analysis, DNA ; Vibrionaceae/genetics ; }, abstract = {Rising concentrations of atmospheric carbon dioxide are acidifying the world's oceans. Surface seawater pH is 0.1 units lower than pre-industrial values and is predicted to decrease by up to 0.4 units by the end of the century. This change in pH may result in changes in the physiology of ocean organisms, in particular, organisms that build their skeletons/shells from calcium carbonate, such as corals. This physiological change may also affect other members of the coral holobiont, for example, the microbial communities associated with the coral, which in turn may affect the coral physiology and health. In the present study, we examined changes in bacterial communities in the coral mucus, tissue and skeleton following exposure of the coral Acropora eurystoma to two different pH conditions: 7.3 and 8.2 (ambient seawater). The microbial community was different at the two pH values, as determined by denaturing gradient gel electrophoresis and 16S rRNA gene sequence analysis. Further analysis of the community in the corals maintained at the lower pH revealed an increase in bacteria associated with diseased and stressed corals, such as Vibrionaceae and Alteromonadaceae. In addition, an increase in the number of potential antibacterial activity was recorded among the bacteria isolated from the coral maintained at pH 7.3. Taken together, our findings highlight the impact that changes in the pH may have on the coral-associated bacterial community and their potential contribution to the coral host.}, }
@article {pmid20456235, year = {2010}, author = {Weis, VM}, title = {The susceptibility and resilience of corals to thermal stress: adaptation, acclimatization or both?.}, journal = {Molecular ecology}, volume = {19}, number = {8}, pages = {1515-1517}, doi = {10.1111/j.1365-294X.2010.04575.x}, pmid = {20456235}, issn = {1365-294X}, mesh = {*Acclimatization/genetics/physiology ; *Adaptation, Physiological/genetics/physiology ; American Samoa ; Animals ; Anthozoa/*genetics/*physiology ; Biomarkers ; Genetic Markers ; Global Warming ; *Hot Temperature ; Stress, Physiological ; Symbiosis ; Ubiquitin/genetics ; }, abstract = {Coral reefs are threatened with worldwide decline from multiple factors, chief among them climate change (Hughes et al. 2003; Hoegh-Guldberg et al. 2007). The foundation of coral reefs is an endosymbiosis between coral hosts and their resident photosynthetic dinoflagellates (genus Symbiodinium) and this partnership (or holobiont) is exquisitely sensitive to temperature stress. The primary response to hyperthermic stress is coral bleaching, which is the loss of symbionts from coral tissues-the collapse of the symbiosis (Weis 2008). Bleaching can result in increased coral mortality which can ultimately lead to severely compromised reef health (Hoegh-Guldberg et al. 2007). Despite this grim picture of coral bleaching and reef degradation, coral susceptibility to stress and bleaching is highly variable (Coles &amp; Brown 2003). There is enormous interest in discovering the factors that determine susceptibility in order to help us predict if and how corals will survive a period of rapid global warming. In this issue, Barshis et al. (2010) examine the ecophysiological and genetic basis for differential responses to stress in Porites lobata in American Samoa. They combine a reciprocal transplant experimental design between two neighbouring, but very different reef environments with state-of-the-art physiological biomarkers and molecular genetic markers for both partners to tease apart the contribution of environmental and fixed influences on stress susceptibility. Their results suggest the presence of a fixed, rather than environmental effect on expression of ubiquitin conjugates, one key marker for physiological stress response. In addition, the authors show genetic differentiation in host populations between the two sites suggesting strong selection for physiological adaptation to differing environments across small geographic distances. These conclusions point the study of coral resilience and susceptibility in a new direction.}, }
@article {pmid20444713, year = {2010}, author = {LaJeunesse, TC and Smith, R and Walther, M and Pinzón, J and Pettay, DT and McGinley, M and Aschaffenburg, M and Medina-Rosas, P and Cupul-Magaña, AL and Pérez, AL and Reyes-Bonilla, H and Warner, ME}, title = {Host-symbiont recombination versus natural selection in the response of coral-dinoflagellate symbioses to environmental disturbance.}, journal = {Proceedings. Biological sciences}, volume = {277}, number = {1696}, pages = {2925-2934}, pmid = {20444713}, issn = {1471-2954}, mesh = {Acclimatization/genetics ; Animals ; Anthozoa/*genetics ; California ; Dinoflagellida/*genetics ; *Environment ; Geography ; *Recombination, Genetic ; Seasons ; *Selection, Genetic ; Species Specificity ; Stress, Physiological ; Symbiosis/*genetics ; Time Factors ; }, abstract = {Mutualisms between reef-building corals and endosymbiotic dinoflagellates are particularly sensitive to environmental stress, yet the ecosystems they construct have endured major oscillations in global climate. During the winter of 2008, an extreme cold-water event occurred in the Gulf of California that bleached corals in the genus Pocillopora harbouring a thermally 'sensitive' symbiont, designated Symbiodinium C1b-c, while colonies possessing Symbiodinium D1 were mostly unaffected. Certain bleached colonies recovered quickly while others suffered partial or complete mortality. In most colonies, no appreciable change was observed in the identity of the original symbiont, indicating that these partnerships are stable. During the initial phases of recovery, a third species of symbiont B1(Aiptasia), genetically identical to that harboured by the invasive anemone, Aiptasia sp., grew opportunistically and was visible as light-yellow patches on the branch tips of several colonies. However, this symbiont did not persist and was displaced in all cases by C1b-c several months later. Colonies with D1 were abundant at inshore habitats along the continental eastern Pacific, where seasonal turbidity is high relative to offshore islands. Environmental conditions of the central and southern coasts of Mexico were not sufficient to explain the exclusivity of D1 Pocillopora in these regions. It is possible that mass mortalities associated with major thermal disturbances during the 1997-1998 El Niño Southern Oscillation eliminated C1b-c holobionts from these locations. The differential loss of Pocillopora holobionts in response to thermal stress suggests that natural selection on existing variation can cause rapid and significant shifts in the frequency of particular coral-algal partnerships. However, coral populations may take decades to recover following episodes of severe selection, thereby raising considerable uncertainty about the long-term viability of these communities.}, }
@article {pmid20361023, year = {2010}, author = {Mao-Jones, J and Ritchie, KB and Jones, LE and Ellner, SP}, title = {How microbial community composition regulates coral disease development.}, journal = {PLoS biology}, volume = {8}, number = {3}, pages = {e1000345}, pmid = {20361023}, issn = {1545-7885}, mesh = {Animals ; Anthozoa/anatomy &amp; histology/*microbiology/*parasitology/physiology ; Bacteria/pathogenicity ; Bacterial Infections/*pathology ; *Ecosystem ; *Models, Theoretical ; Seawater ; *Symbiosis ; Water Microbiology ; }, abstract = {Reef coral cover is in rapid decline worldwide, in part due to bleaching (expulsion of photosynthetic symbionts) and outbreaks of infectious disease. One important factor associated with bleaching and in disease transmission is a shift in the composition of the microbial community in the mucus layer surrounding the coral: the resident microbial community-which is critical to the healthy functioning of the coral holobiont-is replaced by pathogenic microbes, often species of Vibrio. In this paper we develop computational models for microbial community dynamics in the mucus layer in order to understand how the surface microbial community responds to changes in environmental conditions, and under what circumstances it becomes vulnerable to overgrowth by pathogens. Some of our model's assumptions and parameter values are based on Vibrio spp. as a model system for other established and emerging coral pathogens. We find that the pattern of interactions in the surface microbial community facilitates the existence of alternate stable states, one dominated by antibiotic-producing beneficial microbes and the other pathogen-dominated. A shift to pathogen dominance under transient stressful conditions, such as a brief warming spell, may persist long after environmental conditions have returned to normal. This prediction is consistent with experimental findings that antibiotic properties of Acropora palmata mucus did not return to normal long after temperatures had fallen. Long-term loss of antibiotic activity eliminates a critical component in coral defense against disease, giving pathogens an extended opportunity to infect and spread within the host, elevating the risk of coral bleaching, disease, and mortality.}, }
@article {pmid20236189, year = {2010}, author = {Siboni, N and Rasoulouniriana, D and Ben-Dov, E and Kramarsky-Winter, E and Sivan, A and Loya, Y and Hoegh-Guldberg, O and Kushmaro, A}, title = {Stramenopile microorganisms associated with the massive coral Favia sp.}, journal = {The Journal of eukaryotic microbiology}, volume = {57}, number = {3}, pages = {236-244}, doi = {10.1111/j.1550-7408.2010.00469.x}, pmid = {20236189}, issn = {1550-7408}, mesh = {Animals ; Anthozoa/*parasitology/ultrastructure ; Biodiversity ; DNA, Ribosomal/genetics ; Eukaryota/classification/genetics/*isolation &amp; purification ; Molecular Sequence Data ; Phylogeny ; Seawater/parasitology ; }, abstract = {The surfaces of massive corals of the genus Favia from Eilat, Red Sea, and from Heron Island, Great Barrier Reef, are covered by a layer of eukaryotic microorganisms. These microorganisms are embedded in the coral mucus and tissue. In the Gulf of Eilat, the prevalence of corals covered by patches of eukaryotic microorganisms was positively correlated with a decrease in water temperatures (from 25-28 degrees C in the summer to 20-23 degrees C in winter). Comparisons carried out using transmission and scanning electron microscopy showed morphological similarities between the microorganisms from the two geographically distant reefs. The microorganisms found on and in the tissues were approximately 5-15 microm in diameter, surrounded by scales in their cell wall, contained a nucleus, and included unique auto-florescent coccoid bodies of approximately 1 mum. Such morphological characters suggested that these microorganisms are stramenopile protists and in particular thraustochytrids. Molecular analysis, carried out using specific primers for stramenopile 18S rRNA genes, revealed that 90% (111/123) of the clones in the gene libraries were from the Thraustochytriidae. The dominant genera in this family were Aplanochytrium sp., Thraustochytrium sp., and Labyrinthuloides sp. Ten stramenopile strains were isolated and cultured from the corals. Some strains showed > or =97% similarity to clones derived from libraries of mucus-associated microorganisms retrieved directly from these corals. Fatty acid characterization of one of the prevalent strains revealed a high percentage of polyunsaturated fatty acids, including omega-3. The possible association of these stramenopiles in the coral holobiont appeared to be a positive one.}, }
