@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}, doi = {10.3389/fpls.2019.01626}, 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 = {}, doi = {10.1128/mBio.01019-19}, pmid = {31964724}, issn = {2150-7511}, 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 = {2020}, 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 = {}, number = {}, pages = {}, doi = {10.1093/femsle/fnaa014}, pmid = {31960895}, issn = {1574-6968}, 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 = {2019}, 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}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14918}, pmid = {31943674}, issn = {1462-2920}, 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. This article is protected by copyright. All rights reserved.}, }
@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}, support = {200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, 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 = {}, doi = {10.3390/microorganisms8010038}, 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 (Solanumlycopersicum) 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)/ ; }, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14900}, pmid = {31849163}, issn = {1462-2920}, support = {DP170104634//Australian Research Council/ ; DP190103714//Australian Research Council/ ; }, 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}, 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 = {2019}, 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 = {}, number = {}, pages = {106633}, doi = {10.1016/j.vph.2019.106633}, pmid = {31843471}, issn = {1879-3649}, support = {R00 GM118885/GM/NIGMS NIH HHS/United States ; }, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiz201}, pmid = {31841144}, issn = {1574-6941}, 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 which 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}, 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}, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, 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 = {}, doi = {10.3390/microorganisms7120635}, pmid = {31801294}, issn = {2076-2607}, support = {PTDC/BIA-BMA/29985/2017 (POCI-01-0145-FEDER-029985)//Fundação para a Ciência e a Tecnologia/ ; PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017).//Fundação para a Ciência e a Tecnologia/ ; UID/Multi/04423/2019//Fundação para a Ciência e a Tecnologia/ ; }, 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}, 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}, doi = {10.1002/ece3.5749}, 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}, support = {DFG Schi-277/26//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG Schi-277/27//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DFG Schi-277/29//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, 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}, 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}, 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}, 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}, 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}, 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/ ; }, 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 ; 1541511//Division of Environmental Biology/ ; 1651908//Division of Environmental Biology/ ; R15HG010409/GM/NIGMS NIH HHS/United States ; R15HG010409/GF/NIH HHS/United States ; }, 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 &quot;omics&quot; 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 = {2019}, 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 = {}, number = {}, pages = {}, 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/ ; }, 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}, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1111/gcb.14907}, pmid = {31692206}, issn = {1365-2486}, support = {//Labex CORAIL/ ; //IFREMER/ ; }, 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 &quot;hologenome&quot; 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}, 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}, support = {2017M620271//China Postdoctoral Fund/ ; NSFC 31661143029//Projects of International Cooperation and Exchanges/ ; 8730037//Collaborative Research Fund/ ; 2016YFA0601202//National Key Research and Development Program of China (973 program)/ ; 2017YFC1404302//National Key Research and Development Program of China (973 program)/ ; }, 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}, 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}, 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}, 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}, support = {//Mote Marine Laboratory/ ; //Smithsonian Institution/ ; //Faculty of Arts and Sciences, Harvard University/ ; //Museum of Comparative Zoology, Harvard University/ ; }, 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}, 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}, 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}, support = {//Swarthmore College Faculty Research Grant/ ; }, 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}, 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}, 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 &quot;-omics&quot; complexity of coral reef holobionts across the Pacific Ocean.}, journal = {PLoS biology}, volume = {17}, number = {9}, pages = {e3000483}, pmid = {31545807}, issn = {1545-7885}, 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 &quot;-omics&quot; 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}, support = {//UNESCO-L'Oreal For Women in Science Fellowship/ ; P-16-50720//National Science and Technology Development Agency/ ; }, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1007/s10441-019-09364-w}, pmid = {31541308}, issn = {1572-8358}, abstract = {Individuation and organization in complex living multi-level ecosystem occurs as dynamical processes from early ontogeny. The notion of living &quot;holon&quot; 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 &quot;Immunoception&quot; 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}, doi = {10.15698/mic2019.09.689}, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1038/s41437-019-0266-3}, pmid = {31527783}, issn = {1365-2540}, support = {ANR-12-ADAP-0016//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-12-ADAP-0016//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-12-ADAP-0016//Agence Nationale de la Recherche (French National Research Agency)/ ; }, 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}, doi = {10.1186/s40168-019-0743-1}, pmid = {31521200}, issn = {2049-2618}, support = {CRC 1182//Deutsche Forschungsgemeinschaft/ ; }, 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 &quot;metaorganisms.&quot; The goal of the Collaborative Research Center &quot;Origin and Function of Metaorganisms&quot; 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 = {102532/Z/12/Z//Wellcome Trust/International ; MC-A654-5QC80//Medical Research Council/United Kingdom ; }, 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}, doi = {10.3389/fmicb.2019.01860}, 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}, doi = {10.1186/s40168-019-0739-x}, pmid = {31466521}, issn = {2049-2618}, support = {OCE-1558580//Division of Ocean Sciences/ ; }, 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}, doi = {10.3389/fmicb.2019.01693}, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1016/j.pbiomolbio.2019.08.006}, pmid = {31415772}, issn = {1873-1732}, 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 = {}, doi = {10.1128/mSystems.00288-19}, 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 &quot;CandidatusUNitrosopumilus hexadellus,&quot; &quot;CandidatusUNitrosopumilus detritiferus,&quot; and &quot;CandidatusUCenporiarchaeum stylissum&quot; (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that &quot;CaUCenporiarchaeum stylissum&quot; has been exclusively detected in sponges and can hence be classified as a specialist, while &quot;CaUNitrosopumilus detritiferus&quot; and &quot;CaUNitrosopumilus hexadellus&quot; 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 = {}, doi = {10.3390/jcm8081206}, pmid = {31409048}, issn = {2077-0383}, abstract = {Billions of microorganisms, or &quot;microbiota&quot;, 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 &quot;microbiome&quot; 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 = {}, doi = {10.3390/microorganisms7080256}, pmid = {31409030}, issn = {2076-2607}, abstract = {The profound mutualistic symbiosis between corals and their endosymbiotic counterparts, Symbiodiniaceae algae, has been threatened by the increase in seawater temperatures, leading to breakdown of the symbiotic relationship-coral bleaching. To characterize the heat-stress response of the holobiont, we generated vital apo-symbiotic Euphylliaparadivisa corals that lacked the endosymbiotic algae. Using RNA sequencing, we analyzed the gene expression of these apo-symbionts vs. symbiotic ones, to test the effect of the algal presence on the tolerance of the coral. We utilized literature-derived lists of &quot;symbiosis differentially expressed genes&quot; and &quot;coral heat-stress genes&quot; 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}, doi = {10.3389/fpls.2019.00922}, 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}, doi = {10.3389/fmicb.2019.01702}, 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 &quot;Social&quot; 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 ; }, 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 = {2019}, author = {Carrasco, J and Preston, GM}, title = {Growing edible mushrooms: a conversation between bacteria and fungi.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.14765}, pmid = {31361932}, issn = {1462-2920}, support = {742966//European Union's Horizon 2020/ ; }, 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}, doi = {10.1016/j.jare.2019.04.008}, 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}, doi = {10.1016/j.jare.2019.04.007}, 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/ ; }, 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}, 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}, 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/ ; }, 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}, 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 = {2019}, 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 = {}, number = {}, pages = {}, doi = {10.1007/s00248-019-01410-x}, pmid = {31312870}, issn = {1432-184X}, support = {NA14OAR4170071//Hawai'i Sea Grant, University of Hawai'i/ ; }, 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}, doi = {10.1098/rsos.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}, doi = {10.1098/rspb.2019.0882}, pmid = {31311470}, issn = {1471-2954}, 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}, doi = {10.1038/s41467-019-10969-5}, 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}, 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}, 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}, doi = {10.1098/rstb.2018.0546}, pmid = {31203761}, issn = {1471-2970}, 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/ ; }, 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 &quot;chronobiological individuals&quot; should include &quot;a holobiont&quot; 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}, 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}, doi = {10.1186/s40168-019-0697-3}, pmid = {31182168}, issn = {2049-2618}, abstract = {BACKGROUND: Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved &quot;core microbiomes&quot; 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}, doi = {10.1007/s12033-019-00187-1}, 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 ; }, 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 &quot;Anna Karenina Principle&quot; for Bacterial Microbiomes.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {975}, doi = {10.3389/fmicb.2019.00975}, 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}, 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 = {}, doi = {10.3390/biology8020041}, 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 &quot;Experiments&quot; 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}, doi = {10.1002/bies.201800256}, pmid = {31099411}, issn = {1521-1878}, support = {R37 AI050661/AI/NIAID NIH HHS/United States ; P01 GM125576/GM/NIGMS NIH HHS/United States ; P50 GM098911/GM/NIGMS NIH HHS/United States ; }, 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 = {}, doi = {10.1128/mBio.00355-19}, 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 &quot;human-specific-baseline.&quot; 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}, 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}, doi = {10.3389/fmicb.2019.00717}, 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}, doi = {10.1038/s41396-019-0413-0}, pmid = {31015561}, issn = {1751-7370}, 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 = {}, doi = {10.7554/eLife.47626}, pmid = {30994455}, issn = {2050-084X}, 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}, doi = {10.3389/fmicb.2019.00550}, 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}, doi = {10.1007/s00284-019-01684-x}, 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}, doi = {10.1098/rspb.2018.1887}, pmid = {30963929}, issn = {1471-2954}, 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 = {}, doi = {10.1128/mSystems.00213-18}, 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}, doi = {10.1002/ece3.4959}, 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}, 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}, doi = {10.3389/fmicb.2019.00346}, 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}, doi = {10.1007/s11306-018-1401-5}, 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}, 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}, doi = {10.3389/fmicb.2019.00173}, 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}, doi = {10.7717/peerj.6377}, 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}, 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}, doi = {10.1186/s12864-019-5456-0}, 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 = {}, doi = {10.5041/RMMJ.10359}, 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}, doi = {10.1038/s41598-018-37062-z}, pmid = {30718608}, issn = {2045-2322}, 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 = {}, doi = {10.3390/microorganisms7020037}, 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 (Dactylisglomerata L., Festucarubra L. and Loliumperenne 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}, doi = {10.1002/ece3.4756}, 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 (FST = 0.046) and among corals harboring alternative symbiont clades (FST = 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}, doi = {10.7150/jgen.30559}, 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}, doi = {10.1186/s40168-019-0619-4}, 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 &quot;Host-microbiota interactions: from holobiont theory to analysis,&quot; 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 (&quot;detox&quot;). 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}, doi = {10.3389/fphys.2018.01836}, 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}, doi = {10.1007/s00248-018-01315-1}, 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}, doi = {10.1186/s12864-018-5377-3}, 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}, doi = {10.1002/ece3.4678}, 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}, doi = {10.1159/000495115}, pmid = {30566939}, issn = {1662-8128}, 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}, doi = {10.3389/fped.2018.00373}, 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}, doi = {10.3389/fmicb.2018.02959}, 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}, doi = {10.1038/s41396-018-0327-2}, 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}, 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 &quot;phylosymbiosis.&quot; 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}, doi = {10.1007/s00248-018-1285-y}, 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 &quot;holobiont&quot;. 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 &quot;hologenome&quot;, 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 &quot;iron tug-of-war&quot; 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 &quot;friend&quot; 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}, doi = {10.1111/1751-7915.13325}, 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}, doi = {10.1038/s41396-018-0286-7}, 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., &quot;environmentally responsive community,&quot; &quot;resident or individual microbiome,&quot; and &quot;core microbiome&quot;). 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 (&quot;species-specific microbiome&quot;) (∼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}, doi = {10.1007/s00248-018-1255-4}, 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 &quot;hologenome&quot; 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 &quot;early&quot; 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 ; }, 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 &quot;post-paleo&quot; 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 &quot;holistic view&quot; 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 &quot;systems theory of biology&quot; 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 &quot;variable/core&quot; 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}, doi = {10.1007/s00248-018-1201-5}, pmid = {29766224}, issn = {1432-184X}, support = {Doctoral Grant (Convocatoria 528-2011)//Colciencias-Colfuturo/ ; Projects (2012-2014 and 2015-2017//EcosNord-Colciencias/ ; }, mesh = {Animals ; Archaea/*classification/genetics/isolation &amp; purification/physiology ; Bacteria ; Betaproteobacteria/*classification/genetics/isolation &amp; purification/physiology ; DNA, Archaeal/analysis ; DNA, Bacterial/analysis ; France ; Haliclona/*microbiology ; Mediterranean Sea ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Water Microbiology ; }, abstract = {Sponges harbor characteristic microbiomes derived from symbiotic relationships shaping their lifestyle and survival. Haliclona fulva is encrusting marine sponge species dwelling in coralligenous accretions or semidark caves of the Mediterranean Sea and the near Atlantic Ocean. In this work, we characterized the abundance and core microbial community composition found in specimens of H. fulva by means of electron microscopy and 16S amplicon Illumina sequencing. We provide evidence of its low microbial abundance (LMA) nature. We found that the H. fulva core microbiome is dominated by sequences belonging to the orders Nitrosomonadales and Cenarchaeales. Seventy percent of the reads assigned to these phylotypes grouped in a very small number of high-frequency operational taxonomic units, representing niche-specific species Cenarchaeum symbiosum and uncultured Betaproteobacteria HF1, a new eubacterial ribotype variant found in H. fulva. The microbial composition of H. fulva is quite distinct from those reported in sponge species of the same Haliclona genus. We also detected evidence of an excretion/capturing loop between these abundant microorganisms and planktonic microbes by analyzing shifts in seawater planktonic microbial content exposed to healthy sponge specimens maintained in aquaria. Our results suggest that horizontal transmission is very likely the main mechanism for symbionts' acquisition by H. fulva. So far, this is the first shallow water sponge species harboring such a specific and predominant assemblage composed of these eubacterial and archaeal ribotypes. Our data suggests that this symbiotic relationship is very stable over time, indicating that the identified core microbial symbionts may play key roles in the holobiont functioning.}, }
@article {pmid29765310, year = {2018}, author = {Houdek, P}, title = {Economic Holobiont: Influence of Parasites, Microbiota and Chemosignals on Economic Behavior.}, journal = {Frontiers in behavioral neuroscience}, volume = {12}, number = {}, pages = {77}, pmid = {29765310}, issn = {1662-5153}, abstract = {The article is a perspective on utilization of microorganisms and chemosignals in studying human economic behavior. Research in biological roots of economic development has already confirmed that parasitic pressure influenced the creation and development of cultural norms and institutions. However, other effects of microorganisms on human groups and individual decision-making and behavior are heavily understudied. The perspective discusses how parasitic infections, sexually transmitted organisms and microbiota (i.e., &quot;human holobiont&quot;) could causally influence risk-seeking behavior, impulsivity, social dominance, empathy, political views and gender differences. As a case study, the parasite Toxoplasma gondii and its influence on economic preferences, personal characteristics and human appearance are examined. I also briefly review how chemosignals influence decision-making, particularly in the social preferences domain. I mention some predictions that arise from the paradigm of economic holobiont for the economic science. The conclusion summarizes limitations of the discussed findings and the stated speculations.}, }
