@article {pmid34570392, year = {2021}, author = {Florez, JZ and Camus, C and Hengst, MB and Buschmann, AH}, title = {A mesocosm study on kelp (Macrocystis pyrifera)-epiphytic bacteria interactions: Importance of nitrogen availability and kelp genetics.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.13213}, pmid = {34570392}, issn = {1529-8817}, abstract = {Macroalgal holobiont studies involve understanding interaction among the host, its microbiota and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically-distinct populations of 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 = {2021}, 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 = {}, number = {}, pages = {}, 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/ ; }, 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 = {2021}, 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 = {}, number = {}, pages = {}, pmid = {34561754}, issn = {1432-184X}, 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 {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 = {}, number = {}, pages = {e0157721}, doi = {10.1128/mBio.01577-21}, pmid = {34519538}, issn = {2150-7511}, 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 {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}, doi = {10.1016/j.csbj.2021.08.035}, 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}, doi = {10.1371/journal.pone.0256284}, pmid = {34495983}, issn = {1932-6203}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15758}, pmid = {34490980}, issn = {1462-2920}, abstract = {In a 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 firstly 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, DMSP), 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) but also in response to changing microbiota (e.g. chemical defenses). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments. This article is protected by copyright. All rights reserved.}, }
@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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15764}, pmid = {34490977}, issn = {1462-2920}, 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 correlate 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. This article is protected by copyright. All rights reserved.}, }
@article {pmid34481401, year = {2021}, 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}, 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 {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 = {}, number = {}, pages = {}, doi = {10.1111/mec.16163}, pmid = {34473860}, issn = {1365-294X}, 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 fulfill 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 García Guerreiro, MP 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 = {}, number = {}, pages = {}, doi = {10.1093/molbev/msab259}, pmid = {34469576}, issn = {1537-1719}, abstract = {Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, 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 dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. 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 dataset. Our resource will enable population geneticists to analyze spatio-temporal 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}, doi = {10.1002/mbo3.1217}, pmid = {34459547}, issn = {2045-8827}, support = {//Egyptian Ministry of Higher Education &amp; Scientific Research/ ; //Helmholtz Centre for Environmental Research/ ; }, 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 = {}, doi = {10.3390/microorganisms9081730}, 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 = {}, doi = {10.3390/microorganisms9081552}, 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 {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 = {}, number = {}, pages = {e0073421}, doi = {10.1128/mSystems.00734-21}, pmid = {34427504}, issn = {2379-5077}, 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 = {}, number = {}, pages = {e0084121}, doi = {10.1128/mSystems.00841-21}, pmid = {34427502}, issn = {2379-5077}, 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}, 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 {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}, doi = {10.3389/fmicb.2021.702763}, 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}, doi = {10.3389/fmicb.2021.709184}, pmid = {34394058}, issn = {1664-302X}, }
@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}, 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}, 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}, doi = {10.3389/fmicb.2021.649858}, 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 = {}, doi = {10.3390/microorganisms9071462}, 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 {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}, doi = {10.3389/fmicb.2021.666510}, 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 = {}, number = {}, pages = {}, doi = {10.1111/mec.16064}, pmid = {34342082}, issn = {1365-294X}, support = {433042944//Deutsche Forschungsgemeinschaft/ ; 458901010//Deutsche Forschungsgemeinschaft/ ; //Paul G. Allen Family Foundation/ ; 2016403//BiNational Science Foundation grant/ ; //WOA Institution: UNIVERSITAET KONSTANZ/ ; //Blended DEAL: Projekt DEAL/ ; }, 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 = {2021}, 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 = {}, number = {}, pages = {}, pmid = {34331071}, issn = {1432-184X}, 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}, doi = {10.3389/fpls.2021.688533}, 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 {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 15N2 tracer technique), the diazotrophic bacterial community (using nifH gene amplicon sequencing) and the natural δ15N 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 δ15N 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}, 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 = {}, number = {}, pages = {106277}, doi = {10.1016/j.mimet.2021.106277}, pmid = {34237402}, issn = {1872-8359}, 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 = {2021}, author = {Glaze, TD and Erler, DV and Siljanen, HMP}, title = {Microbially facilitated nitrogen cycling in tropical corals.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {34226659}, issn = {1751-7370}, 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}, 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 = {2021}, 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 = {}, number = {}, pages = {}, pmid = {34218251}, issn = {1751-7370}, support = {QMSR- MRRD-MEC-295-1449//Department of Science and Technology (DOST)/ ; }, 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 = {}, doi = {10.3390/microorganisms9071359}, 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/ ; }, 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/ ; }, 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 = {}, number = {}, pages = {}, doi = {10.1111/evo.14301}, pmid = {34192342}, issn = {1558-5646}, 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, are 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. This article is protected by copyright. All rights reserved.}, }