@article {pmid20176062, year = {2010}, author = {Zhao, L and Shen, J}, title = {Whole-body systems approaches for gut microbiota-targeted, preventive healthcare.}, journal = {Journal of biotechnology}, volume = {149}, number = {3}, pages = {183-190}, doi = {10.1016/j.jbiotec.2010.02.008}, pmid = {20176062}, issn = {1873-4863}, mesh = {Chronic Disease ; Humans ; Intestinal Mucosa/metabolism ; Intestines/immunology/*microbiology ; Metabolome ; *Preventive Medicine ; }, abstract = {Humans are superorganisms with two genomes that dictate phenotype, the genetically inherited human genome (25,000 genes) and the environmentally acquired human microbiome (over 1 million genes). The two genomes must work in harmonious integration as a hologenome to maintain health. Nutrition plays a crucial role in directly modulating our microbiomes and health phenotypes. Poorly balanced diets can turn the gut microbiome from a partner for health to a "pathogen" in chronic diseases, e.g. accumulating evidence supports the new hypothesis that obesity and related metabolic diseases develop because of low-grade, systemic and chronic inflammation induced by diet-disrupted gut microbiota. Due to the tight integration of gut microbiota into human global metabolism, molecular profiling of urine metabolites can provide a new window for reflecting physiological functions of gut microbiomes. Changes of gut microbiota and urine metabolites can thus be employed as new systems approaches for quantitative assessment and monitoring of health at the whole-body level with the advantage of measuring human health based on the results of interactions between the two genomes and the environment rather than just host genomic information. Large-scale population-based studies in conjunction with these whole-body level systems methods will generate pre-disease biomarkers with predictive power, thus making preventive health management of populations with rapidly changing disease spectrums possible through re-engineering of the imbalanced gut microbiomes with specially designed foods/diets.}, }
@article {pmid20149089, year = {2010}, author = {DeSalvo, MK and Sunagawa, S and Fisher, PL and Voolstra, CR and Iglesias-Prieto, R and Medina, M}, title = {Coral host transcriptomic states are correlated with Symbiodinium genotypes.}, journal = {Molecular ecology}, volume = {19}, number = {6}, pages = {1174-1186}, doi = {10.1111/j.1365-294X.2010.04534.x}, pmid = {20149089}, issn = {1365-294X}, mesh = {Acclimatization/genetics ; Animals ; Anthozoa/*genetics ; Dinoflagellida/classification/genetics/*physiology ; *Gene Expression Profiling ; Genotype ; Hot Temperature ; Oligonucleotide Array Sequence Analysis ; Symbiosis ; }, abstract = {A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships.}, }
@article {pmid23766005, year = {2010}, author = {Sharon, G and Rosenberg, E}, title = {Healthy corals maintain Vibrio in the VBNC state.}, journal = {Environmental microbiology reports}, volume = {2}, number = {1}, pages = {116-119}, doi = {10.1111/j.1758-2229.2009.00113.x}, pmid = {23766005}, issn = {1758-2229}, abstract = {Vibrio species play an important role in the health and disease of corals. To gain a better understanding of the interactions between Vibrio and coral holobionts we examined the growth of Vibrio in the mucus of the coral Oculina patagonica while the mucus was attached and detached from the coral. Fresh mucus contained ca. 10(2) Vibrio cfu ml(-1) , representing c. 1% of the total viable count. Incubation of detached mucus resulted in a 50 000-fold increase in Vibrio cfu from 1 to 4 h, corresponding to 60% of the total viable counts. This large increase in Vibrio would require an unreasonable doubling time of 11 min. Furthermore, the total microscopic bacterial count increased only 17-fold during the 1-4 h incubation period. These data led to the conclusion that Vibrio species in the mucus were largely in the VBNC state when attached to the coral and 'resuscitated' when the mucus was detached from the coral. We suggest that the coral signal for maintaining Vibrio in the VBNC state is diffusible and unstable. Maintenance of Vibrio in the VBNC state did not require photosynthetic products of the coral holobiont. Vibrio species in the VBNC state may contribute to the health of corals by preventing infections by pathogens.}, }
@article {pmid23766002, year = {2010}, author = {Alves, N and Neto, OS and Silva, BS and De Moura, RL and Francini-Filho, RB and Barreira E Castro, C and Paranhos, R and Bitner-Mathé, BC and Kruger, RH and Vicente, AC and Thompson, CC and Thompson, FL}, title = {Diversity and pathogenic potential of vibrios isolated from Abrolhos Bank corals.}, journal = {Environmental microbiology reports}, volume = {2}, number = {1}, pages = {90-95}, doi = {10.1111/j.1758-2229.2009.00101.x}, pmid = {23766002}, issn = {1758-2229}, abstract = {We performed the first taxonomic characterization of vibrios and other culturable microbiota from apparently healthy and diseased Brazilian-endemic corals at the Abrolhos reef bank. The diseases affecting corals were tissue necrosis in Phyllogorgia dillatata, white plague and bleaching in Mussismilia braziliensis and bleaching in Mussismilia hispida. Bacterial isolates were obtained from mucus of 22 coral specimens originated from the Abrolhos Bank (i.e. Itacolomis reef, Recife de Fora reef and Santa Barbara Island) in 2007. Vibrios counts in the water and coral mucus were approximately 104 cfu ml(-1) and 106 cfu ml(-1) respectively. One hundred and thirty-one representative vibrio isolates were identified. Most vibrio isolates (n = 79) fell into the core group using the pyrH identification marker. According to our analysis, diseased corals did not possess a unique vibrio microbiota. Vibrio species encompassed strains originated from both apparently healthy and diseased corals. The pathogenic potential of representative vibrio isolates (V. alginolyticus 40B, V. harveyi-like 1DA3 and V. coralliilyticus 2DA3) were evaluated in a standardized bioassay using the animal model Drosophila melanogaster and caused 25-88% mortality. This is the first taxonomic characterization of the culturable microbiota from the Brazilian-endemic corals. Endemic Brazilian corals are a reservoir of the vibrio core group. Vibrio alginolyticus, V. harveyi and V. coralliilyticus are dominant in the mucus of these corals and may be a normal component of the holobiont.}, }
@article {pmid20013262, year = {2010}, author = {Lins-de-Barros, MM and Vieira, RP and Cardoso, AM and Monteiro, VA and Turque, AS and Silveira, CB and Albano, RM and Clementino, MM and Martins, OB}, title = {Archaea, Bacteria, and algal plastids associated with the reef-building corals Siderastrea stellata and Mussismilia hispida from Búzios, South Atlantic Ocean, Brazil.}, journal = {Microbial ecology}, volume = {59}, number = {3}, pages = {523-532}, pmid = {20013262}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification ; Atlantic Ocean ; Bacteria/*classification/genetics/isolation &amp; purification ; Brazil ; DNA, Algal/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Ecosystem ; Eukaryota/*classification/genetics/isolation &amp; purification ; Gene Library ; Phylogeny ; Plastids/*genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Symbiosis ; Water Microbiology ; }, abstract = {Reef-building corals may be seen as holobiont organisms, presenting diverse associated microbial communities. Best known is the symbiotic relationship with zooxanthellae, but Archaea, Bacteria, fungi, viruses, and algal plastids are also abundant. Until now, there is little information concerning microbial communities associated with Brazilian corals. The present study aims to describe the diversity of Archaea, Bacteria, and eukaryotic algal plastid communities associated with two sympatric species, Siderastrea stellata and Mussismilia hispida, from Southeastern Brazil, using 16S rRNA gene libraries. Since corals present a high number of other associated invertebrates, coral barcoding (COI) was performed to confirm the exclusive occurrence of coral DNA in our samples. Our analysis yielded 354 distinct microbial OTUs, represented mainly by novel phylotypes. Richness (Chao1 and ACE) and diversity (H') estimations of the microbial communities associated with both species were high and comparable to other studies. Rarefaction analyses showed that microbial diversity of S. stellata is higher than that of M. hispida. Libshuff comparative analyses showed that the highest microbial community similarity between the two coral species occurred in the bacterial libraries, while archaeal and plastidial communities were significantly different. Crenarchaeota dominated archaeal communities, while Proteobacteria was the most abundant bacterial phylum, dominated by alpha-Proteobacteria. Plastids were also represented by novel phylotypes and did not match with any 16S rRNA sequences of Cyanobacteria and zooxanthellae from GenBank. Our data improves the pool of available information on Brazilian coral microbes and shows corals as sources of diverse prokaryotic and picoeukaryotic communities.}, }
@article {pmid19956272, year = {2010}, author = {Thomas, S and Burdett, H and Temperton, B and Wick, R and Snelling, D and McGrath, JW and Quinn, JP and Munn, C and Gilbert, JA}, title = {Evidence for phosphonate usage in the coral holobiont.}, journal = {The ISME journal}, volume = {4}, number = {3}, pages = {459-461}, doi = {10.1038/ismej.2009.129}, pmid = {19956272}, issn = {1751-7370}, mesh = {Alkaline Phosphatase ; Animals ; Anthozoa/*microbiology ; Bacteria/*classification/isolation &amp; purification/*metabolism ; Bacterial Proteins/*genetics ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Organophosphonates/*metabolism ; Phosphoric Monoester Hydrolases/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Phosphonates are characterized by a stable carbon-phosphorus bond and commonly occur as lipid conjugates in invertebrate cell membranes. Phosphonoacetate hydrolase encoded by the phnA gene, catalyses the cleavage of phosphonoacetate to acetate and phosphate. In this study, we demonstrate the unusually high phnA diversity in coral-associated bacteria. The holobiont of eight coral species tested positive when screened for phnA using degenerate primers. In two soft coral species, Sinularia and Discosoma, sequencing of the phnA gene showed 13 distinct groups on the basis of 90% sequence identity across 100% of the sequence. A total of 16 bacterial taxa capable of using phosphonoacetate as the sole carbon and phosphorus source were isolated; 8 of which had a phnA+ genotype. This study enhances our understanding of the wide taxonomic and environmental distribution of phnA, and highlights the importance of phosphonates in marine ecosystems.}, }