@article {pmid29761370, year = {2018}, author = {Bourrat, P and Griffiths, PE}, title = {Multispecies individuals.}, journal = {History and philosophy of the life sciences}, volume = {40}, number = {2}, pages = {33}, doi = {10.1007/s40656-018-0194-1}, pmid = {29761370}, issn = {0391-9714}, support = {DP0878650//Australian Research Council (AU)/ ; }, mesh = {Alismatales/growth &amp; development/physiology ; Animals ; Biological Evolution ; Bivalvia/*microbiology/physiology ; Humans ; Individuality ; Life History Traits ; *Microbiota ; Oligochaeta/*microbiology/physiology ; *Symbiosis ; }, abstract = {We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called 'holobionts'. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of ecological dependence between separate individuals. Some widely used arguments in support of the 'holobiont' concept apply equally to both cases, suggesting that those arguments have misidentified what is at stake when seeking to identify a new level of biological individuality. One important aspect of biological individuality is evolutionary individuality. In line with other work on the evolution of individuality, we show that our cases can be distinguished by focusing on the fitness alignment between the partners of the consortia. We conclude that much of the evidence currently presented for the ubiquity and importance of multi-species individuals is simply not to the point, at least unless the issue of biological individuality is firmly divorced from the question of evolutionary individuality.}, }
@article {pmid29742123, year = {2018}, author = {León-Palmero, E and Joglar, V and Álvarez, PA and Martín-Platero, A and Llamas, I and Reche, I}, title = {Diversity and antimicrobial potential in sea anemone and holothurian microbiomes.}, journal = {PloS one}, volume = {13}, number = {5}, pages = {e0196178}, pmid = {29742123}, issn = {1932-6203}, mesh = {Animals ; Bacteria/isolation &amp; purification ; *Biodiversity ; Holothuria/*microbiology/*physiology ; *Microbiota ; Sea Anemones/*microbiology/*physiology ; Symbiosis ; }, abstract = {Marine invertebrates, as holobionts, contain symbiotic bacteria that coevolve and develop antimicrobial substances. These symbiotic bacteria are an underexplored source of new bioactive molecules to face the emerging antibiotic resistance in pathogens. Here, we explored the antimicrobial activity of bacteria retrieved from the microbiota of two sea anemones (Anemonia sulcata, Actinia equina) and two holothurians (Holothuria tubulosa, Holothuria forskali). We tested the antimicrobial activity of the isolated bacteria against pathogens with interest for human health, agriculture and aquaculture. We isolated 27 strains with antibacterial activity and 12 of these isolates also showed antifungal activity. We taxonomically identified these strains being Bacillus and Vibrio species the most representative producers of antimicrobial substances. Microbiome species composition of the two sea anemones was similar between them but differed substantially of seawater bacteria. In contrast, microbiome species composition of the two holothurian species was different between them and in comparison with the bacteria in holothurian feces and seawater. In all the holobiont microbiomes Bacteroidetes was the predominant phylum. For each microbiome, we determined diversity and the rank-abundance dominance using five fitted models (null, pre-emption, log-Normal, Zipf and Zipf-Mandelbrot). The models with less evenness (i.e. Zipf and Zipf-Mandelblot) showed the best fits in all the microbiomes. Finally, we tracked (using the V4 hypervariable region of 16S rRNA gene) the relative abundance of these 27 isolates with antibacterial activity in the total pool of sequences obtained for the microbiome of each holobiont. Coincidences, although with extremely low frequencies, were detected only in the microbiome of H. forskali. This fact suggests that these isolated bacteria belong to the long tail of rare symbiotic bacteria. Therefore, more and more sophisticated culture techniques are necessary to explore this apparently vast pool of rare symbiontic bacteria and to determine their biotechnological potentiality.}, }
@article {pmid29740401, year = {2018}, author = {Domin, H and Zurita-Gutiérrez, YH and Scotti, M and Buttlar, J and Hentschel Humeida, U and Fraune, S}, title = {Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {728}, pmid = {29740401}, issn = {1664-302X}, abstract = {The maintenance and resilience of host-associated microbiota during development is a fundamental process influencing the fitness of many organisms. Several host properties were identified as influencing factors on bacterial colonization, including the innate immune system, mucus composition, and diet. In contrast, the importance of bacteria-bacteria interactions on host colonization is less understood. Here, we use bacterial abundance data of the marine model organism Nematostella vectensis to reconstruct potential bacteria-bacteria interactions through co-occurrence networks. The analysis indicates that bacteria-bacteria interactions are dynamic during host colonization and change according to the host's developmental stage. To assess the predictive power of inferred interactions, we tested bacterial isolates with predicted cooperative or competitive behavior for their ability to influence bacterial recolonization dynamics. Within 3 days of recolonization, all tested bacterial isolates affected bacterial community structure, while only competitive bacteria increased bacterial diversity. Only 1 week after recolonization, almost no differences in bacterial community structure could be observed between control and treatments. These results show that predicted competitive bacteria can influence community structure for a short period of time, verifying the in silico predictions. However, within 1 week, the effects of the bacterial isolates are neutralized, indicating a high degree of resilience of the bacterial community.}, }
@article {pmid29739445, year = {2018}, author = {Sorek, M and Schnytzer, Y and Waldman Ben-Asher, H and Caspi, VC and Chen, CS and Miller, DJ and Levy, O}, title = {Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian Aiptasia are determined largely by Symbiodinium.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {83}, pmid = {29739445}, issn = {2049-2618}, support = {1294//Taiwan-Israel cooperative program/International ; }, mesh = {Animals ; Biological Clocks/*physiology ; Circadian Rhythm/genetics/*physiology ; Dinoflagellida/*metabolism ; Gene Expression Regulation/*genetics ; Oxygen/metabolism ; Sea Anemones/*genetics/parasitology ; Symbiosis/physiology ; }, abstract = {BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana.<br><br>RESULTS: The results showed that whereas circatidal (approx. 12-h) cycles of activity and gene expression predominated in aposymbiotic morphs, circadian (approx. 24-h) patterns were the more common in symbiotic morphs, where the expression of a significant number of genes shifted from a 12- to 24-h rhythm. The behavioural experiments on symbiotic A. diaphana displayed diel (24-h) rhythmicity in body and tentacle contraction under the light/dark cycles, whereas aposymbiotic morphs showed approximately 12-h (circatidal) rhythmicity. Reinfection experiments represent an important step in understanding the hierarchy of endogenous clocks in symbiotic associations, where the aposymbiotic Aiptasia morphs returned to a 24-h behavioural rhythm after repopulation with algae.<br><br>CONCLUSION: Whilst some modification of host metabolism is to be expected, the extent to which the presence of the algae modified host endogenous behavioural and transcriptional rhythms implies that it is the symbionts that influence the pace. Our results clearly demonstrate the importance of the endosymbiotic algae in determining the timing and the duration of the extension and contraction of the body and tentacles and temporal gene expression.}, }
@article {pmid29738088, year = {2018}, author = {Faure, D and Simon, JC and Heulin, T}, title = {Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.}, journal = {The New phytologist}, volume = {218}, number = {4}, pages = {1321-1324}, doi = {10.1111/nph.15199}, pmid = {29738088}, issn = {1469-8137}, mesh = {*Biological Evolution ; *Ecosystem ; Genomics ; *Host Microbial Interactions/genetics ; Metagenome ; Research Personnel ; }, }
@article {pmid29714033, year = {2018}, author = {Nobori, T and Mine, A and Tsuda, K}, title = {Molecular networks in plant-pathogen holobiont.}, journal = {FEBS letters}, volume = {592}, number = {12}, pages = {1937-1953}, doi = {10.1002/1873-3468.13071}, pmid = {29714033}, issn = {1873-3468}, mesh = {Bacteria/immunology/*pathogenicity ; Gene Regulatory Networks ; Host-Pathogen Interactions ; Plant Diseases/microbiology ; Plant Immunity ; Plant Proteins/*metabolism ; Plants/metabolism/*microbiology ; Signal Transduction ; Virulence Factors/*immunology ; }, abstract = {Plant immune receptors enable detection of a multitude of microbes including pathogens. The recognition of microbes activates various plant signaling pathways, such as those mediated by phytohormones. Over the course of coevolution with microbes, plants have expanded their repertoire of immune receptors and signaling components, resulting in highly interconnected plant immune networks. These immune networks enable plants to appropriately respond to different types of microbes and to coordinate immune responses with developmental programs and environmental stress responses. However, the interconnectivity in plant immune networks is exploited by microbial pathogens to promote pathogen fitness in plants. Analogous to plant immune networks, virulence-related pathways in bacterial pathogens are also interconnected. Accumulating evidence implies that some plant-derived compounds target bacterial virulence networks. Thus, the plant immune and bacterial virulence networks intimately interact with each other. Here, we highlight recent insights into the structures of the plant immune and bacterial virulence networks and the interactions between them. We propose that small molecules derived from plants and/or bacterial pathogens connect the two molecular networks, forming supernetworks in the plant-bacterial pathogen holobiont.}, }
@article {pmid29701776, year = {2018}, author = {Karimi, E and Slaby, BM and Soares, AR and Blom, J and Hentschel, U and Costa, R}, title = {Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges.}, journal = {FEMS microbiology ecology}, volume = {94}, number = {6}, pages = {}, doi = {10.1093/femsec/fiy074}, pmid = {29701776}, issn = {1574-6941}, mesh = {Animals ; Carbon/metabolism ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; Porifera/*microbiology ; Rhodospirillaceae/genetics/*metabolism ; Sulfur/metabolism ; Symbiosis/*physiology ; }, abstract = {Marine sponges are early-branched metazoans known to harbor dense and diverse microbial communities. Yet the role of the so far uncultivable alphaproteobacterial lineages that populate these sessile invertebrates remains unclear. We applied a sequence composition-dependent binning approach to assemble one Rhodospirillaceae genome from the Spongia officinalis microbial metagenome and contrast its functional features with those of closely related sponge-associated and free-living genomes. Both symbiotic and free-living Rhodospirillaceae shared a suite of common features, possessing versatile carbon, nitrogen, sulfur and phosphorus metabolisms. Symbiotic genomes could be distinguished from their free-living counterparts by the lack of chemotaxis and motility traits, enrichment of genes required for the uptake and utilization of organic sulfur compounds-particularly taurine-, higher diversity and abundance of ABC transporters, and a distinct repertoire of genes involved in natural product biosynthesis, plasmid stability, cell detoxification and oxidative stress remediation. These sessile symbionts may more effectively contribute to host fitness via nutrient exchange, and also host detoxification and chemical defense. Considering the worldwide occurrence and high diversity of sponge-associated Rhodospirillaceae verified here using a tailored in silico approach, we suggest that these organisms are not only relevant to holobiont homeostasis but also to nutrient cycling in benthic ecosystems.}, }
@article {pmid29695294, year = {2018}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {The hologenome concept of evolution after 10 years.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {78}, pmid = {29695294}, issn = {2049-2618}, mesh = {Animals ; *Biological Evolution ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genetic Variation ; Genome/genetics ; Humans ; Microbiota/*genetics ; Plants ; Symbiosis/*physiology ; }, abstract = {The holobiont (host with its endocellular and extracellular microbiome) can function as a distinct biological entity, an additional organismal level to the ones previously considered, on which natural selection operates. The holobiont can function as a whole: anatomically, metabolically, immunologically, developmentally, and during evolution. Consideration of the holobiont with its hologenome as an independent level of selection in evolution has led to a better understanding of underappreciated modes of genetic variation and evolution. The hologenome is comprised of two complimentary parts: host and microbiome genomes. Changes in either genome can result in variations that can be selected for or against. The host genome is highly conserved, and genetic changes within it occur slowly, whereas the microbiome genome is dynamic and can change rapidly in response to the environment by increasing or reducing particular microbes, by acquisition of novel microbes, by horizontal gene transfer, and by mutation. Recent experiments showing that microbiota can play an initial role in speciation have been suggested as an additional mode of enhancing evolution. Some of the genetic variations can be transferred to offspring by a variety of mechanisms. Strain-specific DNA analysis has shown that at least some of the microbiota can be maintained across hundreds of thousands of host generations, implying the existence of a microbial core. We argue that rapid changes in the microbiome genome could allow holobionts to adapt and survive under changing environmental conditions thus providing the time necessary for the host genome to adapt and evolve. As Darwin wrote, &quot;It is not the strongest of the species that survives but the most adaptable&quot;.}, }
@article {pmid29695286, year = {2018}, author = {Vannier, N and Mony, C and Bittebiere, AK and Michon-Coudouel, S and Biget, M and Vandenkoornhuyse, P}, title = {A microorganisms' journey between plant generations.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {79}, pmid = {29695286}, issn = {2049-2618}, support = {EC2CO program (MIME project)//Centre National de la Recherche Scientifique/International ; PEPS program (MYCOLAND project)//Centre National de la Recherche Scientifique/International ; }, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics/isolation &amp; purification ; Lamiaceae/*microbiology ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Soil Microbiology ; Symbiosis ; }, abstract = {BACKGROUND: Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network.<br><br>METHODS: We used the clonal plant Glechoma hederacea as plant model and forced newly emitted clonal progeny to root in separated pots while controlling the presence of microorganisms. We used an amplicon sequencing approach of 16S and 18S rRNA targeting bacteria/archaea and fungi respectively to describe the root microbiota of mother and clonal-plant offspring.<br><br>RESULTS: We demonstrated the vertical transmission of a significant proportion of the mother plants' symbiotic bacteria and fungi to the daughters. Interestingly, archaea were not transmitted to the daughter plants. Transmitted communities had lower richness, suggesting a filtration during transmission. We found that the transmitted pool of microorganisms was similar among daughters, constituting the heritability of a specific cohort of microorganisms, opening a new understanding of the plant holobiont. We also found significant effects of distance to the mother plant and of growth time on the richness of the microbiota transmitted.<br><br>CONCLUSIONS: In this clonal plant, microorganisms are transmitted between individuals through connections, thereby ensuring the availability of microbe partners for the newborn plants as well as the dispersion between hosts for the microorganisms. This previously undescribed ecological process allows the dispersal of microorganisms in space and across plant generations. As the vast majority of plants are clonal, this process might be therefore a strong driver of ecosystem functioning and assembly of plant and microorganism communities in a wide range of ecosystems.}, }
@article {pmid29666616, year = {2018}, author = {Mortzfeld, BM and Taubenheim, J and Fraune, S and Klimovich, AV and Bosch, TCG}, title = {Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {629}, pmid = {29666616}, issn = {1664-302X}, abstract = {The aging process is considered to be the result of accumulating cellular deterioration in an individual organism over time. It can be affected by the combined influence of genetic, epigenetic, and environmental factors including life-style-associated events. In the non-senescent freshwater polyp Hydra, one of the classical model systems for evolutionary developmental biology and regeneration, transcription factor FoxO modulates both stem cell proliferation and innate immunity. This provides strong support for the role of FoxO as a critical rate-of-aging regulator. However, how environmental factors interact with FoxO remains unknown. Here, we find that deficiency in FoxO signaling in Hydra leads to dysregulation of antimicrobial peptide expression and that FoxO loss-of-function polyps are impaired in selection for bacteria resembling the native microbiome and more susceptible to colonization of foreign bacteria. These findings reveal a key role of FoxO signaling in the communication between host and microbiota and embed the evolutionary conserved longevity factor FoxO into the holobiont concept.}, }
@article {pmid29657963, year = {2018}, author = {Theis, KR}, title = {Hologenomics: Systems-Level Host Biology.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29657963}, issn = {2379-5077}, abstract = {The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.}, }
@article {pmid29651978, year = {2018}, author = {Vigliotti, C and Bicep, C and Bapteste, E and Lopez, P and Corel, E}, title = {Tracking the Rules of Transmission and Introgression with Networks.}, journal = {Microbiology spectrum}, volume = {6}, number = {2}, pages = {}, doi = {10.1128/microbiolspec.MTBP-0008-2016}, pmid = {29651978}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics/physiology ; Gastrointestinal Tract/*microbiology ; *Gene Regulatory Networks ; Gene Transfer, Horizontal ; Genetic Variation ; Humans ; Interspersed Repetitive Sequences ; Metagenome/genetics ; Microbiota/*genetics/physiology ; Plasmids/genetics ; *Recombination, Genetic ; Sequence Homology ; Viruses/genetics ; }, abstract = {Understanding how an animal organism and its gut microbes form an integrated biological organization, known as a holobiont, is becoming a central issue in biological studies. Such an organization inevitably involves a complex web of transmission processes that occur on different scales in time and space, across microbes and hosts. Network-based models are introduced in this chapter to tackle aspects of this complexity and to better take into account vertical and horizontal dimensions of transmission. Two types of network-based models are presented, sequence similarity networks and bipartite graphs. One interest of these networks is that they can consider a rich diversity of important players in microbial evolution that are usually excluded from evolutionary studies, like plasmids and viruses. These methods bring forward the notion of &quot;gene externalization,&quot; which is defined as the presence of redundant copies of prokaryotic genes on mobile genetic elements (MGEs), and therefore emphasizes a related although distinct process from lateral gene transfer between microbial cells. This chapter introduces guidelines to the construction of these networks, reviews their analysis, and illustrates their possible biological interpretations and uses. The application to human gut microbiomes shows that sequences present in a higher diversity of MGEs have both biased functions and a broader microbial and human host range. These results suggest that an &quot;externalized gut metagenome&quot; is partly common to humans and benefits the gut microbial community. We conclude that testing relationships between microbial genes, microbes, and their animal hosts, using network-based methods, could help to unravel additional mechanisms of transmission in holobionts.}, }