@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/ ; }, 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 {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 drivers1.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.13194}, pmid = {34176151}, issn = {1529-8817}, 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, BurkholderiaCaballeroniaParaburkholderia_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-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM).}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15642}, pmid = {34159693}, issn = {1462-2920}, support = {715513//H2020 European Research Council/ ; }, 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}, doi = {10.1128/mSystems.01249-20}, pmid = {34156291}, issn = {2379-5077}, support = {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)/ ; UIDB/04565/2020//UNL | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; }, 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}, 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 = {}, number = {}, pages = {}, doi = {10.1111/php.13474}, pmid = {34152600}, issn = {1751-1097}, 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-oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 495 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 = {}, number = {}, pages = {}, doi = {10.1152/ajpheart.00225.2021}, pmid = {34142885}, issn = {1522-1539}, support = {K99HL151889//Foundation for the National Institutes of Health (FNIH)/ ; R00GM118885//Foundation for the National Institutes of Health (FNIH)/ ; R01HL149762//Foundation for the National Institutes of Health (FNIH)/ ; 2018/14815-0//The Sao Paulo Research Foundation (FAPESP)/ ; 2013/08216-2//The Sao Paulo Research Foundation/ ; }, 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 crosstalk 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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15647}, pmid = {34139059}, issn = {1462-2920}, support = {841317//European Union's Horizon 2020/ ; }, 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 {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 = {}, number = {}, pages = {}, doi = {10.1093/bbb/zbab106}, pmid = {34113972}, issn = {1347-6947}, 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}, 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 {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 (13C) and nitrate (15N) 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/ ; }, 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 . 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}, 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}, 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 = {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 = 326, ~ 55% of protein coding genes) than between the corresponding Sodalis isolates (n = 235, ~ 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}, 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 {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}, 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 {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 {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 = {}, number = {}, pages = {}, 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 Éirinn)/ ; }, }
@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 °C). One hundred twelve (Pocillopora sp.) and 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 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 {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 = {//doctoral program 'Biointeractions from basics to application' (BioApp) at the University of Innsbruck./ ; }, 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}, 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 = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuab022}, pmid = {33930136}, issn = {1574-6976}, abstract = {Genetic variation in holobionts, (host and microbiome), occurring by changes in both host and microbiome genomes, can be observed from two perspectives: observable variations and the processes that bring about the variation. The observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotic organisms. 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. The result being that, the human gut microbiome, for example, contains 1,000 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, which bring in multiple genes in one step, (2) amplification/reduction of certain microbes in the microbiome, that contribute to holobiont` s adaptation to changing conditions, (3) horizontal gene transfer between microbes and between microbes and host, (4) mutation, which plays an important role in optimizing interactions between different 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, thus a greater chance of vertical transmission and a greater effect of microbiome on evolution of host than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.}, }
@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}, support = {//Canadian Associates of Bermuda Institute of Ocean Sciences/ ; //Bermuda Institute of Ocean Sciences/ ; CP-078ER-17//National Geographic Society/ ; //Heising-Simons Foundation International, LTD/ ; }, 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 {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}, 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 α-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 = {}, number = {}, pages = {}, 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 Tübingen/ ; //European Research Council (ERC)/ ; ERC-2018-COG 820124//DeCoCt research progra/ ; }, 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 ∼104 and ∼105 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 {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}, support = {281125614/GRK 2220//Deutsche Forschungsgemeinschaft/ ; BA 5808/2-1//Deutsche Forschungsgemeinschaft/ ; 851004//ERC Starting Grant Local Knowledge/ ; }, 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 {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 {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 = {2021}, 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 = {}, number = {}, pages = {}, pmid = {33758981}, issn = {1432-184X}, support = {11268//Ministério da Ciência, Tecnologia, Inovações e Comunicações/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.301758/2018-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, 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}, support = {//Australian Research Council/ ; //Betty and Gordon Moore Foundation/ ; }, 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.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.13169}, pmid = {33749821}, issn = {1529-8817}, support = {//Hakai Postdoctoral fellowship/ ; //UBC Four Year Doctoral Fellowship/ ; //Tula Foundation/ ; }, 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}, 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 {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 {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}, doi = {10.1016/j.cell.2021.02.009}, pmid = {33705688}, issn = {1097-4172}, 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 {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}, support = {281361126/GRK2223//Deutsche Forschungsgemeinschaft/ ; VWZN2889/3215/3266//Federal State of Lower Saxony, Nieders chsisches Vorab CDiff and CDInfect/ ; FEDER18-1264962//Junta de Andalucía - Universidad de Sevilla/ ; RTI2018-096936-J-I00//Ministerio de Ciencia e Innovación/ ; }, 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//Grantová agentura České republiky (GAČR)/ ; 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 {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}, 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}, 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 ; }, 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 {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 13C- and 15N-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 13C and 15N 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 = {}, number = {}, pages = {}, pmid = {33576852}, issn = {1432-184X}, support = {41876192//National Natural Science Foundation of China/ ; }, 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}, 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 = {212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1//Biotechnology and Biological Sciences Research Council (GB)/ ; E3//Research England/ ; 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 = {R01 DK117144/DK/NIDDK 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 PPARγ 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 {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}, 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}, 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 ; }, 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 analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 108 16S rRNA gene copies ng-1 DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure 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 clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes 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, 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 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}, support = {N00014-00-1-0609//Office of Naval Research/ ; }, 