@article {pmid19822428, year = {2009}, author = {Bourne, DG and Garren, M and Work, TM and Rosenberg, E and Smith, GW and Harvell, CD}, title = {Microbial disease and the coral holobiont.}, journal = {Trends in microbiology}, volume = {17}, number = {12}, pages = {554-562}, doi = {10.1016/j.tim.2009.09.004}, pmid = {19822428}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; Conservation of Natural Resources ; Ecology ; }, abstract = {Tropical coral reefs harbour a reservoir of enormous biodiversity that is increasingly threatened by direct human activities and indirect global climate shifts. Emerging coral diseases are one serious threat implicated in extensive reef deterioration through disruption of the integrity of the coral holobiont - a complex symbiosis between the coral animal, endobiotic alga and an array of microorganisms. In this article, we review our current understanding of the role of microorganisms in coral health and disease, and highlight the pressing interdisciplinary research priorities required to elucidate the mechanisms of disease. We advocate an approach that applies knowledge gained from experiences in human and veterinary medicine, integrated into multidisciplinary studies that investigate the interactions between host, agent and environment of a given coral disease. These approaches include robust and precise disease diagnosis, standardised ecological methods and application of rapidly developing DNA, RNA and protein technologies, alongside established histological, microbial ecology and ecological expertise. Such approaches will allow a better understanding of the causes of coral mortality and coral reef declines and help assess potential management options to mitigate their effects in the longer term.}, }
@article {pmid19806190, year = {2009}, author = {Garren, M and Raymundo, L and Guest, J and Harvell, CD and Azam, F}, title = {Resilience of coral-associated bacterial communities exposed to fish farm effluent.}, journal = {PloS one}, volume = {4}, number = {10}, pages = {e7319}, pmid = {19806190}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*microbiology ; Aquaculture ; Bacteria/*growth &amp; development ; Carbon ; Chlorophyll/chemistry ; Ecosystem ; Environmental Monitoring ; Environmental Pollutants ; Fishes ; Geologic Sediments ; Water Microbiology ; Water Pollutants, Chemical ; }, abstract = {BACKGROUND: The coral holobiont includes the coral animal, algal symbionts, and associated microbial community. These microbes help maintain the holobiont homeostasis; thus, sustaining robust mutualistic microbial communities is a fundamental part of long-term coral reef survival. Coastal pollution is one major threat to reefs, and intensive fish farming is a rapidly growing source of this pollution.<br><br>We investigated the susceptibility and resilience of the bacterial communities associated with a common reef-building coral, Porites cylindrica, to coastal pollution by performing a clonally replicated transplantation experiment in Bolinao, Philippines adjacent to intensive fish farming. Ten fragments from each of four colonies (total of 40 fragments) were followed for 22 days across five sites: a well-flushed reference site (the original fragment source); two sites with low exposure to milkfish (Chanos chanos) aquaculture effluent; and two sites with high exposure. Elevated levels of dissolved organic carbon (DOC), chlorophyll a, total heterotrophic and autotrophic bacteria abundance, virus like particle (VLP) abundances, and culturable Vibrio abundance characterized the high effluent sites. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis, we observed rapid, dramatic changes in the coral-associated bacterial communities within five days of high effluent exposure. The community composition on fragments at these high effluent sites shifted towards known human and coral pathogens (i.e. Arcobacter, Fusobacterium, and Desulfovibrio) without the host corals showing signs of disease. The communities shifted back towards their original composition by day 22 without reduction in effluent levels.<br><br>SIGNIFICANCE: This study reveals fish farms as a likely source of pathogens with the potential to proliferate on corals and an unexpected short-term resilience of coral-associated bacterial communities to eutrophication pressure. These data highlight a need for improved aquaculture practices that can achieve both sustainable industry goals and long-term coral reef survival.}, }
@article {pmid19691500, year = {2010}, author = {Rypien, KL and Ward, JR and Azam, F}, title = {Antagonistic interactions among coral-associated bacteria.}, journal = {Environmental microbiology}, volume = {12}, number = {1}, pages = {28-39}, doi = {10.1111/j.1462-2920.2009.02027.x}, pmid = {19691500}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Bacteria/genetics/*growth &amp; development/isolation &amp; purification ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; Water Microbiology ; }, abstract = {Reef-building corals are comprised of close associations between the coral animal, symbiotic zooxanthellae, and a diversity of associated microbes (including Bacteria, Archaea and Fungi). Together, these comprise the coral holobiont - a paradigm that emphasizes the potential contributions of each component to the overall function and health of the coral. Little is known about the ecology of the coral-associated microbial community and its hypothesized role in coral health. We explored bacteria-bacteria antagonism among 67 bacterial isolates from the scleractinian coral Montastrea annularis at two temperatures using Burkholder agar diffusion assays. A majority of isolates exhibited inhibitory activity (69.6% of isolates at 25 degrees C, 52.2% at 31 degrees C), with members of the gamma-proteobacteria (Vibrionales and Alteromonadales) being especially antagonistic. Elevated temperatures generally reduced levels of antagonism, although the effects were complex. Several potential pathogens were observed in the microbial community of apparently healthy corals, and 11.6% of isolates were able to inhibit the growth of the coral pathogen Vibrio shiloi at 25 degrees C. Overall, this study demonstrates that antagonism could be a structuring force in coral-associated microbial communities and may contribute to pathogenesis as well as disease resistance.}, }
@article {pmid19629182, year = {2009}, author = {Mieog, JC and Olsen, JL and Berkelmans, R and Bleuler-Martinez, SA and Willis, BL and van Oppen, MJ}, title = {The roles and interactions of symbiont, host and environment in defining coral fitness.}, journal = {PloS one}, volume = {4}, number = {7}, pages = {e6364}, pmid = {19629182}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/classification/*physiology ; Phylogeny ; *Symbiosis ; }, abstract = {BACKGROUND: Reef-building corals live in symbiosis with a diverse range of dinoflagellate algae (genus Symbiodinium) that differentially influence the fitness of the coral holobiont. The comparative role of symbiont type in holobiont fitness in relation to host genotype or the environment, however, is largely unknown. We addressed this knowledge gap by manipulating host-symbiont combinations and comparing growth, survival and thermal tolerance among the resultant holobionts in different environments.<br><br>Offspring of the coral, Acropora millepora, from two thermally contrasting locations, were experimentally infected with one of six Symbiodinium types, which spanned three phylogenetic clades (A, C and D), and then outplanted to the two parental field locations (central and southern inshore Great Barrier Reef, Australia). Growth and survival of juvenile corals were monitored for 31-35 weeks, after which their thermo-tolerance was experimentally assessed. Our results showed that: (1) Symbiodinium type was the most important predictor of holobiont fitness, as measured by growth, survival, and thermo-tolerance; (2) growth and survival, but not heat-tolerance, were also affected by local environmental conditions; and (3) host population had little to no effect on holobiont fitness. Furthermore, coral-algal associations were established with symbiont types belonging to clades A, C and D, but three out of four symbiont types belonging to clade C failed to establish a symbiosis. Associations with clade A had the lowest fitness and were unstable in the field. Lastly, Symbiodinium types C1 and D were found to be relatively thermo-tolerant, with type D conferring the highest tolerance in A. millepora.<br><br>CONCLUSIONS/SIGNIFICANCE: These results highlight the complex interactions that occur between the coral host, the algal symbiont, and the environment to shape the fitness of the coral holobiont. An improved understanding of the factors affecting coral holobiont fitness will assist in predicting the responses of corals to global climate change.}, }
@article {pmid19573132, year = {2009}, author = {Rosenberg, E and Sharon, G and Zilber-Rosenberg, I}, title = {The hologenome theory of evolution contains Lamarckian aspects within a Darwinian framework.}, journal = {Environmental microbiology}, volume = {11}, number = {12}, pages = {2959-2962}, doi = {10.1111/j.1462-2920.2009.01995.x}, pmid = {19573132}, issn = {1462-2920}, mesh = {Adaptation, Biological/genetics/physiology ; Adaptation, Physiological/genetics ; Animals ; Bacteria/genetics ; *Biological Evolution ; Colon/microbiology ; Heredity ; Humans ; *Metagenome ; Plants/genetics ; Symbiosis/genetics/physiology ; }, abstract = {The hologenome theory of evolution emphasizes the role of microorganisms in the evolution of animals and plants. The theory posits that the holobiont (host plus all of its symbiont microbiota) is a unit of selection in evolution. Genetic variation in the holobiont that can occur either in the host and/or in the microbial symbiont genomes (together termed hologenome) can then be transmitted to offspring. In addition to the known modes of variation, i.e. sexual recombination, chromosomal rearrangement and mutation, variation in the holobiont can occur also via two mechanisms that are specific to the hologenome theory: amplification of existing microorganisms and acquisition of novel strains from the environment. These mechanisms are Lamarckian in that (i) they are regulated by 'use and disuse' (of microbes) and (ii) the variations in the hologenome are transmitted to offspring, thus satisfying also the Lamarckian principle of 'inheritance of acquired characteristics'. Accordingly, the hologenome theory incorporates Lamarckian aspects within a Darwinian framework, accentuating both cooperation and competition within the holobiont and with other holobionts.}, }
@article {pmid19397678, year = {2009}, author = {Vega Thurber, R and Willner-Hall, D and Rodriguez-Mueller, B and Desnues, C and Edwards, RA and Angly, F and Dinsdale, E and Kelly, L and Rohwer, F}, title = {Metagenomic analysis of stressed coral holobionts.}, journal = {Environmental microbiology}, volume = {11}, number = {8}, pages = {2148-2163}, doi = {10.1111/j.1462-2920.2009.01935.x}, pmid = {19397678}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa/metabolism/microbiology ; Dinoflagellida/genetics/growth &amp; development/metabolism ; Euryarchaeota/genetics/metabolism ; Fungi/growth &amp; development ; Genomics ; Metagenome/drug effects/*genetics ; Nitrogen/metabolism ; Stress, Physiological/*genetics ; Symbiosis ; Temperature ; Vibrio/pathogenicity ; Virulence/genetics ; }, abstract = {The coral holobiont is the community of metazoans, protists and microbes associated with scleractinian corals. Disruptions in these associations have been correlated with coral disease, but little is known about the series of events involved in the shift from mutualism to pathogenesis. To evaluate structural and functional changes in coral microbial communities, Porites compressa was exposed to four stressors: increased temperature, elevated nutrients, dissolved organic carbon loading and reduced pH. Microbial metagenomic samples were collected and pyrosequenced. Functional gene analysis demonstrated that stressors increased the abundance of microbial genes involved in virulence, stress resistance, sulfur and nitrogen metabolism, motility and chemotaxis, fatty acid and lipid utilization, and secondary metabolism. Relative changes in taxonomy also demonstrated that coral-associated microbiota (Archaea, Bacteria, protists) shifted from a healthy-associated coral community (e.g. Cyanobacteria, Proteobacteria and the zooxanthellae Symbiodinium) to a community (e.g. Bacteriodetes, Fusobacteria and Fungi) of microbes often found on diseased corals. Additionally, low-abundance Vibrio spp. were found to significantly alter microbiome metabolism, suggesting that the contribution of a just a few members of a community can profoundly shift the health status of the coral holobiont.}, }