@article {pmid29650460, year = {2018}, author = {Allemand, D and Furla, P}, title = {How does an animal behave like a plant? Physiological and molecular adaptations of zooxanthellae and their hosts to symbiosis.}, journal = {Comptes rendus biologies}, volume = {341}, number = {5}, pages = {276-280}, doi = {10.1016/j.crvi.2018.03.007}, pmid = {29650460}, issn = {1768-3238}, mesh = {Acclimatization ; Adaptation, Physiological/*physiology ; Animals ; Anthozoa/physiology ; Dinoflagellida/*physiology ; Ecology ; Photosynthesis/physiology ; Sea Anemones/physiology ; Symbiosis/*physiology ; }, abstract = {Cnidarians (corals and sea anemones) harbouring photosynthetic microalgae derive several benefits from their association. To allow this association, numerous symbiotic-dependent adaptations in both partners, resulting from evolutionary pressures, have been selected. The dinoflagellate symbionts (zooxanthellae) are located inside a vesicle in the cnidarian host cell and are therefore exposed to a very different environment compared to the free-living state of these microalgae in terms of ion concentration and carbon content and speciation. In addition, this intracellular localization imposes that they rely completely upon the host for their nutrient supply (nitrogen, CO2). Symbiotic-dependent adaptations imposed to the animal host by phototrophic symbiosis are more relevant to photosynthetic organisms than to metazoans: indeed, the cnidarian host often harbours diurnal changes of morphology to adapt itself to the amount of light and possesses carbon-concentrating mechanisms, antioxidative defences and UV sunscreens similar to that present in phototrophs. These adaptations and the contrasting fragility of the association are discussed from both ecological and evolutionary points of view.}, }
@article {pmid29645277, year = {2019}, author = {Wille, L and Messmer, MM and Studer, B and Hohmann, P}, title = {Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.}, journal = {Plant, cell &amp; environment}, volume = {42}, number = {1}, pages = {20-40}, doi = {10.1111/pce.13214}, pmid = {29645277}, issn = {1365-3040}, abstract = {Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil-borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere-related traits, (c) the role of root exudation in microbe-mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.}, }
@article {pmid29615919, year = {2018}, author = {Rädecker, N and Raina, JB and Pernice, M and Perna, G and Guagliardo, P and Kilburn, MR and Aranda, M and Voolstra, CR}, title = {Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses.}, journal = {Frontiers in physiology}, volume = {9}, number = {}, pages = {214}, pmid = {29615919}, issn = {1664-042X}, abstract = {The symbiosis between cnidarian hosts and microalgae of the genus Symbiodinium provides the foundation of coral reefs in oligotrophic waters. Understanding the nutrient-exchange between these partners is key to identifying the fundamental mechanisms behind this symbiosis, yet has proven difficult given the endosymbiotic nature of this relationship. In this study, we investigated the respective contribution of host and symbiont to carbon and nitrogen assimilation in the coral model anemone Aiptaisa. For this, we combined traditional measurements with nanoscale secondary ion mass spectrometry (NanoSIMS) and stable isotope labeling to investigate patterns of nutrient uptake and translocation both at the organismal scale and at the cellular scale. Our results show that the rate of carbon and nitrogen assimilation in Aiptasia depends on the identity of the host and the symbiont. NanoSIMS analysis confirmed that both host and symbiont incorporated carbon and nitrogen into their cells, implying a rapid uptake and cycling of nutrients in this symbiotic relationship. Gross carbon fixation was highest in Aiptasia associated with their native Symbiodinium communities. However, differences in fixation rates were only reflected in the δ13C enrichment of the cnidarian host, whereas the algal symbiont showed stable enrichment levels regardless of host identity. Thereby, our results point toward a &quot;selfish&quot; character of the cnidarian-Symbiodinium association in which both partners directly compete for available resources. Consequently, this symbiosis may be inherently instable and highly susceptible to environmental change. While questions remain regarding the underlying cellular controls of nutrient exchange and the nature of metabolites involved, the approach outlined in this study constitutes a powerful toolset to address these questions.}, }
@article {pmid29611114, year = {2018}, author = {Wang, J and Chen, L and Zhao, N and Xu, X and Xu, Y and Zhu, B}, title = {Of genes and microbes: solving the intricacies in host genomes.}, journal = {Protein &amp; cell}, volume = {9}, number = {5}, pages = {446-461}, pmid = {29611114}, issn = {1674-8018}, mesh = {Animals ; Biomedical Research ; *Genes ; *Genetic Variation ; *Genome ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Microbiome research is a quickly developing field in biomedical research, and we have witnessed its potential in understanding the physiology, metabolism and immunology, its critical role in understanding the health and disease of the host, and its vast capacity in disease prediction, intervention and treatment. However, many of the fundamental questions still need to be addressed, including the shaping forces of microbial diversity between individuals and across time. Microbiome research falls into the classical nature vs. nurture scenario, such that host genetics shape part of the microbiome, while environmental influences change the original course of microbiome development. In this review, we focus on the nature, i.e., the genetic part of the equation, and summarize the recent efforts in understanding which parts of the genome, especially the human and mouse genome, play important roles in determining the composition and functions of microbial communities, primarily in the gut but also on the skin. We aim to present an overview of different approaches in studying the intricate relationships between host genetic variations and microbes, its underlying philosophy and methodology, and we aim to highlight a few key discoveries along this exploration, as well as current pitfalls. More evidence and results will surely appear in upcoming studies, and the accumulating knowledge will lead to a deeper understanding of what we could finally term a &quot;hologenome&quot;, that is, the organized, closely interacting genome of the host and the microbiome.}, }
@article {pmid29609655, year = {2018}, author = {van de Water, JAJM and Allemand, D and Ferrier-Pagès, C}, title = {Host-microbe interactions in octocoral holobionts - recent advances and perspectives.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {64}, pmid = {29609655}, issn = {2049-2618}, mesh = {Animal Diseases/microbiology ; Animals ; Anthozoa/*microbiology ; Bacteria/classification ; Biological Products ; Coral Reefs ; Drug Discovery ; Ecosystem ; Fungi/classification ; *Host Microbial Interactions ; Host-Pathogen Interactions/immunology ; *Microbiota ; Spatio-Temporal Analysis ; Symbiosis ; Viruses/classification/genetics ; }, abstract = {Octocorals are one of the most ubiquitous benthic organisms in marine ecosystems from the shallow tropics to the Antarctic deep sea, providing habitat for numerous organisms as well as ecosystem services for humans. In contrast to the holobionts of reef-building scleractinian corals, the holobionts of octocorals have received relatively little attention, despite the devastating effects of disease outbreaks on many populations. Recent advances have shown that octocorals possess remarkably stable bacterial communities on geographical and temporal scales as well as under environmental stress. This may be the result of their high capacity to regulate their microbiome through the production of antimicrobial and quorum-sensing interfering compounds. Despite decades of research relating to octocoral-microbe interactions, a synthesis of this expanding field has not been conducted to date. We therefore provide an urgently needed review on our current knowledge about octocoral holobionts. Specifically, we briefly introduce the ecological role of octocorals and the concept of holobiont before providing detailed overviews of (I) the symbiosis between octocorals and the algal symbiont Symbiodinium; (II) the main fungal, viral, and bacterial taxa associated with octocorals; (III) the dominance of the microbial assemblages by a few microbial species, the stability of these associations, and their evolutionary history with the host organism; (IV) octocoral diseases; (V) how octocorals use their immune system to fight pathogens; (VI) microbiome regulation by the octocoral and its associated microbes; and (VII) the discovery of natural products with microbiome regulatory activities. Finally, we present our perspectives on how the field of octocoral research should move forward, and the recognition that these organisms may be suitable model organisms to study coral-microbe symbioses.}, }
@article {pmid29599012, year = {2018}, author = {Bang, C and Dagan, T and Deines, P and Dubilier, N and Duschl, WJ and Fraune, S and Hentschel, U and Hirt, H and Hülter, N and Lachnit, T and Picazo, D and Pita, L and Pogoreutz, C and Rädecker, N and Saad, MM and Schmitz, RA and Schulenburg, H and Voolstra, CR and Weiland-Bräuer, N and Ziegler, M and Bosch, TCG}, title = {Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?.}, journal = {Zoology (Jena, Germany)}, volume = {127}, number = {}, pages = {1-19}, doi = {10.1016/j.zool.2018.02.004}, pmid = {29599012}, issn = {1873-2720}, mesh = {*Adaptation, Physiological/physiology ; Animals ; Ecosystem ; *Extreme Environments ; Microbiota/genetics/*physiology ; Phylogeny ; Symbiosis/physiology ; }, abstract = {From protists to humans, all animals and plants are inhabited by microbial organisms. There is an increasing appreciation that these resident microbes influence the fitness of their plant and animal hosts, ultimately forming a metaorganism consisting of a uni- or multicellular host and a community of associated microorganisms. Research on host-microbe interactions has become an emerging cross-disciplinary field. In both vertebrates and invertebrates a complex microbiome confers immunological, metabolic and behavioural benefits; conversely, its disturbance can contribute to the development of disease states. However, the molecular and cellular mechanisms controlling the interactions within a metaorganism are poorly understood and many key interactions between the associated organisms remain unknown. In this perspective article, we outline some of the issues in interspecies interactions and in particular address the question of how metaorganisms react and adapt to inputs from extreme environments such as deserts, the intertidal zone, oligothrophic seas, and hydrothermal vents.}, }
@article {pmid29587885, year = {2018}, author = {Hassani, MA and Durán, P and Hacquard, S}, title = {Microbial interactions within the plant holobiont.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {58}, pmid = {29587885}, issn = {2049-2618}, support = {758003//European Research Council/International ; }, mesh = {Bacteria/classification ; Biodiversity ; Biological Evolution ; Fungi/classification ; Microbial Consortia ; *Microbial Interactions ; *Microbiota ; Plant Development ; Plants/*microbiology ; }, abstract = {Since the colonization of land by ancestral plant lineages 450 million years ago, plants and their associated microbes have been interacting with each other, forming an assemblage of species that is often referred to as a &quot;holobiont.&quot; Selective pressure acting on holobiont components has likely shaped plant-associated microbial communities and selected for host-adapted microorganisms that impact plant fitness. However, the high microbial densities detected on plant tissues, together with the fast generation time of microbes and their more ancient origin compared to their host, suggest that microbe-microbe interactions are also important selective forces sculpting complex microbial assemblages in the phyllosphere, rhizosphere, and plant endosphere compartments. Reductionist approaches conducted under laboratory conditions have been critical to decipher the strategies used by specific microbes to cooperate and compete within or outside plant tissues. Nonetheless, our understanding of these microbial interactions in shaping more complex plant-associated microbial communities, along with their relevance for host health in a more natural context, remains sparse. Using examples obtained from reductionist and community-level approaches, we discuss the fundamental role of microbe-microbe interactions (prokaryotes and micro-eukaryotes) for microbial community structure and plant health. We provide a conceptual framework illustrating that interactions among microbiota members are critical for the establishment and the maintenance of host-microbial homeostasis.}, }
@article {pmid29587830, year = {2018}, author = {Gobet, A and Mest, L and Perennou, M and Dittami, SM and Caralp, C and Coulombet, C and Huchette, S and Roussel, S and Michel, G and Leblanc, C}, title = {Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {60}, pmid = {29587830}, issn = {2049-2618}, support = {ANR-10-BTBR-02-04-11//Agence Nationale de la Recherche/International ; }, mesh = {Animal Feed ; Animals ; Bacteria/classification/genetics ; *Gastrointestinal Microbiome ; Gastropoda/*microbiology ; *Herbivory ; Polysaccharides ; *Seasons ; }, abstract = {BACKGROUND: Holobionts have a digestive microbiota with catabolic abilities allowing the degradation of complex dietary compounds for the host. In terrestrial herbivores, the digestive microbiota is known to degrade complex polysaccharides from land plants while in marine herbivores, the digestive microbiota is poorly characterized. Most of the latter are generalists and consume red, green, and brown macroalgae, three distinct lineages characterized by a specific composition in complex polysaccharides, which represent half of their biomass. Subsequently, each macroalga features a specific epiphytic microbiota, and the digestive microbiota of marine herbivores is expected to vary with a monospecific algal diet. We investigated the effect of four monospecific diets (Palmaria palmata, Ulva lactuca, Saccharina latissima, Laminaria digitata) on the composition and specificity of the digestive microbiota of a generalist marine herbivore, the abalone, farmed in a temperate coastal area over a year. The microbiota from the abalone digestive gland was sampled every 2 months and explored using metabarcoding.<br><br>RESULTS: Diversity and multivariate analyses showed that patterns of the microbiota were significantly linked to seasonal variations of contextual parameters but not directly to a specific algal diet. Three core genera: Psychrilyobacter, Mycoplasma, and Vibrio constantly dominated the microbiota in the abalone digestive gland. Additionally, a less abundant and diet-specific core microbiota featured genera representing aerobic primary degraders of algal polysaccharides.<br><br>CONCLUSIONS: This study highlights the establishment of a persistent core microbiota in the digestive gland of the abalone since its juvenile state and the presence of a less abundant and diet-specific core community. While composed of different microbial taxa compared to terrestrial herbivores, the digestive gland constitutes a particular niche in the abalone holobiont, where bacteria (i) may cooperate to degrade algal polysaccharides to products assimilable by the host or (ii) may have acquired these functions through gene transfer from the aerobic algal microbiota.}, }
@article {pmid29573244, year = {2018}, author = {Pootakham, W and Mhuantong, W and Putchim, L and Yoocha, T and Sonthirod, C and Kongkachana, W and Sangsrakru, D and Naktang, C and Jomchai, N and Thongtham, N and Tangphatsornruang, S}, title = {Dynamics of coral-associated microbiomes during a thermal bleaching event.}, journal = {MicrobiologyOpen}, volume = {7}, number = {5}, pages = {e00604}, pmid = {29573244}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology/*radiation effects ; Bacteria/*classification/genetics ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Protozoan/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; DNA, Ribosomal Spacer/chemistry/genetics ; Dinoflagellida/*classification/genetics ; Microbiota/*radiation effects ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Temperature ; }, abstract = {Coral-associated microorganisms play an important role in their host fitness and survival. A number of studies have demonstrated connections between thermal tolerance in corals and the type/relative abundance of Symbiodinium they harbor. More recently, the shifts in coral-associated bacterial profiles were also shown to be linked to the patterns of coral heat tolerance. Here, we investigated the dynamics of Porites lutea-associated bacterial and algal communities throughout a natural bleaching event, using full-length 16S rRNA and internal transcribed spacer sequences (ITS) obtained from PacBio circular consensus sequencing. We provided evidence of significant changes in the structure and diversity of coral-associated microbiomes during thermal stress. The balance of the symbiosis shifted from a predominant association between corals and Gammaproteobacteria to a predominance of Alphaproteobacteria and to a lesser extent Betaproteobacteria following the bleaching event. On the contrary, the composition and diversity of Symbiodinium communities remained unaltered throughout the bleaching event. It appears that the switching and/or shuffling of Symbiodinium types may not be the primary mechanism used by P. lutea to cope with increasing seawater temperature. The shifts in the structure and diversity of associated bacterial communities may contribute more to the survival of the coral holobiont under heat stress.}, }
@article {pmid29567394, year = {2018}, author = {Rahman, MM and Flory, E and Koyro, HW and Abideen, Z and Schikora, A and Suarez, C and Schnell, S and Cardinale, M}, title = {Consistent associations with beneficial bacteria in the seed endosphere of barley (Hordeum vulgare L.).}, journal = {Systematic and applied microbiology}, volume = {41}, number = {4}, pages = {386-398}, doi = {10.1016/j.syapm.2018.02.003}, pmid = {29567394}, issn = {1618-0984}, mesh = {Endophytes/growth &amp; development ; Hordeum/growth &amp; development/*microbiology ; Microbiota ; Paenibacillus/classification/growth &amp; development/*isolation &amp; purification ; Pantoea/classification/growth &amp; development/*isolation &amp; purification ; Plant Roots/*microbiology ; Pseudomonas/classification/growth &amp; development/*isolation &amp; purification ; Seeds/*microbiology ; Symbiosis ; }, abstract = {The importance of the plant microbiome for host fitness has led to the concept of the &quot;plant holobiont&quot;. Seeds are reservoirs and vectors for beneficial microbes, which are very intimate partners of higher plants with the potential to connect plant generations. In this study, the endophytic seed microbiota of numerous barley samples, representing different cultivars, geographical sites and harvest years, was investigated. Cultivation-dependent and -independent analyses, microscopy, functional plate assays, greenhouse assays and functional prediction were used, with the aim of assessing the composition, stability and function of the barley seed endophytic bacterial microbiota. Associations were consistently detected in the seed endosphere with Paenibacillus, Pantoea and Pseudomonas spp., which were able to colonize the root with a notable rhizocompetence after seed germination. In greenhouse assays, enrichment with these bacteria promoted barley growth, improved mineral nutrition and induced resistance against the fungal pathogen Blumeria graminis. We demonstrated here that barley, an important crop plant, was consistently associated with beneficial bacteria inside the seeds. The results have relevant implications for plant microbiome ecology and for the holobiont concept, as well as opening up new possibilities for research and application of seed endophytes as bioinoculants in sustainable agriculture.}, }
@article {pmid29566771, year = {2018}, author = {Callens, M and Watanabe, H and Kato, Y and Miura, J and Decaestecker, E}, title = {Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {56}, pmid = {29566771}, issn = {2049-2618}, support = {FWO G060216N//FWO/International ; BOF C16/17/002//KU Leuven/International ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacterial Load ; Biodiversity ; Daphnia/drug effects/growth &amp; development/*microbiology/*physiology ; *Host Microbial Interactions/drug effects ; *Microbiota/drug effects ; }, abstract = {BACKGROUND: Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model Daphnia was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when Daphnia were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota.<br><br>RESULTS: Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of Daphnia by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected Daphnia growth.<br><br>CONCLUSIONS: These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on Daphnia, affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.}, }