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//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 301436/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, 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 {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 {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 M Rosales, S 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}, 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 δ15N 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}, 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 = {2021}, author = {Miquel, PA and Hwang, SY}, title = {On biological individuation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, pmid = {33389691}, issn = {1611-7530}, 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 {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 15N-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 {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 {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 = {DEB 1737869//National Science Foundation/ ; R01GM098856//National Institute for Health Research/ ; }, 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}, 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 {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}, 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}, 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}, support = {KGM4572013//Korea Research Institute of Bioscience and Biotechnology/ ; Genome Technology to Business Translation Program//Ministry of Agriculture, Food and Rural Affairs/ ; HGUARD_2013M3A6B2078954//Ministry of Science, ICT and Future Planning/ ; NRF-2020M3E9A1111636//the National Research Foundation of Korea/ ; }, 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}, doi = {10.1007/978-3-030-51849-3_21}, 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}, doi = {10.1007/978-3-030-51849-3_7}, 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 {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 km2 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 (δ13C) 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}, support = {//King Abdullah University of Science and Technology/ ; }, 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 = {1051-0761}, 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}, 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 13C-citrulline decreases as 13C-arginine increases, consistent with the use of exogenous citrulline for arginine synthesis. In contrast, 13C-citrulline accumulates in larvae as 13C-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 phyla1-10 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 {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 {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}, 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/ ; }, 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 {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 P CO2 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 P CO2) 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 P CO2 on a coral-algal symbiosis (Pocillopora acuta-Symbiodiniaceae) are mediated by light and/or temperature levels. In a 39 day experiment, elevated P CO2 (962 versus 431 µatm P CO2) 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-P CO2 and high-light conditions. Light-enhanced dark respiration increased under elevated P CO2 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 P CO2 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 {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 cm2) 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 {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 Científico e Tecnológico (CNPq)/International ; 140840/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/International ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/International ; E-26/203.320/2017//Fundação de Amparo à 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, É 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 {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 = {//Muséum national d'Histoire naturelle/ ; //Sorbonne-Université (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 (δ13 C and δ15 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 {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 {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//Grantová Agentura České Republiky/ ; CLU-2018-04//Junta de Castilla y León (ES)/ ; }, 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 12137T 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 IA7T as the novel species Arthrobacter ipsi sp. nov. (type strain IA7T = CECT 30100T = LMG 31782T) 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}, doi = {10.1080/21655979.2020.1816788}, pmid = {32881650}, issn = {2165-5987}, 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 {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 Científico e Tecnológico/ ; 304477/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.341847/2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; E-26/203.320/2017//Fundação de Amparo à 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 {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 Innovación/ ; AGL2016-78662R//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, 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 {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}, 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}, doi = {10.1111/nph.16867}, 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}, 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 (TPC4.2)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; //DFG CRC 1182/ ; }, 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}, 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//Università 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 {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}, 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}, 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 - Université 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}, 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 {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}, 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 {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 ; }, 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 {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 ; Environmental DNA/*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 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 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 {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 ; }, }
@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 {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 {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}, 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 {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 Economía y Competitividad/International ; FFU16/02570//Ministerio de Educación, 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 ; }, 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 {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}, 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 {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 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.IMPORTANCE Mycale 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 {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 {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 {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}, doi = {10.1007/978-3-030-34025-4_5}, 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}, 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 {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 Economía 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 1HNMR 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 {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 = {}, number = {}, pages = {}, 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 {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° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °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 suggests high physiological plasticity to support holobiont productivity 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 with the SML across sites may contribute to holobiont function and broaden the ecological 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 {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 {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‐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 {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 [1-13C]-pyruvate and [2,3-13C]-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 13CO2 enhanced host tissue 13C-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 {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}, 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 HL143082/HL/NHLBI NIH HHS/United States ; R01 CA219144/CA/NCI 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 ; Phaeophyta/*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 ; Urodela/*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)//Fundação para a Ciência e a Tecnologia/International ; PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017).