@article {pmid19291243, year = {2009}, author = {Chimetto, LA and Brocchi, M and Gondo, M and Thompson, CC and Gomez-Gil, B and Thompson, FL}, title = {Genomic diversity of vibrios associated with the Brazilian coral Mussismilia hispida and its sympatric zoanthids (Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi).}, journal = {Journal of applied microbiology}, volume = {106}, number = {6}, pages = {1818-1826}, doi = {10.1111/j.1365-2672.2009.04149.x}, pmid = {19291243}, issn = {1365-2672}, mesh = {Animals ; Anthozoa/*microbiology ; Bacterial Proteins/genetics ; Base Sequence ; Brazil ; DNA, Bacterial/genetics ; Molecular Sequence Data ; Mucus/microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Vibrio/*classification/*genetics/isolation &amp; purification ; }, abstract = {AIMS: A taxonomic survey of the vibrios associated with the Brazilian endemic coral Mussismilia hispida and the sympatric zoanthids (i.e. Palythoa caribaeorum, Palythoa variabilis and Zoanthus solanderi).<br><br>METHODS AND RESULTS: Mucus of 54 cnidarian specimens collected in three different places at S&#xe3;o Sebasti&#xe3;o in two consecutive years (i.e. 2005 and 2006) was used for taxonomic characterization of the cnidarian microbiota. Ninety-eight of the 151 vibrio isolates fell within the vibrio core group according to partial 16S rDNA sequences. We performed the sequencing of recA and pyrH genes of all vibrio isolates. The most abundant taxa belonged to the vibrio core group (Vibrio harveyi, Vibrio rotiferianus, Vibrio campbellii and Vibrio alginolyticus), Vibrio mediterranei (=Vibrio shillonii) and Vibrio chagasii. With the exception of V. chagasii which was found only in the mucus of M. hispida, the other species appeared in different hosts with no evidence for the presence of host-specific clones or species. Using rep-PCR analysis, we observed a high genomic heterogeneity within the vibrios. Each vibrio isolate generated a different rep-PCR fingerprint pattern. There was a complete agreement between the grouping based on rep-PCR and concatenated sequences of pyrH, recA and 16S rDNA, but the pyrH gene has the highest discriminatory power for vibrio species identification.<br><br>CONCLUSION: The vibrio core group is dominant in the mucus of these cnidarians. There is a tremendous diversity of vibrio lineages within the coral mucus. pyrH gene sequences permit a clear-cut identification of vibrios.<br><br>The taxonomic resolution provided by pyrH (but not recA) appears to be enough for identifying species of vibrios and for disclosing putative new taxa. The vibrio core group appears to be dominant in the mucus of the Brazilian cnidarians. The overrepresentation of these vibrios may reflect as yet unknown ecological functions in the coral holobiont.}, }
@article {pmid19191871, year = {2009}, author = {Nissimov, J and Rosenberg, E and Munn, CB}, title = {Antimicrobial properties of resident coral mucus bacteria of Oculina patagonica.}, journal = {FEMS microbiology letters}, volume = {292}, number = {2}, pages = {210-215}, doi = {10.1111/j.1574-6968.2009.01490.x}, pmid = {19191871}, issn = {1574-6968}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Bacteria/classification/*drug effects/*growth &amp; development/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Colony Count, Microbial ; }, abstract = {The inhibitory properties of the microbial community of the coral mucus from the Mediterranean coral Oculina patagonica were examined. Out of 156 different colony morphotypes that were isolated from the coral mucus, nine inhibited the growth of Vibrio shiloi, a species previously shown to be a pathogen of this coral. An isolate identified as Pseudoalteromonas sp. was the strongest inhibitor of V. shiloi. Several isolates, especially one identified as Roseobacter sp., also showed a broad spectrum of action against the coral pathogens Vibrio coralliilyticus and Thallassomonas loyana, plus nine other selected Gram-positive and Gram-negative bacteria. Inoculation of a previously established biofilm of the Roseobacter strain with V. shiloi led to a 5-log reduction in the viable count of the pathogen within 3 h, while inoculation of a Pseudoalteromonas biofilm led to complete loss of viability of V. shiloi after 3 h. These results support the concept of a probiotic effect on microbial communities associated with the coral holobiont.}, }
@article {pmid19161430, year = {2009}, author = {Shnit-Orland, M and Kushmaro, A}, title = {Coral mucus-associated bacteria: a possible first line of defense.}, journal = {FEMS microbiology ecology}, volume = {67}, number = {3}, pages = {371-380}, doi = {10.1111/j.1574-6941.2008.00644.x}, pmid = {19161430}, issn = {1574-6941}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Colony Count, Microbial ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Ecosystem ; Microbial Sensitivity Tests ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Water Microbiology ; }, abstract = {Interactions among microorganisms found in coral mucus can be either symbiotic or competitive. It has been hypothesized that microbial communities found on the surface of coral play a role in coral holobiont defense, possibly through production of antimicrobial substances. Selected microorganisms isolated from the mucus layer of a number of coral species were grown using agar-plating techniques. Screening for antimicrobial substances was performed using overlay and drop techniques, employing several indicator microorganisms. Between 25% and 70% of cultivable mucus-associated bacteria from scleractinian corals demonstrated bioactivity. Higher percentages of activity were evident in mucus-associated cultivable bacteria from massive and solitary corals, as compared with bacteria from branching or soft corals. Isolates related to the genera Vibrio and Pseudoalteromonas demonstrated high activity against both Gram-positive and Gram-negative bacteria. Gram-positive bacteria (Bacillus, Planomicrobium) demonstrated lower levels of activity, primarily against other Gram-positive bacteria. In some cases, inhibitory effects were confined to the cell fraction, suggesting the involvement of a cell-bound molecule, sensitive to temperature and most likely proteinaceous in nature. These results demonstrate the existence of microorganisms with antimicrobial activity on the coral surface, possibly acting as a first line of defense to protect the coral host against pathogens.}, }
@article {pmid19129866, year = {2009}, author = {Sunagawa, S and DeSantis, TZ and Piceno, YM and Brodie, EL and DeSalvo, MK and Voolstra, CR and Weil, E and Andersen, GL and Medina, M}, title = {Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata.}, journal = {The ISME journal}, volume = {3}, number = {5}, pages = {512-521}, doi = {10.1038/ismej.2008.131}, pmid = {19129866}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*isolation &amp; purification ; Bacterial Infections/*microbiology ; *Biodiversity ; Caribbean Region ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Microarray Analysis ; Molecular Sequence Data ; Phylogeny ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {Increasing evidence confirms the crucial role bacteria and archaea play within the coral holobiont, that is, the coral host and its associated microbial community. The bacterial component constitutes a community of high diversity, which appears to change in structure in response to disease events. In this study, we highlight the limitation of 16S rRNA gene (16S rDNA) clone library sequencing as the sole method to comprehensively describe coral-associated communities. This limitation was addressed by combining a high-density 16S rRNA gene microarray with, clone library sequencing as a novel approach to study bacterial communities in healthy versus diseased corals. We determined an increase in diversity as well as a significant shift in community structure in Montastraea faveolata colonies displaying phenotypic signs of White Plague Disease type II (WPD-II). An accumulation of species that belong to families that include known coral pathogens (Alteromonadaceae, Vibrionaceae), bacteria previously isolated from diseased, stressed or injured marine invertebrates (for example, Rhodobacteraceae), and other species (for example, Campylobacteraceae) was observed. Some of these species were also present in healthy tissue samples, but the putative primary pathogen, Aurantimonas corallicida, was not detected in any sample by either method. Although an ecological succession of bacteria during disease progression after causation by a primary agent represents a possible explanation for our observations, we also discuss the possibility that a disease of yet to be determined etiology may have affected M. faveolata colonies and resulted in (or be a result of) an increase in opportunistic pathogens.}, }
@article {pmid20375587, year = {2009}, author = {Rosenstiel, P and Philipp, EE and Schreiber, S and Bosch, TC}, title = {Evolution and function of innate immune receptors--insights from marine invertebrates.}, journal = {Journal of innate immunity}, volume = {1}, number = {4}, pages = {291-300}, doi = {10.1159/000211193}, pmid = {20375587}, issn = {1662-8128}, mesh = {Adaptation, Physiological/immunology ; Animals ; *Evolution, Molecular ; Immunity, Innate/genetics/*immunology ; Invertebrates/classification/genetics/*immunology ; Receptors, Immunologic/genetics/*immunology ; Toll-Like Receptors/immunology ; }, abstract = {Innate, nonadaptive immune receptors represent phylogenetically ancient first-line sensors of invariant non-self patterns and other cellular danger signals. From lower animal phyla to vertebrates, most pathogens are immediately detected by various recognition systems and are destroyed by induction of defense effectors like antimicrobial peptides. Toll-like receptors, nucleotide-binding and oligomerization domain-like receptors and scavenger receptor cysteine-rich proteins represent archetypes of the innate immune receptors, which mediate the complex interaction between the host and microbiota at the interface of epithelial barriers. In this review, we will use knowledge gained from marine invertebrates as a paradigm to describe how this constant molecular crosstalk within the holobiont, i.e. the animal with all its associated microorganisms, contributes to epithelial homeostasis, immunological integrity and maintenance of the resident microbial diversity.}, }