@article {pmid29562933, year = {2018}, author = {Ravanbakhsh, M and Sasidharan, R and Voesenek, LACJ and Kowalchuk, GA and Jousset, A}, title = {Microbial modulation of plant ethylene signaling: ecological and evolutionary consequences.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {52}, pmid = {29562933}, issn = {2049-2618}, mesh = {Bacteria/*metabolism ; Environment ; Ethylenes/*metabolism ; Gene Expression Regulation, Plant/*genetics ; Microbiota/physiology ; Plants/*microbiology ; Signal Transduction ; Stress, Physiological/physiology ; Symbiosis/*physiology ; }, abstract = {The plant hormone ethylene is one of the central regulators of plant development and stress resistance. Optimal ethylene signaling is essential for plant fitness and is under strong selection pressure. Plants upregulate ethylene production in response to stress, and this hormone triggers defense mechanisms. Due to the pleiotropic effects of ethylene, adjusting stress responses to maximize resistance, while minimizing costs, is a central determinant of plant fitness. Ethylene signaling is influenced by the plant-associated microbiome. We therefore argue that the regulation, physiology, and evolution of the ethylene signaling can best be viewed as the interactive result of plant genotype and associated microbiota. In this article, we summarize the current knowledge on ethylene signaling and recapitulate the multiple ways microorganisms interfere with it. We present ethylene signaling as a model system for holobiont-level evolution of plant phenotype: this cascade is tractable, extremely well studied from both a plant and a microbial perspective, and regulates fundamental components of plant life history. We finally discuss the potential impacts of ethylene modulation microorganisms on plant ecology and evolution. We assert that ethylene signaling cannot be fully appreciated without considering microbiota as integral regulatory actors, and we more generally suggest that plant ecophysiology and evolution can only be fully understood in the light of plant-microbiome interactions.}, }
@article {pmid29556542, year = {2018}, author = {Wegley Kelly, L and Haas, AF and Nelson, CE}, title = {Ecosystem Microbiology of Coral Reefs: Linking Genomic, Metabolomic, and Biogeochemical Dynamics from Animal Symbioses to Reefscape Processes.}, journal = {mSystems}, volume = {3}, number = {2}, pages = {}, pmid = {29556542}, issn = {2379-5077}, abstract = {Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to broaden our understanding of the ecological roles of environmental microbes. Studies on coral reefs are actively integrating these data streams at multiple levels, from the symbiotic habitat of the coral holobiont to microbially mediated interactions between corals and algae to the effects of these interactions on the microbial community structure, metabolism, and organic geochemistry of the reef ecosystem. Coral reefs endure multiple anthropogenic impacts, including pollution, overfishing, and global change. In this context, we must develop ecosystem microbiology with an eye to providing managers with microbial indicators of reef ecosystem processes, coral health, and resilience to both local and global stressors.}, }
@article {pmid29554951, year = {2018}, author = {Guégan, M and Zouache, K and Démichel, C and Minard, G and Tran Van, V and Potier, P and Mavingui, P and Valiente Moro, C}, title = {The mosquito holobiont: fresh insight into mosquito-microbiota interactions.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {49}, pmid = {29554951}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*metabolism ; Culicidae/*microbiology ; Host-Pathogen Interactions/*physiology ; Microbiota/*physiology ; Mosquito Vectors/*microbiology ; Symbiosis/*physiology ; }, abstract = {The holobiont concept was first developed for coral ecosystems but has been extended to multiple organisms, including plants and other animals. Studies on insect-associated microbial communities have produced strong evidence that symbiotic bacteria play a major role in host biology. However, the understanding of these symbiotic relationships has mainly been limited to phytophagous insects, while the role of host-associated microbiota in haematophagous insect vectors remains largely unexplored. Mosquitoes are a major global public health concern, with a concomitant increase in people at risk of infection. The global emergence and re-emergence of mosquito-borne diseases has led many researchers to study both the mosquito host and its associated microbiota. Although most of these studies have been descriptive, they have led to a broad description of the bacterial communities hosted by mosquito populations. This review describes key advances and progress in the field of the mosquito microbiota research while also encompassing other microbes and the environmental factors driving their composition and diversity. The discussion includes recent findings on the microbiota functional roles and underlines their interactions with the host biology and pathogen transmission. Insight into the ecology of multipartite interactions, we consider that conferring the term holobiont to the mosquito and its microbiota is useful to get a comprehensive understanding of the vector pathosystem functioning so as to be able to develop innovative and efficient novel vector control strategies.}, }
@article {pmid29546438, year = {2018}, author = {Rua, CPJ and de Oliveira, LS and Froes, A and Tschoeke, DA and Soares, AC and Leomil, L and Gregoracci, GB and Coutinho, R and Hajdu, E and Thompson, CC and Berlinck, RGS and Thompson, FL}, title = {Microbial and Functional Biodiversity Patterns in Sponges that Accumulate Bromopyrrole Alkaloids Suggest Horizontal Gene Transfer of Halogenase Genes.}, journal = {Microbial ecology}, volume = {76}, number = {3}, pages = {825-838}, pmid = {29546438}, issn = {1432-184X}, support = {CNE E-26/110.735/2013//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; CIMAR 1986/2014//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; BIOTA/BIOprospecTA grant 2013/50228-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/17616- 7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {Alkaloids/*metabolism ; Animals ; Bacteria/*enzymology/genetics/isolation &amp; purification/metabolism ; Bacterial Proteins/*genetics/metabolism ; *Biodiversity ; Bromine/metabolism ; Gene Transfer, Horizontal ; Hydrolases/*genetics/metabolism ; Phylogeny ; Porifera/chemistry/*microbiology ; Secondary Metabolism ; }, abstract = {Marine sponge holobionts harbor complex microbial communities whose members may be the true producers of secondary metabolites accumulated by sponges. Bromopyrrole alkaloids constitute a typical class of secondary metabolites isolated from sponges that very often display biological activities. Bromine incorporation into secondary metabolites can be catalyzed by either halogenases or haloperoxidases. The diversity of the metagenomes of sponge holobiont species containing bromopyrrole alkaloids (Agelas spp. and Tedania brasiliensis) as well as holobionts devoid of bromopyrrole alkaloids spanning in a vast biogeographic region (approx. Seven thousand km) was studied. The origin and specificity of the detected halogenases was also investigated. The holobionts Agelas spp. and T. brasiliensis did not share microbial halogenases, suggesting a species-specific pattern. Bacteria of diverse phylogenetic origins encoding halogenase genes were found to be more abundant in bromopyrrole-containing sponges. The sponge holobionts (e.g., Agelas spp.) with the greatest number of sequences related to clustered, interspaced, short, palindromic repeats (CRISPRs) exhibited the fewest phage halogenases, suggesting a possible mechanism of protection from phage infection by the sponge host. This study highlights the potential of phages to transport halogenases horizontally across host sponges, particularly in more permissive holobiont hosts, such as Tedania spp.}, }
@article {pmid29540239, year = {2018}, author = {Sevellec, M and Derome, N and Bernatchez, L}, title = {Holobionts and ecological speciation: the intestinal microbiota of lake whitefish species pairs.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {47}, pmid = {29540239}, issn = {2049-2618}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; Base Sequence ; DNA, Bacterial/genetics ; Gastrointestinal Microbiome/*genetics ; Intestines/*microbiology ; Lakes/*microbiology ; RNA, Ribosomal, 16S/genetics ; Salmonidae/*classification/*microbiology ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: It is well established that symbionts have considerable impact on their host, yet the investigation of the possible role of the holobiont in the host's speciation process is still in its infancy. In this study, we compared the intestinal microbiota among five sympatric pairs of dwarf (limnetic) and normal (benthic) lake whitefish Coregonus clupeaformis representing a continuum in the early stage of ecological speciation. We sequenced the 16s rRNA gene V3-V4 regions of the intestinal microbiota present in a total of 108 wild sympatric dwarf and normal whitefish as well as the water bacterial community from five lakes to (i) test for differences between the whitefish intestinal microbiota and the water bacterial community and (ii) test for parallelism in the intestinal microbiota of dwarf and normal whitefish.<br><br>RESULTS: The water bacterial community was distinct from the intestinal microbiota, indicating that intestinal microbiota did not reflect the environment, but rather the intrinsic properties of the host microbiota. Our results revealed a strong influence of the host (dwarf or normal) on the intestinal microbiota with pronounced conservation of the core intestinal microbiota (mean ~ 44% of shared genera). However, no clear evidence for parallelism was observed, whereby non-parallel differences between dwarf and normal whitefish were observed in three of the lakes while similar taxonomic composition was observed for the two other species pairs.<br><br>CONCLUSIONS: This absence of parallelism across dwarf vs. normal whitefish microbiota highlighted the complexity of the holobiont and suggests that the direction of selection could be different between the host and its microbiota.}, }
@article {pmid29523192, year = {2018}, author = {Pita, L and Rix, L and Slaby, BM and Franke, A and Hentschel, U}, title = {The sponge holobiont in a changing ocean: from microbes to ecosystems.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {46}, pmid = {29523192}, issn = {2049-2618}, support = {679849//Horizon 2020/International ; 679849//Horizon 2020/International ; CRC1182-TPB1//Deutsche Forschungsgemeinschaft/International ; }, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*metabolism ; Carbon/metabolism ; Climate Change ; Dysbiosis/*pathology ; Ecosystem ; Microbiota/*physiology ; Nitrogen/metabolism ; Oceans and Seas ; Phosphorus/metabolism ; Porifera/*metabolism/*microbiology ; Symbiosis/*physiology ; }, abstract = {The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as &quot;nested ecosystems.&quot; In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities-a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans.}, }
@article {pmid29507840, year = {2018}, author = {Brüwer, JD and Voolstra, CR}, title = {First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4449}, pmid = {29507840}, issn = {2167-8359}, abstract = {Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.}, }
@article {pmid29505062, year = {2018}, author = {Haag, KL}, title = {Holobionts and their hologenomes: Evolution with mixed modes of inheritance.}, journal = {Genetics and molecular biology}, volume = {41}, number = {1 suppl 1}, pages = {189-197}, pmid = {29505062}, issn = {1415-4757}, abstract = {Symbioses are ubiquitous and have played an influential role in the evolution of life on Earth. Genomic studies are now revealing a huge diversity of associations among hosts and their microbiotas, allowing us to characterize their complex ecological and evolutionary dynamics. The different transmission modes and the asynchronous cell proliferation of the numerous symbionts associated with one host generate a genomic conflict ought to be solved. Two disputing views have been used to model and predict the outcome of such conflicts. The traditional view is based on community ecology, and considers that selection at the level of individuals is sufficient to explain longstanding associations among species. A new perspective considers that the host and its associated microbiota constitute a biological entity called holobiont, and that regarding it as a higher-level unit of selection is unavoidable to understand phenotypic evolution. Novel extended phenotypes are often built through symbiotic interactions, allowing the holobiont to explore and survive in distinct environmental conditions, and may evolve in a Lamarckian fashion.}, }
@article {pmid29499735, year = {2018}, author = {Tetreau, G and Grizard, S and Patil, CD and Tran, FH and Tran Van, V and Stalinski, R and Laporte, F and Mavingui, P and Després, L and Valiente Moro, C}, title = {Bacterial microbiota of Aedes aegypti mosquito larvae is altered by intoxication with Bacillus thuringiensis israelensis.}, journal = {Parasites &amp; vectors}, volume = {11}, number = {1}, pages = {121}, pmid = {29499735}, issn = {1756-3305}, support = {ANR-13-EBID-0007-01//Agence Nationale de la Recherche/International ; }, mesh = {Aedes/*microbiology ; Animals ; Bacillus thuringiensis/*physiology ; DNA Fingerprinting ; Denaturing Gradient Gel Electrophoresis ; Gram-Positive Bacterial Infections ; Larva/*microbiology ; Microbiota/*genetics ; Mosquito Control/methods ; Pest Control, Biological/methods ; }, abstract = {BACKGROUND: Insect microbiota is a dynamic microbial community that can actively participate in defense against pathogens. Bacillus thuringiensis (Bt) is a natural entomopathogen widely used as a bioinsecticide for pest control. Although Bt's mode of action has been extensively studied, whether the presence of microbiota is mandatory for Bt to effectively kill the insect is still under debate. An association between a higher tolerance and a modified microbiota was already evidenced but a critical point remained to be solved: is the modified microbiota a cause or a consequence of a higher tolerance to Bt?<br><br>METHODS: In this study we focused on the mosquito species Aedes aegypti, as no work has been performed on Diptera on this topic to date, and on B. thuringiensis israelensis (Bti), which is used worldwide for mosquito control. To avoid using antibiotics to cure bacterial microbiota, mosquito larvae were exposed to an hourly increasing dose of Bti during 25 hours to separate the most susceptible larvae dying quickly from more tolerant individuals, with longer survival.<br><br>RESULTS: Denaturing gradient gel electrophoresis (DGGE) fingerprinting revealed that mosquito larval bacterial microbiota was strongly affected by Bti infection after only a few hours of exposure. Bacterial microbiota from the most tolerant larvae showed the lowest diversity but the highest inter-individual differences. The proportion of Bti in the host tissue was reduced in the most tolerant larvae as compared to the most susceptible ones, suggesting an active control of Bti infection by the host.<br><br>CONCLUSIONS: Here we show that a modified microbiota is associated with a higher tolerance of mosquitoes to Bti, but that it is rather a consequence of Bti infection than the cause of the higher tolerance. This study paves the way to future investigations aiming at unraveling the role of host immunity, inter-species bacterial competition and kinetics of host colonization by Bti that could be at the basis of the phenotype observed in this study.}, }
@article {pmid29492882, year = {2018}, author = {Grasis, JA}, title = {Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1746}, number = {}, pages = {1-25}, doi = {10.1007/978-1-4939-7683-6_1}, pmid = {29492882}, issn = {1940-6029}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Archaea/*virology ; Bacteria/*virology ; Bacteriophages/*genetics/isolation &amp; purification ; Computational Biology ; Genome, Viral ; *Host-Pathogen Interactions ; *Metagenomics ; }, abstract = {Prokaryotic viruses, or bacteriophages, are viruses that infect bacteria and archaea. These viruses have been known to associate with host systems for decades, yet only recently have their influence on the regulation of host-associated bacteria been appreciated. These studies have been conducted in many host systems, from the base of animal life in the Cnidarian phylum to mammals. These prokaryotic viruses are useful for regulating the number of bacteria in a host ecosystem and for regulating the strains of bacteria useful for the microbiome. These viruses are likely selected by the host to maintain bacterial populations. Viral metagenomics allows researchers to profile the communities of viruses associating with animal hosts, and importantly helps to determine the functional role these viruses play. Further, viral metagenomics show the sphere of viral involvement in gene flow and gene shuffling in an ever-changing host environment. The influence of prokaryotic viruses could, therefore, have a clear impact on host health.}, }
@article {pmid29473977, year = {2018}, author = {Ramsby, BD and Hoogenboom, MO and Whalan, S and Webster, NS}, title = {Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge.}, journal = {Molecular ecology}, volume = {27}, number = {8}, pages = {2124-2137}, doi = {10.1111/mec.14544}, pmid = {29473977}, issn = {1365-294X}, mesh = {Animals ; *Ecology ; Microbiota/*genetics/physiology ; Porifera/genetics/growth &amp; development/*microbiology ; Seawater/microbiology ; Temperature ; }, abstract = {Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The &quot;core&quot; microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.}, }
@article {pmid29468040, year = {2018}, author = {Pogoreutz, C and Rädecker, N and Cárdenas, A and Gärdes, A and Wild, C and Voolstra, CR}, title = {Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome.}, journal = {Ecology and evolution}, volume = {8}, number = {4}, pages = {2240-2252}, pmid = {29468040}, issn = {2045-7758}, abstract = {The importance of Symbiodinium algal endosymbionts and a diverse suite of bacteria for coral holobiont health and functioning are widely acknowledged. Yet, we know surprisingly little about microbial community dynamics and the stability of host-microbe associations under adverse environmental conditions. To gain insight into the stability of coral host-microbe associations and holobiont structure, we assessed changes in the community structure of Symbiodinium and bacteria associated with the coral Pocillopora verrucosa under excess organic nutrient conditions. Pocillopora-associated microbial communities were monitored over 14 days in two independent experiments. We assessed the effect of excess dissolved organic nitrogen (DON) and excess dissolved organic carbon (DOC). Exposure to excess nutrients rapidly affected coral health, resulting in two distinct stress phenotypes: coral bleaching under excess DOC and severe tissue sloughing (>90% tissue loss resulting in host mortality) under excess DON. These phenotypes were accompanied by structural changes in the Symbiodinium community. In contrast, the associated bacterial community remained remarkably stable and was dominated by two Endozoicomonas phylotypes, comprising on average 90% of 16S rRNA gene sequences. This dominance of Endozoicomonas even under conditions of coral bleaching and mortality suggests the bacterial community of P. verrucosa may be rather inflexible and thereby unable to respond or acclimatize to rapid changes in the environment, contrary to what was previously observed in other corals. In this light, our results suggest that coral holobionts might occupy structural landscapes ranging from a highly flexible to a rather inflexible composition with consequences for their ability to respond to environmental change.}, }