//Fundação para a Ciência e a Tecnologia/International ; UID/Multi/04423/2019//Fundação para a Ciência 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 15N- and 13C-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 {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 {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}, doi = {10.1152/physiolgenomics.00089.2019}, pmid = {31762410}, issn = {1531-2267}, 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 {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 β-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 invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 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 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 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 (> 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 {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 {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 {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}, doi = {10.1038/s41564-019-0532-4}, 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 change1. 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 health2,3. 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 V4 over the V1 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 {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 15N2 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 {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 {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 UNitrosopumilus hexadellus," "Candidatus UNitrosopumilus detritiferus," and "Candidatus UCenporiarchaeum 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 UCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "Ca UNitrosopumilus detritiferus" and "Ca UNitrosopumilus 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 Euphyllia paradivisa 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 supérieure/ ; //Centre National de la Recherche Scientifique/ ; PANDA/ERC_/European Research Council/International ; /ERC_/European Research Council/International ; //École Normale Supérieure/ ; }, 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. δ15N and δ13C 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 δ15N 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 {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 {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 (R2 = 0.66) than to the adult microbiota (R2 = 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, ÁT 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 {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//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 23038.002486/2018-26//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Programa de Excelência Acadêmica/ ; 304477/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 140840/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível 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 = {}, number = {}, pages = {}, 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 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 {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 {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 {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//Niedersächsisches Ministerium für Wissenschaft und Kultur/ ; Starting Grant//Georg-August-Universität Göttingen/ ; }, 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 {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}, 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 {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 13C-assimilation in Symbiodinium, but increased 13C-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 13C-turnover in Symbiodinium, but did not impact host 13C-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 9T 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 9T (ATCC 43555T), 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 (105 and 104 of bacterial 16S rRNA and fungal ITS copies per gram of sand to up to 108 and 107 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 13C 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 13C-labelled glucose and reduced abundance and diversity of 13C-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 13C-labelled scyllo-inositol, a potential interpartner signalling molecule in symbiosis specificity. 13C-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//Grantová Agentura České Republiky/International ; 15-13265S//Grantová Agentura České Republiky/International ; 16-20049S//Grantová Agentura České Republiky/International ; 16-23773S//Grantová Agentura České 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//Jóven 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 {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//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 {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: 41st 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 {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 = 0·001) and Faith's PD (P = 0·004). Flowers and fruit hosted distinct bacterial community structures (R2 = 0·27, P = 0·001), with specific taxonomic differences in taxa that included the Xanthomonadaceae (higher in flowers), and the Pseudomonadaceae, Methylobacteriaceae and Rhizobiales (higher in fruit) (FDR-P < 0·05). Bacterial community profiles of netted plants were overall statistically similar to non-netted plants for both flowers and fruit (P > 0·10). However, less variation between samples was observed among flowers (~50% less, P = 0·004) and green fruit (~10% less, P = 0·038) 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 (δ13C and δ15N) 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 δ13C and δ15N 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 d13C compared to the E-NE side. In 2013, SI signatures of sponges did not differ between the two sides and were overall lighter in δ13C and δ15N 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): δ13C -24.9‰, δ15N +4.3‰) and benthic-derived food (macroalgae: δ13C -15.4‰, δ15N +0.8‰). Enriched δ13C 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 δ13C and δ15N in sponges in October 2013 compared to October 2011 concurred with significantly elevated POM concentrations. The contemporaneous decrease in δ15N suggests that sponges obtain their N mostly from benthic-derived food with a lower δ15N 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 δ13C and 3‰ ± sd 0.5 for δ15N 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 Jagielloński 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 = {Lycopersicon esculentum/*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 {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 = {}, number = {}, pages = {}, 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 {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 {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, JÉ and Huang, C and Liao, Q and Braga Gomes, P and Daniel Pérez, C and de Brandão Prieto-da-Silva, ÁR 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 {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 = {Th