@article {pmid19052667, year = {2008}, author = {Shapshak, P and Chiappelli, F and Commins, D and Singer, E and Levine, AJ and Somboonwit, C and Minagar, A and Pellionisz, AJ}, title = {Molecular epigenetics, chromatin, and NeuroAIDS/HIV: translational implications.}, journal = {Bioinformation}, volume = {3}, number = {1}, pages = {53-57}, pmid = {19052667}, issn = {0973-2063}, support = {U24 MH100929/MH/NIMH NIH HHS/United States ; R01 GM056529/GM/NIGMS NIH HHS/United States ; T32 AI007126/AI/NIAID NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; R01 DA012580/DA/NIDA NIH HHS/United States ; R24 NS038841/NS/NINDS NIH HHS/United States ; R21 DA014533/DA/NIDA NIH HHS/United States ; }, abstract = {We describe current research that applies epigenetics to a novel understanding of the immuno-neuropathogenesis of HIV-1 viral infection and NeuroAIDS. We propose the hypothesis that HIV-1 alters the structure-function relationship of chromatin, coding DNA and non-coding DNA, including RNA transcribed from these regions resulting in pathogenesis in AIDS, drug abuse, and NeuroAIDS. We discuss the general implications of molecular epigenetics with special emphasis on drug abuse, bar-codes, pyknons, and miRNAs for translational and clinical research. We discuss the application of the recent recursive algorithm of biology to this field and propose to synthesize the Genomic and Epigenomic views into a holistic approach of HoloGenomics.}, }
@article {pmid19052666, year = {2008}, author = {Chiappelli, F and Shapshak, P and Commins, D and Singer, E and Minagar, A and Oluwadara, O and Prolo, P and Pellionisz, AJ}, title = {Molecular epigenetics, chromatin, and NeuroAIDS/HIV: immunopathological implications.}, journal = {Bioinformation}, volume = {3}, number = {1}, pages = {47-52}, pmid = {19052666}, issn = {0973-2063}, support = {R01 GM056529/GM/NIGMS NIH HHS/United States ; T32 AI007126/AI/NIAID NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; R24 NS038841/NS/NINDS NIH HHS/United States ; R21 DA014533/DA/NIDA NIH HHS/United States ; }, abstract = {Epigenetics studies factors related to the organism and environment that modulate inheritance from generation to generation. Molecular epigenetics examines non-coding DNA (ncdDNA) vs. coding DNA (cdDNA), and pertains to every domain of physiology, including immune and brain function. Molecular cartography, including genomics, proteomics, and interactomics, seeks to recognize and to identify the multi-faceted and intricate array of interacting genes and gene products that characterize the function and specialization of each individual cell in the context of cell-cell interaction, tissue, and organ function. Molecular cartography, epigenetics, and chromatin assembly, repair and remodeling (CARR), which, together with the RNA interfering signaling complex (RISC), is responsible for much of the control and regulation of gene expression, intersect.We describe current and ongoing studies aimed to apply these overlapping areas of research, CARR and RISC, to a novel understanding of the immuno-neuropathology of HIV-1 infection, as an example. Taken together, the arguments presented here lead to a novel working hypothesis of molecular immune epigenetics as it pertains to HIV/AIDS, and the immunopathology of HIV-1-infected CD4+ cells. Specifically, we discuss these views in the context of the structure-function relationship of chromatin, the cdDNA/ncdDNA ratio, and possible nucleotide divergence in the untranslated regions (UTRs) of mature mRNA intronic and intergenic DNA sequences, and putative catastrophic consequences for immune surveillance and the preservation of health in HIV/AIDS. Here, we discuss the immunopathology of HIV Infection, with emphasis on CARR in cellular, humoral and molecular immune epigenetics.}, }
@article {pmid19005495, year = {2009}, author = {Rosenberg, E and Kushmaro, A and Kramarsky-Winter, E and Banin, E and Yossi, L}, title = {The role of microorganisms in coral bleaching.}, journal = {The ISME journal}, volume = {3}, number = {2}, pages = {139-146}, doi = {10.1038/ismej.2008.104}, pmid = {19005495}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; *Antibiosis ; Eukaryota/*growth &amp; development ; Vibrio/*growth &amp; development/*metabolism ; }, abstract = {Coral bleaching is the disruption of the symbiosis between the coral host and its endosymbiotic algae. The prevalence and severity of the disease have been correlated with high seawater temperature. During the last decade, the major hypothesis to explain coral bleaching is that high water temperatures cause irreversible damage to the symbiotic algae resulting in loss of pigment and/or algae from the holobiont. Here, we discuss the evidence for an alternative but not mutually exclusive concept, the microbial hypothesis of coral bleaching.}, }
@article {pmid18996547, year = {2009}, author = {Obura, DO}, title = {Reef corals bleach to resist stress.}, journal = {Marine pollution bulletin}, volume = {58}, number = {2}, pages = {206-212}, doi = {10.1016/j.marpolbul.2008.10.002}, pmid = {18996547}, issn = {0025-326X}, mesh = {Animals ; Anthozoa/*physiology ; Eukaryota/physiology ; Stress, Physiological/*physiology ; Symbiosis/physiology ; }, abstract = {A rationale is presented here for a primary role of bleaching in regulation of the coral-zooxanthellae symbiosis under conditions of stress. Corals and zooxanthellae have fundamentally different metabolic rates, requiring active homeostasis to limit zooxanthellae production and manage translocated products to maintain the symbiosis. The control processes for homeostasis are compromised by environmental stress, resulting in metabolic imbalance between the symbionts. For the coral-zooxanthella symbiosis the most direct way to minimize metabolic imbalance under stress is to reduce photosynthetic production by zooxanthellae. Two mechanisms have been demonstrated that do this: reduction of the chlorophyll concentration in individual zooxanthellae and reduction of the relative biomass of zooxanthellae. Both mechanisms result in visual whitening of the coral, termed bleaching. Arguments are presented here that bleaching provides the final control to minimize physiological damage from stress as an adversity response to metabolic imbalance. As such, bleaching meets the requirements of a stress response syndrome/general adaptive mechanism that is sensitive to internal states rather than external parameters. Variation in bleaching responses among holobionts reflects genotypic and phenotypic differentiation, allowing evolutionary change by natural selection. Thus, reef corals bleach to resist stress, and thereby have some capacity to adapt to and survive change. The extreme thermal anomalies causing mass coral bleaching worldwide lie outside the reaction norms for most coral-zooxanthellae holobionts, revealing the limitations of bleaching as a control mechanism.}, }
@article {pmid18707612, year = {2008}, author = {Siboni, N and Ben-Dov, E and Sivan, A and Kushmaro, A}, title = {Global distribution and diversity of coral-associated Archaea and their possible role in the coral holobiont nitrogen cycle.}, journal = {Environmental microbiology}, volume = {10}, number = {11}, pages = {2979-2990}, doi = {10.1111/j.1462-2920.2008.01718.x}, pmid = {18707612}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*classification/genetics/isolation &amp; purification/*metabolism ; Australia ; *Biodiversity ; DNA, Archaeal/chemistry/genetics ; DNA, Ribosomal/genetics ; Israel ; Molecular Sequence Data ; Nitrogen/*metabolism ; Phylogeny ; RNA, Archaeal/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Diversity, distribution and genetic comparison of Archaea associated with the surface mucus of corals from three genera, namely Acanthastrea sp., Favia sp. and Fungia sp., from the Gulf of Eilat, Israel and from Heron Island, Australia were studied. Sequencing of the 16S rRNA gene of the coral-associated Archaea revealed dominance of Crenarchaeota (79%, on average). In this phylum, 87% of the sequences were similar (>or= 97%) to the Thermoprotei, with 76% of these being similar (>or= 97%) to the ammonium oxidizer, Nitrosopumilus maritimus. Most of the coral-associated euryarchaeotal sequences (69%) were related to marine group II, while other euryarchaeotal clades were found to be related to anaerobic methanotrophs (8%), anaerobic nitrate reducers (i.e. denitrification, 15%) and marine group III (8%). Most of the crenarchaeotal and euryarchaeotal coral-associated 16S rRNA gene sequences from Heron Island (61%) and from the Gulf of Eilat (71%) were closely related (>or= 97%) to sequences previously derived from corals from the Virgin Islands. Analysis of archaeal amoA sequences obtained from the fungiid coral, Fungia granulosa, divided into three clades, all related to archaeal sequences previously obtained from the marine environment. These sequences were distantly related to amoA sequences previously found in association with other coral species. Preliminary experiments suggest that there is active oxidation of ammonia to nitrite in the mucus of F. granulosa. Thus, coral-associated Archaea may contribute to nitrogen recycling in the holobiont, presumably by acting as a nutritional sink for excess ammonium trapped in the mucus layer, through nitrification and denitrification processes.}, }
@article {pmid18643952, year = {2008}, author = {Dove, SG and Lovell, C and Fine, M and Deckenback, J and Hoegh-Guldberg, O and Iglesias-Prieto, R and Anthony, KR}, title = {Host pigments: potential facilitators of photosynthesis in coral symbioses.}, journal = {Plant, cell &amp; environment}, volume = {31}, number = {11}, pages = {1523-1533}, doi = {10.1111/j.1365-3040.2008.01852.x}, pmid = {18643952}, issn = {1365-3040}, mesh = {Acclimatization ; Analysis of Variance ; Animals ; Anthozoa/chemistry/*metabolism ; Dinoflagellida/chemistry/*metabolism ; Light ; Oxygen/metabolism ; *Photosynthesis ; Pigmentation/physiology ; Pigments, Biological/chemistry/*physiology ; Species Specificity ; *Symbiosis ; }, abstract = {Reef-building corals occur as a range of colour morphs because of varying types and concentrations of pigments within the host tissues, but little is known about their physiological or ecological significance. Here, we examined whether specific host pigments act as an alternative mechanism for photoacclimation in the coral holobiont. We used the coral Montipora monasteriata (Forskål 1775) as a case study because it occurs in multiple colour morphs (tan, blue, brown, green and red) within varying light-habitat distributions. We demonstrated that two of the non-fluorescent host pigments are responsive to changes in external irradiance, with some host pigments up-regulating in response to elevated irradiance. This appeared to facilitate the retention of antennal chlorophyll by endosymbionts and hence, photosynthetic capacity. Specifically, net P(max) Chl a(-1) correlated strongly with the concentration of an orange-absorbing non-fluorescent pigment (CP-580). This had major implications for the energetics of bleached blue-pigmented (CP-580) colonies that maintained net P(max) cm(-2) by increasing P(max) Chl a(-1). The data suggested that blue morphs can bleach, decreasing their symbiont populations by an order of magnitude without compromising symbiont or coral health.}, }