@article {pmid29463295, year = {2018}, author = {Brener-Raffalli, K and Clerissi, C and Vidal-Dupiol, J and Adjeroud, M and Bonhomme, F and Pratlong, M and Aurelle, D and Mitta, G and Toulza, E}, title = {Thermal regime and host clade, rather than geography, drive Symbiodinium and bacterial assemblages in the scleractinian coral Pocillopora damicornis sensu lato.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {39}, pmid = {29463295}, issn = {2049-2618}, support = {ANR-12-ADAP-0016//Agence Nationale de la Recherche/International ; }, mesh = {Acinetobacter/genetics/*isolation &amp; purification ; Animals ; Anthozoa/*microbiology/*parasitology ; Arcobacter/genetics/*isolation &amp; purification ; DNA, Intergenic/genetics ; Dinoflagellida/genetics/*isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Oceanospirillaceae/genetics/*isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Symbiosis/physiology ; }, abstract = {BACKGROUND: Although the term holobiont has been popularized in corals with the advent of the hologenome theory of evolution, the underlying concepts are still a matter of debate. Indeed, the relative contribution of host and environment and especially thermal regime in shaping the microbial communities should be examined carefully to evaluate the potential role of symbionts for holobiont adaptation in the context of global changes. We used the sessile, long-lived, symbiotic and environmentally sensitive reef-building coral Pocillopora damicornis to address these issues.<br><br>RESULTS: We sampled Pocillopora damicornis colonies corresponding to two different mitochondrial lineages in different geographic areas displaying different thermal regimes: Djibouti, French Polynesia, New Caledonia, and Taiwan. The community composition of bacteria and the algal endosymbiont Symbiodinium were characterized using high-throughput sequencing of 16S rRNA gene and internal transcribed spacer, ITS2, respectively. Bacterial microbiota was very diverse with high prevalence of Endozoicomonas, Arcobacter, and Acinetobacter in all samples. While Symbiodinium sub-clade C1 was dominant in Taiwan and New Caledonia, D1 was dominant in Djibouti and French Polynesia. Moreover, we also identified a high background diversity (i.e., with proportions < 1%) of A1, C3, C15, and G Symbiodinum sub-clades. Using redundancy analyses, we found that the effect of geography was very low for both communities and that host genotypes and temperatures differently influenced Symbiodinium and bacterial microbiota. Indeed, while the constraint of host haplotype was higher than temperatures on bacterial composition, we showed for the first time a strong relationship between the composition of Symbiodinium communities and minimal sea surface temperatures.<br><br>CONCLUSION: Because Symbiodinium assemblages are more constrained by the thermal regime than bacterial communities, we propose that their contribution to adaptive capacities of the holobiont to temperature changes might be higher than the influence of bacterial microbiota. Moreover, the link between Symbiodinium community composition and minimal temperatures suggests low relative fitness of clade D at lower temperatures. This observation is particularly relevant in the context of climate change, since corals will face increasing temperatures as well as much frequent abnormal cold episodes in some areas of the world.}, }
@article {pmid29453252, year = {2018}, author = {Romano, S}, title = {Ecology and Biotechnological Potential of Bacteria Belonging to the Genus Pseudovibrio.}, journal = {Applied and environmental microbiology}, volume = {84}, number = {8}, pages = {}, pmid = {29453252}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/microbiology ; Biotechnology ; Environment ; Porifera/microbiology ; Rhodobacteraceae/growth &amp; development/metabolism/*physiology ; *Symbiosis ; }, abstract = {Members of the genus Pseudovibrio have been isolated worldwide from a great variety of marine sources as both free-living and host-associated bacteria. So far, the available data depict a group of alphaproteobacteria characterized by a versatile metabolism, which allows them to use a variety of substrates to meet their carbon, nitrogen, sulfur, and phosphorous requirements. Additionally, Pseudovibrio-related bacteria have been shown to proliferate under extreme oligotrophic conditions, tolerate high heavy-metal concentrations, and metabolize potentially toxic compounds. Considering this versatility, it is not surprising that they have been detected from temperate to tropical regions and are often the most abundant isolates obtained from marine invertebrates. Such an association is particularly recurrent with marine sponges and corals, animals that play a key role in benthic marine systems. The data so far available indicate that these bacteria are mainly beneficial to the host, and besides being involved in major nutrient cycles, they could provide the host with both vitamins/cofactors and protection from potential pathogens via the synthesis of antimicrobial secondary metabolites. In fact, the biosynthetic abilities of Pseudovibrio spp. have been emerging in recent years, and both genomic and analytic studies have underlined how these organisms promise novel natural products of biotechnological value.}, }
@article {pmid29441234, year = {2018}, author = {Bonthond, G and Merselis, DG and Dougan, KE and Graff, T and Todd, W and Fourqurean, JW and Rodriguez-Lanetty, M}, title = {Inter-domain microbial diversity within the coral holobiont Siderastrea siderea from two depth habitats.}, journal = {PeerJ}, volume = {6}, number = {}, pages = {e4323}, pmid = {29441234}, issn = {2167-8359}, abstract = {Corals host diverse microbial communities that are involved in acclimatization, pathogen defense, and nutrient cycling. Surveys of coral-associated microbes have been particularly directed toward Symbiodinium and bacteria. However, a holistic understanding of the total microbiome has been hindered by a lack of analyses bridging taxonomically disparate groups. Using high-throughput amplicon sequencing, we simultaneously characterized the Symbiodinium, bacterial, and fungal communities associated with the Caribbean coral Siderastrea siderea collected from two depths (17 and 27 m) on Conch reef in the Florida Keys. S. siderea hosted an exceptionally diverse Symbiodinium community, structured differently between sampled depth habitats. While dominated at 27 m by a Symbiodinium belonging to clade C, at 17 m S. siderea primarily hosted a mixture of clade B types. Most fungal operational taxonomic units were distantly related to available reference sequences, indicating the presence of a high degree of fungal novelty within the S. siderea holobiont and a lack of knowledge on the diversity of fungi on coral reefs. Network analysis showed that co-occurrence patterns in the S. siderea holobiont were prevalent among bacteria, however, also detected between fungi and bacteria. Overall, our data show a drastic shift in the associated Symbiodinium community between depths on Conch Reef, which might indicate that alteration in this community is an important mechanism facilitating local physiological adaptation of the S. siderea holobiont. In contrast, bacterial and fungal communities were not structured differently between depth habitats.}, }
@article {pmid29435256, year = {2018}, author = {Leite, DCA and Salles, JF and Calderon, EN and van Elsas, JD and Peixoto, RS}, title = {Specific plasmid patterns and high rates of bacterial co-occurrence within the coral holobiont.}, journal = {Ecology and evolution}, volume = {8}, number = {3}, pages = {1818-1832}, pmid = {29435256}, issn = {2045-7758}, abstract = {Despite the importance of coral microbiomes for holobiont persistence, the interactions among these are not well understood. In particular, knowledge of the co-occurrence and taxonomic importance of specific members of the microbial core, as well as patterns of specific mobile genetic elements (MGEs), is lacking. We used seawater and mucus samples collected from Mussismilia hispida colonies on two reefs located in Bahia, Brazil, to disentangle their associated bacterial communities, intertaxa correlations, and plasmid patterns. Proxies for two broad-host-range (BHR) plasmid groups, IncP-1β and PromA, were screened. Both groups were significantly (up to 252 and 100%, respectively) more abundant in coral mucus than in seawater. Notably, the PromA plasmid group was detected only in coral mucus samples. The core bacteriome of M. hispida mucus was composed primarily of members of the Proteobacteria, followed by those of Firmicutes. Significant host specificity and co-occurrences among different groups of the dominant phyla (e.g., Bacillaceae and Pseudoalteromonadaceae and the genera Pseudomonas, Bacillus, and Vibrio) were detected. These relationships were observed for both the most abundant phyla and the bacteriome core, in which most of the operational taxonomic units showed intertaxa correlations. The observed evidence of host-specific bacteriome and co-occurrence (and potential symbioses or niche space co-dominance) among the most dominant members indicates a taxonomic selection of members of the stable bacterial community. In parallel, host-specific plasmid patterns could also be, independently, related to the assembly of members of the coral microbiome.}, }
@article {pmid29433554, year = {2018}, author = {Cregger, MA and Veach, AM and Yang, ZK and Crouch, MJ and Vilgalys, R and Tuskan, GA and Schadt, CW}, title = {The Populus holobiont: dissecting the effects of plant niches and genotype on the microbiome.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {31}, pmid = {29433554}, issn = {2049-2618}, mesh = {Archaea/*classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Fungi/*classification/genetics/isolation &amp; purification ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Microbiota ; Organ Specificity ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Plant Stems/microbiology ; Populus/*genetics/microbiology ; Rhizosphere ; Sequence Analysis, DNA/*methods ; Soil Microbiology ; }, abstract = {BACKGROUND: Microorganisms serve important functions within numerous eukaryotic host organisms. An understanding of the variation in the plant niche-level microbiome, from rhizosphere soils to plant canopies, is imperative to gain a better understanding of how both the structural and functional processes of microbiomes impact the health of the overall plant holobiome. Using Populus trees as a model ecosystem, we characterized the archaeal/bacterial and fungal microbiome across 30 different tissue-level niches within replicated Populus deltoides and hybrid Populus trichocarpa × deltoides individuals using 16S and ITS2 rRNA gene analyses.<br><br>RESULTS: Our analyses indicate that archaeal/bacterial and fungal microbiomes varied primarily across broader plant habitat classes (leaves, stems, roots, soils) regardless of plant genotype, except for fungal communities within leaf niches, which were greatly impacted by the host genotype. Differences between tree genotypes are evident in the elevated presence of two potential fungal pathogens, Marssonina brunnea and Septoria sp., on hybrid P. trichocarpa × deltoides trees which may in turn be contributing to divergence in overall microbiome composition. Archaeal/bacterial diversity increased from leaves, to stem, to root, and to soil habitats, whereas fungal diversity was the greatest in stems and soils.<br><br>CONCLUSIONS: This study provides a holistic understanding of microbiome structure within a bioenergy relevant plant host, one of the most complete niche-level analyses of any plant. As such, it constitutes a detailed atlas or map for further hypothesis testing on the significance of individual microbial taxa within specific niches and habitats of Populus and a baseline for comparisons to other plant species.}, }
@article {pmid29430857, year = {2018}, author = {Voss, JD and Goodson, MS and Leon, JC}, title = {Phenotype diffusion and one health: A proposed framework for investigating the plurality of obesity epidemics across many species.}, journal = {Zoonoses and public health}, volume = {65}, number = {3}, pages = {279-290}, doi = {10.1111/zph.12445}, pmid = {29430857}, issn = {1863-2378}, mesh = {Animals ; *Epidemics ; Humans ; Obesity/epidemiology/*veterinary ; *One Health ; }, abstract = {We propose the idea of &quot;phenotype diffusion,&quot; which is a rapid convergence of an observed trait in some human and animal populations. The words phenotype and diffusion both imply observations independent of mechanism as phenotypes are observed traits with multiple possible genetic mechanisms and diffusion is an observed state of being widely distributed. Recognizing shared changes in phenotype in multiple species does not by itself reveal a particular mechanism such as a shared exposure, shared adaptive need, particular stochastic process or a transmission pathway. Instead, identifying phenotype diffusion suggests the mechanism should be explored to help illuminate the ways human and animal health are connected and new opportunities for optimizing these links. Using the plurality of obesity epidemics across multiple species as a prototype for shared changes in phenotype, the goal of this review was to explore eco-evolutionary theories that could inform further investigation. First, evolutionary changes described by hologenome evolution, pawnobe evolution, transposable element (TE) thrust and the drifty gene hypothesis will be discussed within the context of the selection asymmetries among human and animal populations. Secondly, the ecology of common source exposures (bovine milk, xenohormesis and &quot;obesogens&quot;), niche evolution and the hygiene hypothesis will be summarized. Finally, we synthesize these considerations. For example, many agricultural breeds have been aggressively selected for weight gain, microbiota (e.g., adenovirus 36, toxoplasmosis) associated with (or infecting) these breeds cause experimental weight gain in other animals, and these same microbes are associated with human obesity. We propose applications of phenotype diffusion could include zoonotic biosurveillance, biocontainment, antibiotic stewardship and environmental priorities. The One Health field is focused on the connections between the health of humans, animals and the environment, and so identification of phenotype diffusion is highly relevant for practitioners (public health officials, physicians and veterinarians) in this field.}, }
@article {pmid29423641, year = {2018}, author = {Feng, G and Sun, W and Zhang, F and Orlić, S and Li, Z}, title = {Functional Transcripts Indicate Phylogenetically Diverse Active Ammonia-Scavenging Microbiota in Sympatric Sponges.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {20}, number = {2}, pages = {131-143}, pmid = {29423641}, issn = {1436-2236}, mesh = {Ammonia/*metabolism ; Animals ; Archaea/classification/enzymology/genetics ; Bacteria/classification/enzymology/genetics ; Glutamate-Ammonia Ligase/genetics ; Microbiota/genetics/*physiology ; Oxidoreductases/genetics ; Phylogeny ; Porifera/*physiology ; Seawater ; Symbiosis ; Transcriptome ; }, abstract = {Symbiotic ammonia scavengers contribute to effective removal of ammonia in sponges. However, the phylogenetic diversity and in situ activity of ammonia-scavenging microbiota between different sponge species are poorly addressed. Here, transcribed ammonia monooxygenase genes (amoA), hydrazine synthase genes (hzsA), and glutamine synthetase genes (glnA) were analyzed to reveal the active ammonia-scavenging microbiota in the sympatric sponges Theonella swinhoei, Plakortis simplex, and Phakellia fusca, and seawater. Archaeal amoA and bacterial glnA transcripts rather than bacterial amoA, hzsA, and archaeal glnA transcripts were detected in the investigated sponges and seawater. The transcribed amoA genes were ascribed to two Thaumarchaeota ecotypes, while the transcribed glnA genes were interspersed among the lineages of Cyanobacteria, Tectomicrobia, Poribacteria, Alpha-, Beta-, Gamma-, and Epsilonproteobacteria. In addition, transcribed abundances of archaeal amoA and bacterial glnA genes in these sponges have been quantified, showing significant variation among the investigated sponges and seawater. The transcriptome-based qualitative and quantitative analyses clarified the different phylogenetic diversity and transcription expression of functional genes related to microbially mediated ammonia scavenging in different sympatric sponges, contributing to the understanding of in situ active ecological functions of sponge microbial symbionts in holobiont nitrogen cycling.}, }
@article {pmid29410656, year = {2018}, author = {Rubio-Portillo, E and Kersting, DK and Linares, C and Ramos-Esplá, AA and Antón, J}, title = {Biogeographic Differences in the Microbiome and Pathobiome of the Coral Cladocora caespitosa in the Western Mediterranean Sea.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {22}, pmid = {29410656}, issn = {1664-302X}, abstract = {The endemic Mediterranean zooxanthellate scleractinian reef-builder Cladocora caespitosa is among the organisms most affected by warming-related mass mortality events in the Mediterranean Sea. Corals are known to contain a diverse microbiota that plays a key role in their physiology and health. Here we report the first study that examines the microbiome and pathobiome associated with C. caespitosa in three different Mediterranean locations (i.e., Genova, Columbretes Islands, and Tabarca Island). The microbial communities associated with this species showed biogeographical differences, but shared a common core microbiome that probably plays a key role in the coral holobiont. The putatively pathogenic microbial assemblage (i.e., pathobiome) of C. caespitosa also seemed to depend on geographic location and the human footprint. In locations near the coast and with higher human influence, the pathobiome was entirely constituted by Vibrio species, including the well-known coral pathogens Vibrio coralliilyticus and V. mediterranei. However, in the Columbretes Islands, located off the coast and the most pristine of the analyzed locations, no changes among microbial communities associated to healthy and necrosed samples were detected. Hence, our results provide new insights into the microbiome of the temperate corals and its role in coral health status, highlighting its dependence on the local environmental conditions and the human footprint.}, }
@article {pmid29403516, year = {2018}, author = {Saminathan, T and García, M and Ghimire, B and Lopez, C and Bodunrin, A and Nimmakayala, P and Abburi, VL and Levi, A and Balagurusamy, N and Reddy, UK}, title = {Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits.}, journal = {Frontiers in plant science}, volume = {9}, number = {}, pages = {4}, pmid = {29403516}, issn = {1664-462X}, abstract = {The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.}, }
@article {pmid29396559, year = {2018}, author = {Massé, A and Domart-Coulon, I and Golubic, S and Duché, D and Tribollet, A}, title = {Early skeletal colonization of the coral holobiont by the microboring Ulvophyceae Ostreobium sp.}, journal = {Scientific reports}, volume = {8}, number = {1}, pages = {2293}, pmid = {29396559}, issn = {2045-2322}, mesh = {Animal Shells/*microbiology ; Animals ; Anthozoa/*microbiology ; Chlorophyta/classification/genetics/*growth &amp; development ; Genetic Variation ; Metagenome ; Ribulose-Bisphosphate Carboxylase/genetics ; *Symbiosis ; }, abstract = {Ostreobium sp. (Bryopsidales, Ulvophyceae) is a major microboring alga involved in tropical reef dissolution, with a proposed symbiotic lifestyle in living corals. However, its diversity and colonization dynamics in host's early life stages remained unknown. Here, we mapped microborer distribution and abundance in skeletons of the branching coral Pocillopora damicornis from the onset of calcification in primary polyps (7 days) to budding juvenile colonies (1 and 3 months) growing on carbonate and non-carbonate substrates pre-colonized by natural biofilms, and compared them to adult colonies (in aquarium settings). Primary polyps were surprisingly already colonized by microboring filaments and their level of invasion depended on the nature of settlement substrate and the extent of its pre-colonization by microborers. Growth of early coral recruits was unaffected even when microborers were in close vicinity to the polyp tissue. In addition to morphotype observations, chloroplast-encoded rbcL gene sequence analyses revealed nine new Ostreobium clades (OTU99%) in Pocillopora coral. Recruits and adults shared one dominant rbcL clade, undetected in larvae, but also present in aquarium seawater, carbonate and non-carbonate settlement substrates, and in corals from reef settings. Our results show a substratum-dependent colonization by Ostreobium clades, and indicate horizontal transmission of Ostreobium-coral associations.}, }
@article {pmid29395346, year = {2018}, author = {Limborg, MT and Alberdi, A and Kodama, M and Roggenbuck, M and Kristiansen, K and Gilbert, MTP}, title = {Applied Hologenomics: Feasibility and Potential in Aquaculture.}, journal = {Trends in biotechnology}, volume = {36}, number = {3}, pages = {252-264}, doi = {10.1016/j.tibtech.2017.12.006}, pmid = {29395346}, issn = {1879-3096}, mesh = {Animals ; *Aquaculture ; Epigenomics ; *Feasibility Studies ; Fishes/*microbiology ; Food Industry ; Gastrointestinal Microbiome/genetics/immunology ; Genome, Microbial/genetics/immunology ; Humans ; Immune System/immunology/microbiology ; *Metagenomics ; Proteomics ; Transcriptome ; }, abstract = {Aquaculture will play an essential role in feeding a growing human population, but several biological challenges impede sustainable growth of production. Emerging evidence across all areas of life has revealed the importance of the intimate biological interactions between animals and their associated gut microbiota. Based on challenges in aquaculture, we leverage current knowledge in molecular biology and host microbiota interactions to propose an applied holo-omic framework that integrates molecular data including genomes, transcriptomes, epigenomes, proteomes, and metabolomes for analyzing fish and their gut microbiota as interconnected and coregulated systems. With an eye towards aquaculture, we discuss the feasibility and potential of our holo-omic framework to improve growth, health, and sustainability in any area of food production, including livestock and agriculture.}, }