@article {pmid18549407, year = {2008}, author = {Zilber-Rosenberg, I and Rosenberg, E}, title = {Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution.}, journal = {FEMS microbiology reviews}, volume = {32}, number = {5}, pages = {723-735}, doi = {10.1111/j.1574-6976.2008.00123.x}, pmid = {18549407}, issn = {0168-6445}, mesh = {Adaptation, Biological/genetics/*physiology ; Adaptation, Physiological/*genetics ; Animals ; *Biological Evolution ; Host-Parasite Interactions/genetics/*physiology ; Plants/genetics ; Symbiosis/genetics/*physiology ; }, abstract = {We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the 'superorganism' proposed by Wilson and Sober.}, }
@article {pmid18479440, year = {2008}, author = {Marhaver, KL and Edwards, RA and Rohwer, F}, title = {Viral communities associated with healthy and bleaching corals.}, journal = {Environmental microbiology}, volume = {10}, number = {9}, pages = {2277-2286}, pmid = {18479440}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*virology ; *Biodiversity ; DNA, Viral/genetics ; Ecology ; *Genome, Viral ; Genomic Library ; Sequence Alignment ; Sequence Analysis, DNA ; Symbiosis ; Viruses/*genetics/isolation &amp; purification ; *Water Microbiology ; }, abstract = {The coral holobiont is the integrated assemblage of the coral animal, its symbiotic algae, protists, fungi and a diverse consortium of Bacteria and Archaea. Corals are a model system for the study of symbiosis, the breakdown of which can result in disease and mortality. Little is known, however, about viruses that infect corals and their symbionts. Here we present metagenomic analyses of the viral communities associated with healthy and partially bleached specimens of the Caribbean reef-building coral Diploria strigosa. Surprisingly, herpes-like sequences accounted for 4-8% of the total sequences in each metagenome; this abundance of herpes-like sequences is unprecedented in other marine viral metagenomes. Viruses similar to those that infect algae and plants were also present in the coral viral assemblage. Among the phage identified, cyanophages were abundant in both healthy and bleaching corals and vibriophages were also present. Therefore, coral-associated viruses could potentially infect all components of the holobiont--coral, algal and microbial. Thus, we expect viruses to figure prominently in the preservation and breakdown of coral health.}, }
@article {pmid18393989, year = {2008}, author = {Harel, M and Ben-Dov, E and Rasoulouniriana, D and Siboni, N and Kramarsky-Winter, E and Loya, Y and Barak, Z and Wiesman, Z and Kushmaro, A}, title = {A new Thraustochytrid, strain Fng1, isolated from the surface mucus of the hermatypic coral Fungia granulosa.}, journal = {FEMS microbiology ecology}, volume = {64}, number = {3}, pages = {378-387}, doi = {10.1111/j.1574-6941.2008.00464.x}, pmid = {18393989}, issn = {0168-6496}, mesh = {Amino Acids/metabolism ; Animals ; Anthozoa/*parasitology ; Carbohydrate Metabolism ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Eukaryota/*classification/cytology/genetics/*isolation &amp; purification/ultrastructure ; Fatty Acids/analysis ; Microscopy ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Sequence Analysis, DNA ; }, abstract = {Recent evidence suggests that there is a dynamic microbial biota living on the surface and in the mucus layer of many hermatypic coral species that plays an essential role in coral well-being. Most of the studies published to date emphasize the importance of prokaryotic communities associated with the coral mucus in coral health and disease. In this study, we report the presence of a protist (Fng1) in the mucus of the hermatypic coral Fungia granulosa from the Gulf of Eilat. This protist was identified morphologically and molecularly as belonging to the family Thraustochytridae (phylum Stramenopile, order Labyrinthulida), a group of heterotrophs widely distributed in the marine environment. Morphological examination of this strain revealed a nonmotile organism c. 35 mum in diameter, which is able to thrive on carbon-deprived media, and whose growth and morphology are inoculum dependent. Its fatty acid production profile revealed an array of polyunsaturated fatty acids. A similar protist was also isolated from the mucus of the coral Favia sp. In light of these findings, its possible contribution to the coral holobiont is discussed.}, }
@article {pmid18268342, year = {2008}, author = {Starcevic, A and Akthar, S and Dunlap, WC and Shick, JM and Hranueli, D and Cullum, J and Long, PF}, title = {Enzymes of the shikimic acid pathway encoded in the genome of a basal metazoan, Nematostella vectensis, have microbial origins.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {105}, number = {7}, pages = {2533-2537}, pmid = {18268342}, issn = {1091-6490}, mesh = {Animals ; Genome/*genetics ; Phylogeny ; Sea Anemones/classification/*enzymology/*genetics ; Shikimic Acid/*metabolism ; }, abstract = {The shikimic acid pathway is responsible for the biosynthesis of many aromatic compounds by a broad range of organisms, including bacteria, fungi, plants, and some protozoans. Animals are considered to lack this pathway, as evinced by their dietary requirement for shikimate-derived aromatic amino acids. We challenge the universality of this traditional view in this report of genes encoding enzymes for the shikimate pathway in an animal, the starlet sea anemone Nematostella vectensis. Molecular evidence establishes horizontal transfer of ancestral genes of the shikimic acid pathway into the N. vectensis genome from both bacterial and eukaryotic (dinoflagellate) donors. Bioinformatic analysis also reveals four genes that are closely related to those of Tenacibaculum sp. MED152, raising speculation for the existence of a previously unsuspected bacterial symbiont. Indeed, the genome of the holobiont (i.e., the entity consisting of the host and its symbionts) comprises a high content of Tenacibaculum-like gene orthologs, including a 16S rRNA sequence that establishes the phylogenetic position of this associate to be within the family Flavobacteriaceae. These results provide a complementary view for the biogenesis of shikimate-related metabolites in marine Cnidaria as a "shared metabolic adaptation" between the partners.}, }
@article {pmid18059488, year = {2008}, author = {Ainsworth, TD and Fine, M and Roff, G and Hoegh-Guldberg, O}, title = {Bacteria are not the primary cause of bleaching in the Mediterranean coral Oculina patagonica.}, journal = {The ISME journal}, volume = {2}, number = {1}, pages = {67-73}, doi = {10.1038/ismej.2007.88}, pmid = {18059488}, issn = {1751-7362}, mesh = {Animals ; Anthozoa/*microbiology/physiology/ultrastructure ; Bacterial Physiological Phenomena ; Ecosystem ; In Situ Hybridization, Fluorescence ; Israel ; Microscopy, Electron, Scanning Transmission ; Symbiosis ; Vibrio/*physiology ; }, abstract = {Coral bleaching occurs when the endosymbiosis between corals and their symbionts disintegrates during stress. Mass coral bleaching events have increased over the past 20 years and are directly correlated with periods of warm sea temperatures. However, some hypotheses have suggested that reef-building corals bleach due to infection by bacterial pathogens. The 'Bacterial Bleaching' hypothesis is based on laboratory studies of the Mediterranean invading coral, Oculina patagonica, and has further generated conclusions such as the coral probiotic hypothesis and coral hologenome theory of evolution. We aimed to investigate the natural microbial ecology of O. patagonica during the annual bleaching using fluorescence in situ hybridization to map bacterial populations within the coral tissue layers, and found that the coral bleaches on the temperate rocky reefs of the Israeli coastline without the presence of Vibrio shiloi or bacterial penetration of its tissue layers. Bacterial communities were found associated with the endolithic layer of bleached coral regions, and a community dominance shift from an apparent cyanobacterial-dominated endolithic layer to an algal-dominated layer was found in bleached coral samples. While bacterial communities certainly play important roles in coral stasis and health, we suggest environmental stressors, such as those documented with reef-building corals, are the primary triggers leading to bleaching of O. patagonica and suggest that bacterial involvement in patterns of bleaching is that of opportunistic colonization.}, }
@article {pmid18043672, year = {2007}, author = {Santiago-Vázquez, LZ and Brück, TB and Brück, WM and Duque-Alarcón, AP and McCarthy, PJ and Kerr, RG}, title = {The diversity of the bacterial communities associated with the azooxanthellate hexacoral Cirrhipathes lutkeni.}, journal = {The ISME journal}, volume = {1}, number = {7}, pages = {654-659}, doi = {10.1038/ismej.2007.77}, pmid = {18043672}, issn = {1751-7362}, mesh = {Actinobacteria/classification/genetics ; Alphaproteobacteria/classification/genetics ; Animals ; Anthozoa/*microbiology ; Bacteria/classification/*genetics/growth &amp; development ; *Biodiversity ; Chloroflexi/classification/genetics ; Cytophagaceae/classification/genetics ; Flavobacterium/classification/genetics ; Gammaproteobacteria/classification/genetics ; Genetic Variation ; In Situ Hybridization, Fluorescence ; Molecular Sequence Data ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {This study examined the symbiotic microbiota of the hexacoral Cirrhipathes lutkeni using traditional plate culture, fluorescence in situ hybridization (FISH) and 16S rDNA characterization. FISH counts for the whole coral (holobiont) showed a major presence of gamma-Proteobacteria (22%) and Actinobacteria (19%), followed by alpha-Proteobacteria (14%), Firmicutes (9%), Cytophaga-Flavobacterium (7%), beta-Proteobacteria (6%) and Chloroflexi (2%). In contrast to the diversity observed by FISH, plate cultures were found to be selective for gamma-Proteobacteria (22 cultures) with the exception of an Actinobacterium. The methods employed in this study detected 76% of all microbes estimated by DAPI staining of C. lutkeni homogenates. The absence of zooxanthellae in this particular hexacoral was confirmed by PCR and spectrophotometry using fresh tissue isolated from the holobiont. This is the first study describing the microbial associations of shallow-water hexacorallia, which opens further insight into coral microbial ecology and may enhance the search for novel natural products in the near future.}, }
@article {pmid17937669, year = {2007}, author = {Kooperman, N and Ben-Dov, E and Kramarsky-Winter, E and Barak, Z and Kushmaro, A}, title = {Coral mucus-associated bacterial communities from natural and aquarium environments.}, journal = {FEMS microbiology letters}, volume = {276}, number = {1}, pages = {106-113}, doi = {10.1111/j.1574-6968.2007.00921.x}, pmid = {17937669}, issn = {0378-1097}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/*isolation &amp; purification ; *Biodiversity ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; }, abstract = {The microbial biota dwelling in the mucus, on the surface, and in the tissues of many coral species may have an important role in holobiont physiology and health. This microbiota differs with coral species, water depth, and geographic location. Here we compare the surface mucus microbiota of the coral Fungia granulosa from the natural environment with that from individuals maintained in aquaria. Molecular analysis revealed that the microbial community of the mucus microlayer of the coral F. granulosa includes a wide range of bacteria and that these change with environment. Coral mucus from the natural environment contained a significantly higher diversity of microorganisms than did mucus from corals maintained in the closed-system aquaria. A microbial community shift, with the loss of several groups, including actinobacterial and cyanobacterial groups, was observed in corals maintained in aquaria. The most abundant bacterial class in F. granulosa mucus was the Alphaproteobacteria, regardless of whether the corals were from aquaria or freshly collected from their natural environment. A significantly higher percentage of bacteria from the Betaproteobacteria class was evident in aquarium corals (24%) when compared with corals from the natural environment (3%). The differences in mucus-inhabiting microbial communities between corals from captive and natural environments suggest an adaptation of the mucus bacterial communities to the different conditions.}, }
@article {pmid17922755, year = {2007}, author = {Wegley, L and Edwards, R and Rodriguez-Brito, B and Liu, H and Rohwer, F}, title = {Metagenomic analysis of the microbial community associated with the coral Porites astreoides.}, journal = {Environmental microbiology}, volume = {9}, number = {11}, pages = {2707-2719}, doi = {10.1111/j.1462-2920.2007.01383.x}, pmid = {17922755}, issn = {1462-2912}, mesh = {Animals ; Anthozoa/genetics/*microbiology/virology ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Carbon/metabolism ; Databases, Nucleic Acid ; *Ecosystem ; Eukaryotic Cells/classification/*physiology ; Fungi/classification/*genetics/metabolism ; *Genome ; Nitrogen/metabolism ; Oxidative Stress ; Sulfur/metabolism ; Virulence Factors/genetics ; }, abstract = {The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific; coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide diversity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs.}, }
@article {pmid17560324, year = {2007}, author = {Dunlap, WC and Battershill, CN and Liptrot, CH and Cobb, RE and Bourne, DG and Jaspars, M and Long, PF and Newman, DJ}, title = {Biomedicinals from the phytosymbionts of marine invertebrates: a molecular approach.}, journal = {Methods (San Diego, Calif.)}, volume = {42}, number = {4}, pages = {358-376}, doi = {10.1016/j.ymeth.2007.03.001}, pmid = {17560324}, issn = {1046-2023}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Biological Factors/*chemistry/genetics ; Cell Line, Tumor ; Cyanobacteria/*chemistry/genetics ; Fresh Water ; Genomics/methods ; Humans ; Marine Biology ; Mice ; Molecular Structure ; Phylogeny ; Porifera/*chemistry/genetics ; RNA, Ribosomal, 16S/*genetics ; *Symbiosis ; }, abstract = {Marine invertebrate animals such as sponges, gorgonians, tunicates and bryozoans are sources of biomedicinally relevant natural products, a small but growing number of which are advancing through clinical trials. Most metazoan and anthozoan species harbour commensal microorganisms that include prokaryotic bacteria, cyanobacteria (blue-green algae), eukaryotic microalgae, and fungi within host tissues where they reside as extra- and intra-cellular symbionts. In some sponges these associated microbes may constitute as much as 40% of the holobiont volume. There is now abundant evidence to suggest that a significant portion of the bioactive metabolites thought originally to be products of the source animal are often synthesized by their symbiotic microbiota. Several anti-cancer metabolites from marine sponges that have progressed to pre-clinical or clinical-trial phases, such as discodermolide, halichondrin B and bryostatin 1, are thought to be products derived from their microbiotic consortia. Freshwater and marine cyanobacteria are well recognised for producing numerous and structurally diverse bioactive and cytotoxic secondary metabolites suited to drug discovery. Sea sponges often contain dominant taxa-specific populations of cyanobacteria, and it is these phytosymbionts (= photosymbionts) that are considered to be the true biogenic source of a number of pharmacologically active polyketides and nonribosomally synthesized peptides produced within the sponge. Accordingly, new collections can be pre-screened in the field for the presence of phytobionts and, together with metagenomic screening using degenerate PCR primers to identify key polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes, afford a biodiscovery rationale based on the therapeutic prospects of phytochemical selection. Additionally, new cloning and biosynthetic expression strategies may provide a sustainable method for the supply of new pharmaceuticals derived from the uncultured phytosymbionts of marine organisms.}, }
@article {pmid17514404, year = {2007}, author = {Brück, TB and Brück, WM and Santiago-Vázquez, LZ and McCarthy, PJ and Kerr, RG}, title = {Diversity of the bacterial communities associated with the azooxanthellate deep water octocorals Leptogorgia minimata, Iciligorgia schrammi, and Swiftia exertia.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {9}, number = {5}, pages = {561-576}, pmid = {17514404}, issn = {1436-2228}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics/growth &amp; development/isolation &amp; purification ; Base Sequence ; *Biodiversity ; Colony Count, Microbial ; Dinoflagellida/genetics/isolation &amp; purification ; In Situ Hybridization, Fluorescence/veterinary ; Molecular Sequence Data ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {This study examined the microbiota associated with the marine azooxanthellate octocorals Leptogorgia minimata, Swiftia exertia, and Iciligorgia schrammi collected from moderate depths (45 m). Traditional aerobic plate culture, fluorescence in situ hybridization (FISH), and molecular identification of the 16S rDNA region were used for this purpose. In general, cultures were found to be selective for Gammaproteobacteria, Alphaproteobacteria, and Firmicutes. Interestingly, FISH counts for Firmicutes in the whole coral (holobiont) were near the detection limit of this assay, representing less than 6% of the total detectable microbiota in all counts. Proteobacteria, especially Alpha- and Gammaproteobacteria, made up the majority of the total microbiota in the holobionts. In addition, the absence of zooxanthellae in these three corals was confirmed by the use of polymerase chain reaction (PCR) and dinoflagellate-specific primers, and spectrophotometric chlorophyll pigment measurements. No evidence of zooxanthellae could be found in any of the corals by either of these techniques. This is the first study examining the microbiota marine octocorals, which grow at moderate depth (40 to 100 m) in the absence of direct sunlight.}, }
@article {pmid17384666, year = {2007}, author = {Rosenberg, E and Koren, O and Reshef, L and Efrony, R and Zilber-Rosenberg, I}, title = {The role of microorganisms in coral health, disease and evolution.}, journal = {Nature reviews. Microbiology}, volume = {5}, number = {5}, pages = {355-362}, doi = {10.1038/nrmicro1635}, pmid = {17384666}, issn = {1740-1534}, mesh = {*Adaptation, Physiological ; Animals ; *Anthozoa/microbiology/parasitology/ultrastructure/virology ; Aspergillus/growth &amp; development/pathogenicity ; Bacteria/growth &amp; development/*pathogenicity ; *Biological Evolution ; Dinoflagellida/growth &amp; development ; *Probiotics ; Seawater/microbiology ; *Symbiosis ; }, abstract = {Coral microbiology is an emerging field, driven largely by a desire to understand, and ultimately prevent, the worldwide destruction of coral reefs. The mucus layer, skeleton and tissues of healthy corals all contain large populations of eukaryotic algae, bacteria and archaea. These microorganisms confer benefits to their host by various mechanisms, including photosynthesis, nitrogen fixation, the provision of nutrients and infection prevention. Conversely, in conditions of environmental stress, certain microorganisms cause coral bleaching and other diseases. Recent research indicates that corals can develop resistance to specific pathogens and adapt to higher environmental temperatures. To explain these findings the coral probiotic hypothesis proposes the occurrence of a dynamic relationship between symbiotic microorganisms and corals that selects for the coral holobiont that is best suited for the prevailing environmental conditions. Generalization of the coral probiotic hypothesis has led us to propose the hologenome theory of evolution.}, }
@article {pmid17107548, year = {2006}, author = {Reshef, L and Koren, O and Loya, Y and Zilber-Rosenberg, I and Rosenberg, E}, title = {The coral probiotic hypothesis.}, journal = {Environmental microbiology}, volume = {8}, number = {12}, pages = {2068-2073}, doi = {10.1111/j.1462-2920.2006.01148.x}, pmid = {17107548}, issn = {1462-2912}, mesh = {*Adaptation, Physiological ; Animals ; Anthozoa/growth &amp; development/*microbiology ; Bacteria/growth &amp; development ; Biological Evolution ; Ecosystem ; Immunity, Innate ; *Probiotics ; Seawater/microbiology ; Symbiosis/*physiology ; }, abstract = {Emerging diseases have been responsible for the death of about 30% of corals worldwide during the last 30 years. Coral biologists have predicted that by 2050 most of the world's coral reefs will be destroyed. This prediction is based on the assumption that corals can not adapt rapidly enough to environmental stress-related conditions and emerging diseases. Our recent studies of the Vibrio shiloi/Oculina patagonica model system of the coral bleaching disease indicate that corals can indeed adapt rapidly to changing environmental conditions by altering their population of symbiotic bacteria. These studies have led us to propose the Coral Probiotic Hypothesis. This hypothesis posits that a dynamic relationship exists between symbiotic microorganisms and environmental conditions which brings about the selection of the most advantageous coral holobiont. Changing their microbial partners would allow the corals to adapt to changing environmental conditions more rapidly (days to weeks) than via mutation and selection (many years). An important outcome of the Probiotic Hypothesis would be development of resistance of the coral holobiont to diseases. The following evidence supports this hypothesis: (i) Corals contain a large and diverse bacterial population associated with their mucus and tissues; (ii) the coral-associated bacterial population undergoes a rapid change when environmental conditions are altered; and (iii) although lacking an adaptive immune system (no antibodies), corals can develop resistance to pathogens. The Coral Probiotic Hypothesis may help explain the evolutionary success of corals and moderate the predictions of their demise.}, }