@article {pmid29386628, year = {2018}, author = {Achlatis, M and Pernice, M and Green, K and Guagliardo, P and Kilburn, MR and Hoegh-Guldberg, O and Dove, S}, title = {Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge.}, journal = {The ISME journal}, volume = {12}, number = {5}, pages = {1308-1318}, pmid = {29386628}, issn = {1751-7370}, mesh = {Ammonium Compounds/*metabolism ; Animals ; Bicarbonates/*metabolism ; Coral Reefs ; Dinoflagellida/*metabolism ; Ecosystem ; Porifera/*metabolism ; Single-Cell Analysis ; *Symbiosis ; }, abstract = {Some of the most aggressive coral-excavating sponges host intracellular dinoflagellates from the genus Symbiodinium, which are hypothesized to provide the sponges with autotrophic energy that powers bioerosion. Investigations of the contribution of Symbiodinium to host metabolism and particularly inorganic nutrient recycling are complicated, however, by the presence of alternative prokaryotic candidates for this role. Here, novel methods are used to study nutrient assimilation and transfer within and between the outer-layer cells of the Indopacific bioeroding sponge Cliona orientalis. Combining stable isotope labelling, transmission electron microscopy (TEM) and nanoscale secondary ion mass spectrometry (NanoSIMS), we visualize and measure metabolic activity at the individual cell level, tracking the fate of 15N-ammonium and 13C-bicarbonate within the intact holobiont. We found strong uptake of both inorganic sources (especially 13C-bicarbonate) by Symbiodinium cells. Labelled organic nutrients were translocated from Symbiodinium to the Symbiodinium-hosting sponge cells within 6 h, and occasionally to other sponge cells within 3 days. By contrast, prokaryotic symbionts were not observed to participate in inorganic nutrient assimilation in the outer layers of the sponge. Our findings strongly support the metabolic interaction between the sponge and dinoflagellates, shedding light on the ecological advantages and adaptive capacity of photosymbiotic bioeroding sponges in oligotrophic marine habitats.}, }
@article {pmid29382945, year = {2018}, author = {Frischkorn, KR and Haley, ST and Dyhrman, ST}, title = {Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre.}, journal = {The ISME journal}, volume = {12}, number = {4}, pages = {997-1007}, pmid = {29382945}, issn = {1751-7370}, mesh = {Carbon/metabolism ; *Gene Expression Regulation, Bacterial ; Heterotrophic Processes ; *Microbial Interactions ; Microbiota/*genetics ; Nitrogen/metabolism ; Oceans and Seas ; Periodicity ; Seawater/microbiology ; Transcriptome ; Trichodesmium/*genetics/metabolism ; }, abstract = {Trichodesmium is a widespread, N2 fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmium ubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmium holobiont could influence the fate of fixed carbon and nitrogen. Metatranscriptome sequencing was performed on Trichodesmium colonies collected during high-frequency Lagrangian sampling in the North Pacific Subtropical Gyre (NPSG) to identify possible interactions between the Trichodesmium host and microbiome over day-night cycles. Here we show significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day-night periodicity. The functions of the co-expressed genes suggested a suite of interactions within the holobiont linked to key resources including nitrogen, carbon, and iron. Evidence of microbiome reliance on Trichodesmium-derived vitamin B12 was also detected in co-expression patterns, highlighting a dependency that could shape holobiont community structure. Collectively, these patterns of expression suggest that biotic interactions could influence colony cycling of resources like nitrogen and vitamin B12, and decouple activities, like N2 fixation, from typical abiotic drivers of Trichodesmium physiological ecology.}, }
@article {pmid29379177, year = {2018}, author = {Baker, DM and Freeman, CJ and Wong, JCY and Fogel, ML and Knowlton, N}, title = {Climate change promotes parasitism in a coral symbiosis.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {921-930}, pmid = {29379177}, issn = {1751-7370}, mesh = {Acclimatization/*physiology ; Animals ; Anthozoa/metabolism/*physiology ; Carbon/metabolism ; *Climate Change ; *Coral Reefs ; Cyanobacteria/metabolism/*physiology ; Dinoflagellida/metabolism/*physiology ; Nitrogen/metabolism ; Symbiosis/*physiology ; *Temperature ; }, abstract = {Coastal oceans are increasingly eutrophic, warm and acidic through the addition of anthropogenic nitrogen and carbon, respectively. Among the most sensitive taxa to these changes are scleractinian corals, which engineer the most biodiverse ecosystems on Earth. Corals' sensitivity is a consequence of their evolutionary investment in symbiosis with the dinoflagellate alga, Symbiodinium. Together, the coral holobiont has dominated oligotrophic tropical marine habitats. However, warming destabilizes this association and reduces coral fitness. It has been theorized that, when reefs become warm and eutrophic, mutualistic Symbiodinium sequester more resources for their own growth, thus parasitizing their hosts of nutrition. Here, we tested the hypothesis that sub-bleaching temperature and excess nitrogen promotes symbiont parasitism by measuring respiration (costs) and the assimilation and translocation of both carbon (energy) and nitrogen (growth; both benefits) within Orbicella faveolata hosting one of two Symbiodinium phylotypes using a dual stable isotope tracer incubation at ambient (26 °C) and sub-bleaching (31 °C) temperatures under elevated nitrate. Warming to 31 °C reduced holobiont net primary productivity (NPP) by 60% due to increased respiration which decreased host %carbon by 15% with no apparent cost to the symbiont. Concurrently, Symbiodinium carbon and nitrogen assimilation increased by 14 and 32%, respectively while increasing their mitotic index by 15%, whereas hosts did not gain a proportional increase in translocated photosynthates. We conclude that the disparity in benefits and costs to both partners is evidence of symbiont parasitism in the coral symbiosis and has major implications for the resilience of coral reefs under threat of global change.}, }
@article {pmid29378627, year = {2018}, author = {Broberg, M and Doonan, J and Mundt, F and Denman, S and McDonald, JE}, title = {Integrated multi-omic analysis of host-microbiota interactions in acute oak decline.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {21}, pmid = {29378627}, issn = {2049-2618}, support = {TH0108//Department for Environment, Food and Rural Affairs/International ; }, mesh = {Bacterial Proteins/genetics/metabolism ; Enterobacteriaceae/genetics/metabolism/*pathogenicity ; Gene Expression Profiling ; Genomics/*methods ; Host-Pathogen Interactions ; Microbiota ; Plant Diseases/*microbiology ; Proteomics ; Quercus/*microbiology ; Sequence Analysis, DNA ; Sequence Analysis, RNA ; Virulence Factors/*genetics/*metabolism ; }, abstract = {BACKGROUND: Britain's native oak species are currently under threat from acute oak decline (AOD), a decline-disease where stem bleeds overlying necrotic lesions in the inner bark and larval galleries of the bark-boring beetle, Agrilus biguttatus, represent the primary symptoms. It is known that complex interactions between the plant host and its microbiome, i.e. the holobiont, significantly influence the health status of the plant. In AOD, necrotic lesions are caused by a microbiome shift to a pathobiome consisting predominantly of Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana and potentially other bacteria. However, the specific mechanistic processes of the microbiota causing tissue necrosis, and the host response, have not been established and represent a barrier to understanding and managing this decline.<br><br>RESULTS: We profiled the metagenome, metatranscriptome and metaproteome of inner bark tissue from AOD symptomatic and non-symptomatic trees to characterise microbiota-host interactions. Active bacterial virulence factors such as plant cell wall-degrading enzymes, reactive oxygen species defence and flagella in AOD lesions, along with host defence responses including reactive oxygen species, cell wall modification and defence regulators were identified. B. goodwinii dominated the lesion microbiome, with significant expression of virulence factors such as the phytopathogen effector avrE. A smaller proportion of microbiome activity was attributed to G. quercinecans and R. victoriana. In addition, we describe for the first time the potential role of two previously uncharacterised Gram-positive bacteria predicted from metagenomic binning and identified as active in the AOD lesion metatranscriptome and metaproteome, implicating them in lesion formation.<br><br>CONCLUSIONS: This multi-omic study provides novel functional insights into microbiota-host interactions in AOD, a complex arboreal decline disease where polymicrobial-host interactions result in lesion formation on tree stems. We present the first descriptions of holobiont function in oak health and disease, specifically, the relative lesion activity of B. goodwinii, G. quercinecans, Rahnella victoriana and other bacteria. Thus, the research presented here provides evidence of some of the mechanisms used by members of the lesion microbiome and a template for future multi-omic research into holobiont characterisation, plant polymicrobial diseases and pathogen defence in trees.}, }
@article {pmid29374490, year = {2018}, author = {Liu, J and Abdelfattah, A and Norelli, J and Burchard, E and Schena, L and Droby, S and Wisniewski, M}, title = {Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.}, journal = {Microbiome}, volume = {6}, number = {1}, pages = {18}, pmid = {29374490}, issn = {2049-2618}, support = {2017YFD0201100//National Key Research and Development Program of China/International ; IS 2513-16//U.S. - Israel Binational Agricultural Research and Development Fund/International ; R2016LX01//Foundation for High-level Talents of Chongqing University of Arts and Sciences/International ; }, mesh = {Actinobacteria/classification/genetics/isolation &amp; purification ; Ascomycota/classification/genetics/isolation &amp; purification ; Bacteria/*classification/genetics/isolation &amp; purification ; Basidiomycota/classification/genetics/isolation &amp; purification ; Endophytes ; Firmicutes/classification/genetics/isolation &amp; purification ; Fungi/*classification/genetics/isolation &amp; purification ; Fusobacteria/classification/genetics/isolation &amp; purification ; Genotype ; High-Throughput Nucleotide Sequencing/*methods ; Malus/*genetics/microbiology ; Microbiota ; Phylogeny ; Plant Roots/microbiology ; Proteobacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/*genetics ; }, abstract = {BACKGROUND: High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, &quot;Royal Gala,&quot; &quot;Golden Delicious,&quot; and &quot;Honey Crisp,&quot; and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component.<br><br>RESULTS: Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9).<br><br>CONCLUSIONS: The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the &quot;holobiont&quot; concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.}, }
@article {pmid29367878, year = {2018}, author = {Marzinelli, EM and Qiu, Z and Dafforn, KA and Johnston, EL and Steinberg, PD and Mayer-Pinto, M}, title = {Coastal urbanisation affects microbial communities on a dominant marine holobiont.}, journal = {NPJ biofilms and microbiomes}, volume = {4}, number = {}, pages = {1}, pmid = {29367878}, issn = {2055-5008}, abstract = {Host-associated microbial communities play a fundamental role in the life of eukaryotic hosts. It is increasingly argued that hosts and their microbiota must be studied together as 'holobionts' to better understand the effects of environmental stressors on host functioning. Disruptions of host-microbiota interactions by environmental stressors can negatively affect host performance and survival. Substantial ecological impacts are likely when the affected hosts are habitat-forming species (e.g., trees, kelps) that underpin local biodiversity. In marine systems, coastal urbanisation via the addition of artificial structures is a major source of stress to habitat formers, but its effect on their associated microbial communities is unknown. We characterised kelp-associated microbial communities in two of the most common and abundant artificial structures in Sydney Harbour-pier-pilings and seawalls-and in neighbouring natural rocky reefs. The kelp Ecklonia radiata is the dominant habitat-forming species along 8000 km of the temperate Australian coast. Kelp-associated microbial communities on pilings differed significantly from those on seawalls and natural rocky reefs, possibly due to differences in abiotic (e.g., shade) and biotic (e.g., grazing) factors between habitats. Many bacteria that were more abundant on kelp on pilings belonged to taxa often associated with macroalgal diseases, including tissue bleaching in Ecklonia. There were, however, no differences in kelp photosynthetic capacity between habitats. The observed differences in microbial communities may have negative effects on the host by promoting fouling by macroorganisms or by causing and spreading disease over time. This study demonstrates that urbanisation can alter the microbiota of key habitat-forming species with potential ecological consequences.}, }
@article {pmid29366516, year = {2017}, author = {Sandoval-Motta, S and Aldana, M and Frank, A}, title = {Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome.}, journal = {Archives of medical research}, volume = {48}, number = {8}, pages = {780-789}, doi = {10.1016/j.arcmed.2018.01.002}, pmid = {29366516}, issn = {1873-5487}, mesh = {Animals ; *Evolution, Molecular ; *Heredity ; Humans ; *Microbiota ; *Selection, Genetic ; }, abstract = {The importance of microorganisms in human biology is undeniable. The amount of research that supports that microbes have a fundamental role in animal and plant physiology is substantial and increasing every year. Even though we are only beginning to comprehend the broadness and complexity of microbial communities, evolutionary theories need to be recast in the light of such discoveries to fully understand and incorporate the role of microbes in our evolution. Fundamental evolutionary concepts such as diversity, heredity, selection, speciation, etc., which constitute the modern synthesis, are now being challenged, or at least expanded, by the emerging notion of the holobiont, which defines the genetic and metabolic networks of the host and its microbes as a single evolutionary unit. Several concepts originally developed to study ecosystems, can be used to understand the physiology and evolution of such complex systems that constitute &quot;individuals.&quot; In this review, we discuss these ecological concepts and also provide examples that range from squids, insects and koalas to other mammals and humans, suggesting that microorganisms have a fundamental role not only in physiology but also in evolution. Current evolutionary theories need to take into account the dynamics and interconnectedness of the host-microbiome network, as animals and plants not only owe their symbiogenetic origin to microbes, but also share a long evolutionary history together.}, }
@article {pmid29334418, year = {2018}, author = {van de Water, JAJM and Chaib De Mares, M and Dixon, GB and Raina, JB and Willis, BL and Bourne, DG and van Oppen, MJH}, title = {Antimicrobial and stress responses to increased temperature and bacterial pathogen challenge in the holobiont of a reef-building coral.}, journal = {Molecular ecology}, volume = {27}, number = {4}, pages = {1065-1080}, doi = {10.1111/mec.14489}, pmid = {29334418}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/drug effects/genetics/*microbiology ; Anti-Infective Agents/*pharmacology ; *Coral Reefs ; Gene Expression Regulation/drug effects ; Seawater ; Stress, Physiological/*drug effects/genetics ; *Temperature ; Transcriptome/genetics ; }, abstract = {Global increases in coral disease prevalence have been linked to ocean warming through changes in coral-associated bacterial communities, pathogen virulence and immune system function. However, the interactive effects of temperature and pathogens on the coral holobiont are poorly understood. Here, we assessed three compartments of the holobiont (host, Symbiodinium and bacterial community) of the coral Montipora aequituberculata challenged with the pathogen Vibrio coralliilyticus and the commensal bacterium Oceanospirillales sp. under ambient (27°C) and elevated (29.5 and 32°C) seawater temperatures. Few visual signs of bleaching and disease development were apparent in any of the treatments, but responses were detected in the holobiont compartments. V. coralliilyticus acted synergistically and negatively impacted the photochemical efficiency of Symbiodinium at 32°C, while Oceanospirillales had no significant effect on photosynthetic efficiency. The coral, however, exhibited a minor response to the bacterial challenges, with the response towards V. coralliilyticus being significantly more pronounced, and involving the prophenoloxidase-activating system and multiple immune system-related genes. Elevated seawater temperatures did not induce shifts in the coral-associated bacterial community, but caused significant gene expression modulation in both Symbiodinium and the coral host. While Symbiodinium exhibited an antiviral response and upregulated stress response genes, M. aequituberculata showed regulation of genes involved in stress and innate immune response processes, including immune and cytokine receptor signalling, the complement system, immune cell activation and phagocytosis, as well as molecular chaperones. These observations show that M. aequituberculata is capable of maintaining a stable bacterial community under elevated seawater temperatures and thereby contributes to preventing disease development.}, }
@article {pmid29324042, year = {2018}, author = {Bartholomay, LC and Michel, K}, title = {Mosquito Immunobiology: The Intersection of Vector Health and Vector Competence.}, journal = {Annual review of entomology}, volume = {63}, number = {}, pages = {145-167}, doi = {10.1146/annurev-ento-010715-023530}, pmid = {29324042}, issn = {1545-4487}, support = {R21 AI117204/AI/NIAID NIH HHS/United States ; R01 AI095842/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Culicidae/*immunology/microbiology ; Host-Pathogen Interactions/*immunology ; Microbiota ; }, abstract = {As holometabolous insects that occupy distinct aquatic and terrestrial environments in larval and adult stages and utilize hematophagy for nutrient acquisition, mosquitoes are subjected to a wide variety of symbiotic interactions. Indeed, mosquitoes play host to endosymbiotic, entomopathogenic, and mosquito-borne organisms, including protozoa, viruses, bacteria, fungi, fungal-like organisms, and metazoans, all of which trigger and shape innate infection-response capacity. Depending on the infection or interaction, the mosquito may employ, for example, cellular and humoral immune effectors for septic infections in the hemocoel, humoral infection responses in the midgut lumen, and RNA interference and programmed cell death for intracellular pathogens. These responses often function in concert, regardless of the infection type, and provide a robust front to combat infection. Mosquito-borne pathogens and entomopathogens overcome these immune responses, employing avoidance or suppression strategies. Burgeoning methodologies are capitalizing on this concerted deployment of immune responses to control mosquito-borne disease.}, }
@article {pmid29312241, year = {2017}, author = {Florez, JZ and Camus, C and Hengst, MB and Buschmann, AH}, title = {A Functional Perspective Analysis of Macroalgae and Epiphytic Bacterial Community Interaction.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2561}, pmid = {29312241}, issn = {1664-302X}, abstract = {Macroalgae are photosynthetic, multicellular, sessile eukaryotic organisms that offer diverse habitats for the colonization of epiphytic bacteria, therefore establishing biological interactions of diverse complexity. This review focusses on the interactions between macroalgae and their Epiphytic Bacterial Community (EBC); the main aims are to ascertain whether (1) the epiphytic bacterial groups differ at the phylum and genus levels of the macroalgae; (2) the methodologies used so far to study these microorganisms are related in any way to eventual variations of the EBCs on macroalgae; and (3) the EBC of macroalgae has a functional means rather a simple taxonomic grouping. Results showed firstly the taxonomic grouping of macroalgae does not explain the composition and structure of the EBCs. Secondly, the methodology used is important for describing EBCs; and thirdly, multiple bacteria can have the same function and thus to describe the functionality of EBCs it is important to recognize host-specific and generalist bacteria. We recommend the incorporation of a complementary approach between the taxonomic composition and the functional composition analyzes of EBCs, as well as the use of methodological tools that allow analysis of interactions between the EBCs and their hosts, based on the &quot;holobiont&quot; concept.}, }