@article {pmid15755882, year = {2005}, author = {Baruch, R and Avishai, N and Rabinowitz, C}, title = {UV incites diverse levels of DNA breaks in different cellular compartments of a branching coral species.}, journal = {The Journal of experimental biology}, volume = {208}, number = {Pt 5}, pages = {843-848}, doi = {10.1242/jeb.01496}, pmid = {15755882}, issn = {0022-0949}, mesh = {Animals ; Anthozoa/*genetics ; Cell Fractionation ; Comet Assay ; *DNA Damage ; Eukaryota/*genetics ; Seawater ; *Symbiosis ; *Ultraviolet Rays ; }, abstract = {This study evaluates in vitro the effects of UVB irradiation on three cellular compartments of a shallow water coral species. Coral tissues were dissociated by Ca(2+)-Mg(2+)-free artificial seawater. Cell suspensions were divided into the major cellular compartments (animal cells, algal cells, holobiont entities) by sucrose gradient and then by detergent treatments. Cell fractions were irradiated by UVB lamp (4.05, 8.1 and 12.2 kJ m(-2)) and subjected to the comet assay. UVB radiation, at levels that induced a moderate DNA breakage to the non-symbiotic coral and algal cell compartments, caused dramatic increase in DNA breakage to the holobiont entities. After a 1 h repair period, DNA breakage levels in the algal and animal cell fractions were augmented as compared with a reduction in DNA breakage in the holobiont fraction. This discordancy in DNA breakage between the three cellular compartments reveals that the holobiont cell fraction is more vulnerable to increased natural UV irradiation and associated anthropogenic genotoxic impacts, providing another possible explanation for recent increase in worldwide coral bleaching events.}, }
@article {pmid15178799, year = {2004}, author = {Little, AF and van Oppen, MJ and Willis, BL}, title = {Flexibility in algal endosymbioses shapes growth in reef corals.}, journal = {Science (New York, N.Y.)}, volume = {304}, number = {5676}, pages = {1492-1494}, doi = {10.1126/science.1095733}, pmid = {15178799}, issn = {1095-9203}, mesh = {Adaptation, Physiological ; Animals ; Anthozoa/*growth &amp; development/physiology ; Dinoflagellida/genetics/*physiology ; Ecosystem ; Environment ; Eukaryota ; Genome, Protozoan ; Larva/growth &amp; development ; Polymorphism, Single-Stranded Conformational ; *Symbiosis ; }, abstract = {The relation between corals and their algal endosymbionts has been a key to the success of scleractinian (stony) corals as modern reef-builders, but little is known about early stages in the establishment of the symbiosis. Here, we show that initial uptake of zooxanthellae by juvenile corals during natural infection is nonspecific (a potentially adaptive trait); the association is flexible and characterized by a change in (dominant) zooxanthella strains over time; and growth rates of experimentally infected coral holobionts are partly contingent on the zooxanthella strain harbored, with clade C-infected juveniles growing two to three times as fast as those infected with clade D.}, }
@article {pmid21665677, year = {2002}, author = {Jackson, RC and Ngo, N and Ngo, H}, title = {Chromosome-specific desynapsis in the n = 2 race of Haplopappus gracilis (Compositae).}, journal = {American journal of botany}, volume = {89}, number = {5}, pages = {777-782}, doi = {10.3732/ajb.89.5.777}, pmid = {21665677}, issn = {0002-9122}, abstract = {During cytological screening for pollen sterility in a wild population of Haplopappus gracilis (n = 2), several partially sterile plants were found that had good pachytene pairing but varying numbers of univalents. Some plants had chromosome A bivalents or A univalents, while in the same cells chromosome B had only bivalents. In other plants the reverse condition occurred; the B chromosome had B bivalents or B univalents and only A bivalents. This demonstrates a chromosome-specific effect for the desynapsis genes. Hybridization between the two homozygous mutant genotypes produced only normal bivalents; this indicates the two mutants are not alleles and each is recessive. An F2 generation showed independent assortment of the desynaptic mutations. The chromosome A bivalent is the larger of the two and normally has one or two chiasmata; the B bivalent normally has a single chiasma. Chiasmata distribution was tested in the desynaptic mutant A bivalents and showed an acceptable fit to a binomial distribution. This occurs also in heterozygous, asynaptic pairing control gene mutations. Analysis of the NOR bivalent in two hologenomic desynaptic mutations in tomato also showed a good fit to a binomial distribution of chiasmata. This indicates the same methods are applicable to diverse species.}, }
@article {pmid8155852, year = {1993}, author = {Jorgensen, R}, title = {The origin of land plants: a union of alga and fungus advanced by flavonoids?.}, journal = {Bio Systems}, volume = {31}, number = {2-3}, pages = {193-207}, doi = {10.1016/0303-2647(93)90049-i}, pmid = {8155852}, issn = {0303-2647}, mesh = {*Biological Evolution ; Chlorophyta/physiology ; Flavonoids/physiology ; Fungi/physiology ; Models, Biological ; Phylogeny ; *Plants/genetics/microbiology/radiation effects ; Signal Transduction ; *Symbiosis/physiology ; Ultraviolet Rays ; }, abstract = {This paper addresses the hypothesis that land plants have a biphyletic origin as the product of an endocellular mutualism between a green alga and a tip-growing, fungus-like organism, culminating in the acquisition of part of the latter's genome by the host alga (Atsatt, P.R., 1988, Are vascular plants 'inside-out' lichens? Ecology 69, 17-23). According to this hypothesis, the tip-growing symbiont's capacity for invasive growth was exploited during the further evolution of the holobiont for the development of various specialized plant cell types, but especially those displaying tip growth. Here, noting the recent discovery of the dependence of pollen tube tip growth on flavonoids, this hypothesis is refined and extended by suggesting that a symbiotic relationship was advanced by the evolution of UV-protective flavonoids in the alga, followed by the evolution of a growth response by the tip-growing symbiont to the presence of those flavonoids, allowing the symbiont to continue to live with the alga in its new, high-light habitat. This growth response then evolved into a dependence on flavonoids in the context of an obligate, mutualistic relationship progressing toward endosymbiosis and incorporation of the endocytobiont's genetic capacity for cell polarization, tip growth and their control into the host alga's genome. Land plants and advanced charophycean algae (which are the closest green-algal relatives of land plants) are likely products of this process, while a primitive charophycean alga (lacking both tip growth and cell polarization) is proposed to have been the likely host for the endocytobiont. A series of tests of this hypothesis, based mainly on the identification and molecular phylogenetic analysis of appropriate genes, are proposed. Whether the endocytobiont could have been a relative of the earliest endomycorrhizal fungi is assessed.}, }
@article {pmid8155845, year = {1993}, author = {Zrzavý, J and Skála, Z}, title = {Holobionts, hybrids, and cladistic classification.}, journal = {Bio Systems}, volume = {31}, number = {2-3}, pages = {127-30; discussion 130-3}, doi = {10.1016/0303-2647(93)90040-j}, pmid = {8155845}, issn = {0303-2647}, mesh = {Biological Evolution ; Classification ; Hybridization, Genetic ; Models, Genetic ; *Phylogeny ; Symbiosis/*genetics ; }, abstract = {David P. Mindell assumes that incorporation of the holobionts (evolutionarily stable symbiotic complexes) and hybrids into phylogenetic trees necessarily distorts the hierarchical structure of cladistic classification, and must lead to reformulation of some basic cladistic concepts (BioSystems, 27, 53-62, 1992). He does not regard the Eukarya and Eubacteria as monophyletic taxa, the former being 'polyphyletic', the latter 'paraphyletic'. We attempt to show that the existence of holobionts/hybrids is not a cladistic problem. Cladistics is a systematic methodology, not a system of evolutionary hypotheses; cladograms are statements about distribution of shared characters (synapomorphies) and, consequently, the cladograms are always branching and hierarchically structured. A taxon is monophyletic if it has a single root in the cladogram, not a single ancestor 'in reality'. Cladistic methodology does not provide a clue for distinguishing whether a conflicting distribution of the potential synapomorphies is due to reticulation (e.g., symbiogenesis) or convergent evolution. Consequently, both Eubacteria and Eukarya either are or are not monophyletic taxa if they are or are not determined to be so during cladistic analysis.}, }
@article {pmid1391691, year = {1992}, author = {Mindell, DP}, title = {Phylogenetic consequences of symbioses: Eukarya and Eubacteria are not monophyletic taxa.}, journal = {Bio Systems}, volume = {27}, number = {1}, pages = {53-62}, doi = {10.1016/0303-2647(92)90046-2}, pmid = {1391691}, issn = {0303-2647}, mesh = {Animal Population Groups/*genetics ; Animals ; Archaea/*classification ; Bacteria/*classification ; Fungi/*classification ; *Phylogeny ; Plants/*classification ; *Symbiosis ; }, abstract = {In the past systematists have not been concerned with distinguishing the different phylogenetic histories for symbiont taxa that have merged within a composite taxon, or holobiont. I suggest that symbionts can retain their status as discrete taxa and that their independent histories can be included in phylogenetic analyses intending to discover monophyletic groups. Use of reticulate branches to include independent histories for different symbionts, incorporates our improving understanding of evolution and provides greater accuracy in denoting monophyletic groups. In an expanded view, a monophyletic group includes only and all the descendants of the merged-symbionts' common ancestor. Holobiont taxa will have constituent symbionts included in different monophyletic groups and there will be a reduction in the number of monophyletic groups recognized, particularly at higher taxonomic levels. As a consequence of considering symbioses in phylogenetic analyses, the proposed taxa Eubacteria and Eukarya are seen to be non-monophyletic, and, thus, poor indicators of evolutionary history.}, }
@article {pmid24247535, year = {1986}, author = {Jackson, RC and Murray, BG}, title = {Quantitative analysis of diploid translocation heterozygotes: test of models and equations.}, journal = {TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik}, volume = {71}, number = {4}, pages = {600-606}, pmid = {24247535}, issn = {0040-5752}, abstract = {Equations have been derived for two different models of chromosome pairing and chiasmata distribution. The first model represents the normal condition and assumes complete synapsis of homologous bivalents and the arms of interchange quadrivalents. This is followed by a nonrandom distribution of chiasmata among bivalents and multivalents such that each bivalent or bivalent-equivalent always has at least one chiasma. Univalents occur only as part of a III, I configuration at diakinesis or metaphase I. The second model assumes that a hologenomic mutation is present in which all chromosomes of a genome are equally affected. Two different assumptions can be made for such a mutation, and both give the same results: (1) homologous or homoeologous chromosome arms may be randomly paired or unpaired, but synapsis always leads to a crossover; (2) homologous or homoeologous arms always pair, but chiasmata are randomly distributed among the arms. The meiotic configurations at diakinesis or metaphase I are the same for both assumptions. Meiotic configurations of normal diploid interchange heterozygotes show good agreement with numbers predicted by the equations for nonrandom chiasmata distribution among configurations. Inter-specific hybrids with supernumerary chromosomes produced meiotic configurations frequencies in agreement with predictions of equations for random chiasmata distribution, but a hybrid without supernumeraries fitted the nonrandom expectations.}, }