@article {pmid29312170, year = {2017}, author = {KleinJan, H and Jeanthon, C and Boyen, C and Dittami, SM}, title = {Exploring the Cultivable Ectocarpus Microbiome.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {2456}, pmid = {29312170}, issn = {1664-302X}, abstract = {Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal-bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.}, }
@article {pmid29308251, year = {2017}, author = {Sangsawang, L and Casareto, BE and Ohba, H and Vu, HM and Meekaew, A and Suzuki, T and Yeemin, T and Suzuki, Y}, title = {13C and 15N assimilation and organic matter translocation by the endolithic community in the massive coral Porites lutea.}, journal = {Royal Society open science}, volume = {4}, number = {12}, pages = {171201}, pmid = {29308251}, issn = {2054-5703}, abstract = {Corals evolved by establishing symbiotic relationships with various microorganisms (the zooxanthellae, filamentous algae, cyanobacteria, bacteria, archaea, fungi and viruses), forming the 'coral holobiont'. Among them, the endolithic community is the least studied. Its main function was considered to be translocation of photo-assimilates to the coral host, particularly during bleaching. Here, we hypothesize that (i) endolithic algae may show similar primary production rates in healthy or bleached corals by changing their pigment ratios, and therefore that similar production and translocation of organic matter may occur at both conditions and (ii) diazotrophs are components of the endolithic community; therefore, N2 fixation and translocation of organic nitrogen may occur. We tested these hypotheses in incubation of Porites lutea with 13C and 15N tracers to measure primary production and N2 fixation in coral tissues and endoliths. Assimilation of the 13C atom (%) was observed in healthy and bleached corals when the tracer was injected in the endolithic band, showing translocation in both conditions. N2 fixation was found in coral tissues and endolithic communities with translocation of organic nitrogen. Thus, the endolithic community plays an important role in supporting the C and N metabolism of the holobiont, which may be crucial under changing environmental conditions.}, }
@article {pmid29271225, year = {2018}, author = {Sebastián Domingo, JJ and Sánchez Sánchez, C}, title = {From the intestinal flora to the microbiome.}, journal = {Revista espanola de enfermedades digestivas : organo oficial de la Sociedad Espanola de Patologia Digestiva}, volume = {110}, number = {1}, pages = {51-56}, doi = {10.17235/reed.2017.4947/2017}, pmid = {29271225}, issn = {1130-0108}, mesh = {Gastroenterology/*history ; Gastrointestinal Diseases/microbiology ; *Gastrointestinal Microbiome ; History, 17th Century ; History, 19th Century ; Humans ; Intestines/*microbiology ; }, abstract = {In this article, the history of the microbiota is reviewed and the related concepts of the microbiota, microbiome, metagenome, pathobiont, dysbiosis, holobiont, phylotype and enterotype are defined. The most precise and current knowledge about the microbiota is presented and the metabolic, nutritional and immunomodulatory functions are reviewed. Some gastrointestinal diseases whose pathogenesis is associated with the intestinal microbiota, including inflammatory bowel disease, irritable bowel syndrome and celiac disease, among others, are briefly discussed. Finally, some prominent and promising data with regard to the fecal microbiota transplantation in certain digestive illness are discussed.}, }
@article {pmid29266341, year = {2018}, author = {Elgart, M and Soen, Y}, title = {Microbiome-Germline Interactions and Their Transgenerational Implications.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {40}, number = {4}, pages = {e1700018}, doi = {10.1002/bies.201700018}, pmid = {29266341}, issn = {1521-1878}, mesh = {Bacteria/genetics ; Epigenesis, Genetic/*genetics ; Gastrointestinal Microbiome/genetics ; Germ Cells/*physiology ; Microbiota/genetics/*physiology ; Symbiosis/genetics/physiology ; }, abstract = {It is becoming increasingly clear that most, if not all, animals and plants are associated with a diverse array of resident gut microbiota. This symbiosis is regulated by host-microbiome interactions which influence the development, homeostasis, adaptation and evolution of the host. Recent evidence indicated that these interactions can also affect the host germline and have a potential of supporting transgenerational effects, including inheritance of acquired characteristics. Taken together, the influence of gut bacteria on the host soma and germline could potentially give rise to emergent phenotypes, which may be partially inherited by three distinguishable modes of transgenerational influence of gut bacteria: 1) &quot;soma-to-soma&quot; 2) &quot;soma-to-germline&quot; and 3) &quot;soma-germline-soma&quot;. Here, we discuss these possibilities in light of evidence supporting bacterial-mediated modes of transgenerational inheritance.}, }
@article {pmid29245010, year = {2017}, author = {Kundu, P and Blacher, E and Elinav, E and Pettersson, S}, title = {Our Gut Microbiome: The Evolving Inner Self.}, journal = {Cell}, volume = {171}, number = {7}, pages = {1481-1493}, doi = {10.1016/j.cell.2017.11.024}, pmid = {29245010}, issn = {1097-4172}, mesh = {Aging ; Animals ; Bacteria/classification/*growth &amp; development/metabolism ; Biological Evolution ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Organ Specificity ; Puberty ; Symbiosis ; }, abstract = {The &quot;holobiont&quot; concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality.}, }
@article {pmid29244764, year = {2017}, author = {Ugarelli, K and Chakrabarti, S and Laas, P and Stingl, U}, title = {The Seagrass Holobiont and Its Microbiome.}, journal = {Microorganisms}, volume = {5}, number = {4}, pages = {}, pmid = {29244764}, issn = {2076-2607}, abstract = {Seagrass meadows are ecologically and economically important components of many coastal areas worldwide. Ecosystem services provided by seagrasses include reducing the number of microbial pathogens in the water, providing food, shelter and nurseries for many species, and decreasing the impact of waves on the shorelines. A global assessment reported that 29% of the known areal extent of seagrasses has disappeared since seagrass areas were initially recorded in 1879. Several factors such as direct and indirect human activity contribute to the demise of seagrasses. One of the main reasons for seagrass die-offs all over the world is increased sulfide concentrations in the sediment that result from the activity of sulfate-reducing prokaryotes, which perform the last step of the anaerobic food chain in marine sediments and reduce sulfate to H₂S. Recent seagrass die-offs, e.g., in the Florida and Biscayne Bays, were caused by an increase in pore-water sulfide concentrations in the sediment, which were the combined result of unfavorable environmental conditions and the activities of various groups of heterotrophic bacteria in the sulfate-rich water-column and sediment that are stimulated through increased nutrient concentrations. Under normal circumstances, seagrasses are able to withstand low levels of sulfide, probably partly due to microbial symbionts, which detoxify sulfide by oxidizing it to sulfur or sulfate. Novel studies are beginning to give greater insights into the interactions of microbes and seagrasses, not only in the sulfur cycle. Here, we review the literature on the basic ecology and biology of seagrasses and focus on studies describing their microbiome.}, }
@article {pmid29222444, year = {2018}, author = {Lesser, MP and Morrow, KM and Pankey, SM and Noonan, SHC}, title = {Diazotroph diversity and nitrogen fixation in the coral Stylophora pistillata from the Great Barrier Reef.}, journal = {The ISME journal}, volume = {12}, number = {3}, pages = {813-824}, pmid = {29222444}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/genetics ; *Coral Reefs ; Dinoflagellida/*metabolism ; Heterotrophic Processes ; Metagenome ; Nitrogen/*metabolism ; Nitrogen Fixation/*physiology/radiation effects ; Photosynthesis/*physiology/radiation effects ; Photosystem II Protein Complex/metabolism ; Sequence Analysis, DNA ; }, abstract = {Diazotrophs, both Bacteria and Archaea, capable of fixing nitrogen (N2), are present in the tissues and mucous, of corals and can supplement the coral holobiont nitrogen budget with fixed nitrogen (N) in the form of ammonia (NH3). Stylophora pistillata from Heron Island on the Great Barrier Reef collected at 5 and 15 m, and experimentally manipulated in the laboratory, showed that the rates of net photosynthesis, steady state quantum yields of photosystem II (PSII) fluorescence (∆Fv/Fm') and calcification varied based on irradiance as expected. Rates of N2 fixation were, however, invariant across treatments while the amount of fixed N contributing to Symbiodinium spp. N demand is irradiance dependent. Additionally, both the Symbiodinium and diazotrophic communities are significantly different based on depth, and novel Cluster V nifH gene phylotypes, which are not known to fix nitrogen, were recovered. A functional analysis using PICRUSt also showed that shallow corals were enriched in genes involved in nitrogen metabolism, and N2 fixation specifically. Corals have evolved a number of strategies to derive nitrogen from organic (e.g., heterotrophic feeding) and inorganic sources (e.g., N2 fixation) to maintain critical pathways such as protein synthesis to succeed ecologically in nitrogen-limited habitats.}, }
@article {pmid29211049, year = {2017}, author = {Shapiro, JA}, title = {Living Organisms Author Their Read-Write Genomes in Evolution.}, journal = {Biology}, volume = {6}, number = {4}, pages = {}, pmid = {29211049}, issn = {2079-7737}, abstract = {Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with &quot;non-coding&quot; DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called &quot;non-coding&quot; RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.}, }
@article {pmid29194919, year = {2018}, author = {Lavy, A and Keren, R and Yu, K and Thomas, BC and Alvarez-Cohen, L and Banfield, JF and Ilan, M}, title = {A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {800-814}, pmid = {29194919}, issn = {1462-2920}, support = {P42 ES004705/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; *Gammaproteobacteria/classification/genetics/metabolism ; Genome, Bacterial/genetics ; Indian Ocean ; Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; Oxidation-Reduction ; Phylogeny ; Polyketide Synthases/genetics ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sulfides/*metabolism ; Sulfur/*metabolism ; Symbiosis/physiology ; }, abstract = {Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbour a multitude of associated microorganisms that could affect sulfur cycling within the holobiont. We reconstructed the genome of a Chromatiales (class Gammaproteobacteria) bacterium from a metagenomic sequence dataset of a T. swinhoei-associated microbial community. This relatively abundant bacterium has the metabolic capability to oxidize sulfide yet displays reduced metabolic potential suggestive of its lifestyle as an obligatory symbiont. This bacterium was detected in multiple sponge orders, according to similarities in key genes such as 16S rRNA and polyketide synthase genes. Due to its sulfide oxidation metabolism and occurrence in many members of the Porifera phylum, we suggest naming the newly described taxon Candidatus Porisulfidus.}, }
@article {pmid29192903, year = {2018}, author = {Ziegler, M and Eguíluz, VM and Duarte, CM and Voolstra, CR}, title = {Rare symbionts may contribute to the resilience of coral-algal assemblages.}, journal = {The ISME journal}, volume = {12}, number = {1}, pages = {161-172}, pmid = {29192903}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; Coral Reefs ; Dinoflagellida/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; *Symbiosis ; }, abstract = {The association between corals and photosynthetic dinoflagellates (Symbiodinium spp.) is the key to the success of reef ecosystems in highly oligotrophic environments, but it is also their Achilles' heel due to its vulnerability to local stressors and the effects of climate change. Research during the last two decades has shaped a view that coral host-Symbiodinium pairings are diverse, but largely exclusive. Deep sequencing has now revealed the existence of a rare diversity of cryptic Symbiodinium assemblages within the coral holobiont, in addition to one or a few abundant algal members. While the contribution of the most abundant resident Symbiodinium species to coral physiology is widely recognized, the significance of the rare and low abundant background Symbiodinium remains a matter of debate. In this study, we assessed how coral-Symbiodinium communities assemble and how rare and abundant components together constitute the Symbiodinium community by analyzing 892 coral samples comprising >110 000 unique Symbiodinium ITS2 marker gene sequences. Using network modeling, we show that host-Symbiodinium communities assemble in non-random 'clusters' of abundant and rare symbionts. Symbiodinium community structure follows the same principles as bacterial communities, for which the functional significance of rare members (the 'rare bacterial biosphere') has long been recognized. Importantly, the inclusion of rare Symbiodinium taxa in robustness analyses revealed a significant contribution to the stability of the host-symbiont community overall. As such, it highlights the potential functions rare symbionts may provide to environmental resilience of the coral holobiont.}, }
@article {pmid29175233, year = {2018}, author = {Miller, WB}, title = {Biological information systems: Evolution as cognition-based information management.}, journal = {Progress in biophysics and molecular biology}, volume = {134}, number = {}, pages = {1-26}, doi = {10.1016/j.pbiomolbio.2017.11.005}, pmid = {29175233}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Cells/cytology/metabolism ; Cognition ; Humans ; }, abstract = {An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses.}, }
@article {pmid29170664, year = {2017}, author = {Grasis, JA}, title = {The Intra-Dependence of Viruses and the Holobiont.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {1501}, pmid = {29170664}, issn = {1664-3224}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, abstract = {Animals live in symbiosis with the microorganisms surrounding them. This symbiosis is necessary for animal health, as a symbiotic breakdown can lead to a disease state. The functional symbiosis between the host, and associated prokaryotes, eukaryotes, and viruses in the context of an environment is the holobiont. Deciphering these holobiont associations has proven to be both difficult and controversial. In particular, holobiont association with viruses has been of debate even though these interactions have been occurring since cellular life began. The controversy stems from the idea that all viruses are parasitic, yet their associations can also be beneficial. To determine viral involvement within the holobiont, it is necessary to identify and elucidate the function of viral populations in symbiosis with the host. Viral metagenome analyses identify the communities of eukaryotic and prokaryotic viruses that functionally associate within a holobiont. Similarly, analyses of the host in response to viral presence determine how these interactions are maintained. Combined analyses reveal how viruses interact within the holobiont and how viral symbiotic cooperation occurs. To understand how the holobiont serves as a functional unit, one must consider viruses as an integral part of disease, development, and evolution.}, }
@article {pmid29167578, year = {2017}, author = {Jarett, JK and MacManes, MD and Morrow, KM and Pankey, MS and Lesser, MP}, title = {Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {16039}, pmid = {29167578}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics ; Dinoflagellida/genetics ; Genomics/*methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Montastraea cavernosa is a common coral in the Caribbean basin found in several color morphs. To investigate the causes for brown and orange morphs we undertook a genomics approach on corals collected at the same time and depth in the Bahamas. The coral holobiont includes the host, symbiotic dinoflagellates (Symbiodinium spp.), and a diverse microbiome. While the coral host showed significant genetic differentiation between color morphs both the composition of the Symbiodinium spp. communities and the prokaryotic communities did not. Both targeted and global gene expression differences in the transcriptome of the host show no difference in fluorescent proteins while the metatranscriptome of the microbiome shows that pigments such as phycoerythrin and orange carotenoid protein of cyanobacterial origin are significantly greater in orange morphs, which is also consistent with the significantly greater number of cyanobacteria quantified by 16S rRNA reads and flow cytometry. The microbiome of orange color morphs expressed significantly more nitrogenase (nifH) transcripts consistent with their known ability to fix nitrogen. Both coral and Symbiodinium spp. transcriptomes from orange morphs had significantly increased expression of genes related to immune response and apoptosis, which may potentially be involved in maintaining and regulating the unique symbiont population in orange morphs.}, }
@article {pmid29158985, year = {2017}, author = {Weynberg, KD and Laffy, PW and Wood-Charlson, EM and Turaev, D and Rattei, T and Webster, NS and van Oppen, MJH}, title = {Coral-associated viral communities show high levels of diversity and host auxiliary functions.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e4054}, pmid = {29158985}, issn = {2167-8359}, abstract = {Stony corals (Scleractinia) are marine invertebrates that form the foundation and framework upon which tropical reefs are built. The coral animal associates with a diverse microbiome comprised of dinoflagellate algae and other protists, bacteria, archaea, fungi and viruses. Using a metagenomics approach, we analysed the DNA and RNA viral assemblages of seven coral species from the central Great Barrier Reef (GBR), demonstrating that tailed bacteriophages of the Caudovirales dominate across all species examined, and ssDNA viruses, notably the Microviridae, are also prevalent. Most sequences with matches to eukaryotic viruses were assigned to six viral families, including four Nucleocytoplasmic Large DNA Viruses (NCLDVs) families: Iridoviridae, Phycodnaviridae, Mimiviridae, and Poxviridae, as well as Retroviridae and Polydnaviridae. Contrary to previous findings, Herpesvirales were rare in these GBR corals. Sequences of a ssRNA virus with similarities to the dinornavirus, Heterocapsa circularisquama ssRNA virus of the Alvernaviridae that infects free-living dinoflagellates, were observed in three coral species. We also detected viruses previously undescribed from the coral holobiont, including a virus that targets fungi associated with the coral species Acropora tenuis. Functional analysis of the assembled contigs indicated a high prevalence of latency-associated genes in the coral-associated viral assemblages, several host-derived auxiliary metabolic genes (AMGs) for photosynthesis (psbA, psbD genes encoding the photosystem II D1 and D2 proteins respectively), as well as potential nematocyst toxins and antioxidants (genes encoding green fluorescent-like chromoprotein). This study expands the currently limited knowledge on coral-associated viruses by characterising viral composition and function across seven GBR coral species.}, }
@article {pmid29108677, year = {2017}, author = {Ellison, MA and Ferrier, MD and Carney, SL}, title = {Salinity stress results in differential Hsp70 expression in the Exaiptasia pallida and Symbiodinium symbiosis.}, journal = {Marine environmental research}, volume = {132}, number = {}, pages = {63-67}, doi = {10.1016/j.marenvres.2017.10.006}, pmid = {29108677}, issn = {1879-0291}, mesh = {Animals ; Dinoflagellida/*physiology ; HSP70 Heat-Shock Proteins/*metabolism ; Salinity ; Sea Anemones/*physiology ; Stress, Physiological/*physiology ; Symbiosis ; }, abstract = {Abiotic factors affect cnidarian-algal symbiosis and, if severe enough, can result in bleaching. Increased temperature and light are well characterized causes of bleaching, but other factors like salinity can also stress the holobiont. In cnidarian-dinoflagellate systems, the expression of host genes, including heat shock protein 70 (Hsp70), changes due to thermal and light stress. In this experiment, we characterized to what extent salinity stress affects Hsp70 expression in the holobiont by simultaneously measuring host and symbiont Hsp70 expression in response to up to 8 h of hypo- and hypersaline conditions in the sea anemone Exaiptasia pallida and its intracellular symbiont Symbiodinium minutum. We show that E. pallida Hsp70 expression increases (6-11-fold) at high salinities whereas Symbiodinium Hsp70 expression shows little change (1.4-2.6-fold). These data suggest that cnidarian Hsp70 response is similar across multiple abiotic stressors further validating the Hsp70 gene as a biomarker for abiotic stress.}, }
@article {pmid29098358, year = {2018}, author = {Baumann, JH and Davies, SW and Aichelman, HE and Castillo, KD}, title = {Coral Symbiodinium Community Composition Across the Belize Mesoamerican Barrier Reef System is Influenced by Host Species and Thermal Variability.}, journal = {Microbial ecology}, volume = {75}, number = {4}, pages = {903-915}, pmid = {29098358}, issn = {1432-184X}, support = {15802-1//Rufford Foundation/ ; OCE 1459522//Division of Ocean Sciences/ ; }, mesh = {Animals ; Anthozoa/genetics/*parasitology ; Belize ; DNA/analysis ; Dinoflagellida/*classification/genetics/*physiology ; Environmental Monitoring ; Genetic Variation ; *Host Specificity ; Hot Temperature ; Oceans and Seas ; Phylogeny ; Symbiosis/physiology ; Temperature ; Thermotolerance ; }, abstract = {Reef-building corals maintain a symbiotic relationship with dinoflagellate algae of the genus Symbiodinium, and this symbiosis is vital for the survival of the coral holobiont. Symbiodinium community composition within the coral host has been shown to influence a coral's ability to resist and recover from stress. A multitude of stressors including ocean warming, ocean acidification, and eutrophication have been linked to global scale decline in coral health and cover in recent decades. Three distinct thermal regimes (highTP, modTP, and lowTP) following an inshore-offshore gradient of declining average temperatures and thermal variation were identified on the Belize Mesoamerican Barrier Reef System (MBRS). Quantitative metabarcoding of the ITS-2 locus was employed to investigate differences and similarities in Symbiodinium genetic diversity of the Caribbean corals Siderastrea siderea, S. radians, and Pseudodiploria strigosa between the three thermal regimes. A total of ten Symbiodinium lineages were identified across the three coral host species. S. siderea was associated with distinct Symbiodinium communities; however, Symbiodinium communities of its congener, S. radians and P. strigosa, were more similar to one another. Thermal regime played a role in defining Symbiodinium communities in S. siderea but not S. radians or P. strigosa. Against expectations, Symbiodinium trenchii, a symbiont known to confer thermal tolerance, was dominant only in S. siderea at one sampled offshore site and was rare inshore, suggesting that coral thermal tolerance in more thermally variable inshore habitats is achieved through alternative mechanisms. Overall, thermal parameters alone were likely not the only primary drivers of Symbiodinium community composition, suggesting that environmental variables unrelated to temperature (i.e., light availability or nutrients) may play key roles in structuring coral-algal communities in Belize and that the relative importance of these environmental variables may vary by coral host species.}, }
@article {pmid29078340, year = {2017}, author = {Hartmann, AC and Petras, D and Quinn, RA and Protsyuk, I and Archer, FI and Ransome, E and Williams, GJ and Bailey, BA and Vermeij, MJA and Alexandrov, T and Dorrestein, PC and Rohwer, FL}, title = {Meta-mass shift chemical profiling of metabolomes from coral reefs.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {114}, number = {44}, pages = {11685-11690}, pmid = {29078340}, issn = {1091-6490}, support = {P41 GM103484/GM/NIGMS NIH HHS/United States ; R03 CA211211/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*metabolism ; Coral Reefs ; Metabolome ; Metabolomics/*methods ; Transcriptome ; }, abstract = {Untargeted metabolomics of environmental samples routinely detects thousands of small molecules, the vast majority of which cannot be identified. Meta-mass shift chemical (MeMSChem) profiling was developed to identify mass differences between related molecules using molecular networks. This approach illuminates metabolome-wide relationships between molecules and the putative chemical groups that differentiate them (e.g., H2, CH2, COCH2). MeMSChem profiling was used to analyze a publicly available metabolomic dataset of coral, algal, and fungal mat holobionts (i.e., the host and its associated microbes and viruses) sampled from some of Earth's most remote and pristine coral reefs. Each type of holobiont had distinct mass shift profiles, even when the analysis was restricted to molecules found in all samples. This result suggests that holobionts modify the same molecules in different ways and offers insights into the generation of molecular diversity. Three genera of stony corals had distinct patterns of molecular relatedness despite their high degree of taxonomic relatedness. MeMSChem profiles also partially differentiated between individuals, suggesting that every coral reef holobiont is a potential source of novel chemical diversity.}, }
@article {pmid29038057, year = {2017}, author = {Ahila, NK and Prakash, S and Manikandan, B and Ravindran, J and Prabhu, NM and Kannapiran, E}, title = {Bio-prospecting of coral (Porites lutea) mucus associated bacteria, Palk Bay reefs, Southeast coast of India.}, journal = {Microbial pathogenesis}, volume = {113}, number = {}, pages = {113-123}, doi = {10.1016/j.micpath.2017.09.056}, pmid = {29038057}, issn = {1096-1208}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Bacillus/genetics/isolation &amp; purification/*metabolism ; Coral Reefs ; Enterobacter cloacae/genetics/isolation &amp; purification ; India ; Microbiota ; Mucus/*microbiology ; RNA, Ribosomal, 16S/genetics ; Vibrio/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Coral mucus is one of the key localization in the coral holobiont, as this serves as an energy rich substrate for a wide range of abundant, diverse and multifunctional microbiota. However, very little is known about the functional role of bacterial communities in their associations with corals. In the present study, a total of 48 isolates were obtained from Porites lutea wherein the genus of Bacillus sp. and Vibrio sp. were predominant. Bio-prospecting the coral mucus revealed the existence of (10.42%) antagonistic bacteria against the tested bacterial pathogens. Molecular taxonomy (16S rRNA) proved the identity of these antagonistic bacteria belong to Enterobacter cloacae (CM1), Bacillus subtilis (CM2), Bacillus sp. (CM11) and Bacillus marisflavi (CM12). The secondary screening emphasized that the ethyl acetate extract of B. subtilis showed strong antagonistic effect, followed by the chloroform extract of E. cloacae and ethyl acetate extract of B. marisflavi. The antagonistic activity was statistically confirmed by Principal Component Analysis and Hierarchical Cluster Analysis. The privileged coral mucus associated bacterial (CMAB) solvent extracts inhibited the bacterial pathogens at 100 μg/ml (MIC) and ceased the growth at 200 μg/ml (MBC). The hemolytic and brine shrimp lethality assays disclosed the non-toxic nature of solvent extracts of CMAB. Altogether, the present investigation brought out the diversity of bacteria associated with the mucus of P. lutea. In addition, bio-prospecting corroborated the CMAB as the potential source of pharmacologically important bioactive compounds against a wide range of bacterial pathogens.}, }
@article {pmid29027742, year = {2018}, author = {Mera, H and Bourne, DG}, title = {Disentangling causation: complex roles of coral-associated microorganisms in disease.}, journal = {Environmental microbiology}, volume = {20}, number = {2}, pages = {431-449}, doi = {10.1111/1462-2920.13958}, pmid = {29027742}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Coral Reefs ; Microbiota ; }, abstract = {Rapidly changing climate regimes combined with other anthropogenic pressures are implicated in increased disease epizootics among reef building corals, resulting in changing habitat structure. These accumulated stressors directly contribute to disease outbreaks by compromising the coral host immune system, modulating virulence of microbial pathogens and/or disrupting the balance within the microbiome of the holobiont. Disentangling coral disease causation has been challenging, and while progress has been made for certain diseases in terms of the roles the associated microorganisms play, it is evident that like in other marine or terrestrial systems, compromised host health cannot always be attributed to a single causative agent. Here, we summarize the current state in knowledge of microbial induced coral diseases, and discuss challenges and strategies to further disentangle disease causation. With the major environmental pressures coral reefs face over the next century, understanding interactions between host, environmental and microbial causative agent(s) that lead to disease, is still a priority to enable development of effective strategies for building resilience into coral populations.}, }
@article {pmid28967236, year = {2018}, author = {Sapp, M and Ploch, S and Fiore-Donno, AM and Bonkowski, M and Rose, LE}, title = {Protists are an integral part of the Arabidopsis thaliana microbiome.}, journal = {Environmental microbiology}, volume = {20}, number = {1}, pages = {30-43}, doi = {10.1111/1462-2920.13941}, pmid = {28967236}, issn = {1462-2920}, mesh = {Arabidopsis/*parasitology ; Cercozoa/*classification/genetics/*isolation &amp; purification ; DNA, Intergenic/genetics ; Microbiota/physiology ; Oomycetes/*classification/genetics/*isolation &amp; purification ; Plant Leaves/*parasitology ; Plant Roots/*parasitology ; RNA, Ribosomal, 18S/genetics ; Rhizosphere ; Soil/parasitology ; }, abstract = {Although protists occupy a vast range of habitats and are known to interact with plants among other things via disease suppression, competition or growth stimulation, their contributions to the 'phytobiome' are not well described. To contribute to a more comprehensive picture of the plant holobiont, we examined cercozoan and oomycete taxa living in association with the model plant Arabidopsis thaliana grown in two different soils. Soil, roots, leaves and wooden toothpicks were analysed before and after surface sterilization. Cercozoa were identified using 18S rRNA gene metabarcoding, whereas the Internal Transcribed Spacer 1 was used to determine oomycetes. Subsequent analyses revealed strong spatial structuring of protist communities between compartments, although oomycetes appeared more specialized than Cercozoa. With regards to oomycetes, only members of the Peronosporales and taxa belonging to the genus Globisporangium were identified as shared members of the A. thaliana microbiome. This also applied to cercozoan taxa belonging to the Glissomonadida and Cercomonadida. We identified a strong influence by edaphic factors on the rhizosphere, but not for the phyllosphere. Distinct differences of Cercozoa found preferably in wood or fresh plant material imply specific niche adaptations. Our results highlight the importance of micro-eukaryotes for the plant holobiont.}, }
@article {pmid28915923, year = {2017}, author = {Sharp, KH and Pratte, ZA and Kerwin, AH and Rotjan, RD and Stewart, FJ}, title = {Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {120}, pmid = {28915923}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Dinoflagellida/*physiology ; *Microbiota ; Seasons ; *Symbiosis ; }, abstract = {BACKGROUND: Understanding the associations among corals, their photosynthetic zooxanthella symbionts (Symbiodinium), and coral-associated prokaryotic microbiomes is critical for predicting the fidelity and strength of coral symbioses in the face of growing environmental threats. Most coral-microbiome associations are beneficial, yet the mechanisms that determine the composition of the coral microbiome remain largely unknown. Here, we characterized microbiome diversity in the temperate, facultatively symbiotic coral Astrangia poculata at four seasonal time points near the northernmost limit of the species range. The facultative nature of this system allowed us to test seasonal influence and symbiotic state (Symbiodinium density in the coral) on microbiome community composition.<br><br>RESULTS: Change in season had a strong effect on A. poculata microbiome composition. The seasonal shift was greatest upon the winter to spring transition, during which time A. poculata microbiome composition became more similar among host individuals. Within each of the four seasons, microbiome composition differed significantly from that of surrounding seawater but was surprisingly uniform between symbiotic and aposymbiotic corals, even in summer, when differences in Symbiodinium density between brown and white colonies are the highest, indicating that the observed seasonal shifts are not likely due to fluctuations in Symbiodinium density.<br><br>CONCLUSIONS: Our results suggest that symbiotic state may not be a primary driver of coral microbial community organization in A. poculata, which is a surprise given the long-held assumption that excess photosynthate is of importance to coral-associated microbes. Rather, other environmental or host factors, in this case, seasonal changes in host physiology associated with winter quiescence, may drive microbiome diversity. Additional studies of A. poculata and other facultatively symbiotic corals will provide important comparisons to studies of reef-building tropical corals and therefore help to identify basic principles of coral microbiome assembly, as well as functional relationships among holobiont members.}, }
@article {pmid28894639, year = {2017}, author = {Naim, MA and Smidt, H and Sipkema, D}, title = {Fungi found in Mediterranean and North Sea sponges: how specific are they?.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3722}, pmid = {28894639}, issn = {2167-8359}, abstract = {Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.}, }
@article {pmid28893194, year = {2017}, author = {Frazier, M and Helmkampf, M and Bellinger, MR and Geib, SM and Takabayashi, M}, title = {De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly.}, journal = {BMC genomics}, volume = {18}, number = {1}, pages = {710}, pmid = {28893194}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/*genetics/*growth &amp; development ; *Gene Expression Profiling ; Morphogenesis/genetics ; }, abstract = {BACKGROUND: Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals (&quot;healthy&quot;), GA lesion tissue from diseased corals (&quot;GA-affected&quot;) and apparently healthy tissue from diseased corals (&quot;GA-unaffected&quot;). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease.<br><br>RESULTS: The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system.<br><br>CONCLUSION: This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.}, }
@article {pmid28892512, year = {2017}, author = {Mezzasalma, V and Sandionigi, A and Bruni, I and Bruno, A and Lovicu, G and Casiraghi, M and Labra, M}, title = {Grape microbiome as a reliable and persistent signature of field origin and environmental conditions in Cannonau wine production.}, journal = {PloS one}, volume = {12}, number = {9}, pages = {e0184615}, pmid = {28892512}, issn = {1932-6203}, mesh = {Agriculture ; Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Barcoding, Taxonomic ; *Environment ; Fungi/classification/genetics ; Geography ; Metagenome ; Metagenomics/methods ; *Microbiota ; Vitis/*microbiology ; *Wine ; }, abstract = {Grape berries harbor a wide range of microbes originating from the vineyard environment, many of which are recognized for their role in the must fermentation process shaping wine quality. To better clarify the contribution of the microbiome of grape fruits during wine fermentation, we used high-throughput sequencing to identify bacterial and fungi communities associated with berries and musts of Cannonau. This is the most important cultivar-wine of Sardinia (Italy) where most vineyards are cultivated without phytochemical treatments. Results suggested that microbiomes of berries collected at four different localities share a core composition characterized by Enterobacteriales, Pseudomonadales, Bacillales, and Rhodospirillales. However, any area seems to enrich berries microbiome with peculiar microbial traits. For example, berries belonging to the biodynamic vineyards of Mamoiada were rich in Bacillales typical of manure (i.e. Lysinibacillus, Bacillus, and Sporosarcina), whereas in the Santadi locality, berries showed soil bacteria such as Pasteurellales and Bacteroidales as well as Rhodospirillales and Lactobacillales which are commonly involved in wine fermentation. In the case of fungi, the most abundant taxa were Dothioraceae, Pleosporaceae, and Saccharomycodaceae, and although the proportion of these families varied among localities, they occurred ubiquitously in all vineyards. During vinification processes performed at the same wine cellar under controlled conditions and without using any yeast starter, more than 50% of bacteria groups of berries reached musts, and each locality had its own private bacteria signature, even if Saccharomyces cerevisiae represented the most abundant fungal species. This work suggests that natural berries microbiome could be influenced by pedoclimatic and anthropologic conditions (e.g., farming management), and the fruits' microorganisms persist during the fermentation process. For these reasons, a reliable wine genotyping should include the entire holobiont (plant and all its symbionts), and bioprospecting activities on grape microbiota could lead to improved viticulture yields and wine quality.}, }
@article {pmid28887506, year = {2017}, author = {Evans, JS and Erwin, PM and Shenkar, N and López-Legentil, S}, title = {Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {11033}, pmid = {28887506}, issn = {2045-2322}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; *Biota ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; High-Throughput Nucleotide Sequencing ; North Carolina ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, DNA ; Urochordata/*microbiology ; }, abstract = {Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 47 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.}, }
@article {pmid28861262, year = {2017}, author = {Rädecker, N and Pogoreutz, C and Ziegler, M and Ashok, A and Barreto, MM and Chaidez, V and Grupstra, CGB and Ng, YM and Perna, G and Aranda, M and Voolstra, CR}, title = {Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa.}, journal = {Ecology and evolution}, volume = {7}, number = {16}, pages = {6614-6621}, pmid = {28861262}, issn = {2045-7758}, abstract = {The productivity of coral reefs in oligotrophic tropical waters is sustained by an efficient uptake and recycling of nutrients. In reef-building corals, the engineers of these ecosystems, this nutrient recycling is facilitated by a constant exchange of nutrients between the animal host and endosymbiotic photosynthetic dinoflagellates (zooxanthellae), bacteria, and other microbes. Due to the complex interactions in this so-called coral holobiont, it has proven difficult to understand the environmental limitations of productivity in corals. Among others, the micronutrient iron has been proposed to limit primary productivity due to its essential role in photosynthesis and bacterial processes. Here, we tested the effect of iron enrichment on the physiology of the coral Pocillopora verrucosa from the central Red Sea during a 12-day experiment. Contrary to previous reports, we did not see an increase in zooxanthellae population density or gross photosynthesis. Conversely, respiration rates were significantly increased, and microbial nitrogen fixation was significantly decreased. Taken together, our data suggest that iron is not a limiting factor of primary productivity in Red Sea corals. Rather, increased metabolic demands in response to iron enrichment, as evidenced by increased respiration rates, may reduce carbon (i.e., energy) availability in the coral holobiont, resulting in reduced microbial nitrogen fixation. This decrease in nitrogen supply in turn may exacerbate the limitation of other nutrients, creating a negative feedback loop. Thereby, our results highlight that the effects of iron enrichment appear to be strongly dependent on local environmental conditions and ultimately may depend on the availability of other nutrients.}, }
@article {pmid28857164, year = {2017}, author = {Brodie, J and Ball, SG and Bouget, FY and Chan, CX and De Clerck, O and Cock, JM and Gachon, C and Grossman, AR and Mock, T and Raven, JA and Saha, M and Smith, AG and Vardi, A and Yoon, HS and Bhattacharya, D}, title = {Biotic interactions as drivers of algal origin and evolution.}, journal = {The New phytologist}, volume = {216}, number = {3}, pages = {670-681}, doi = {10.1111/nph.14760}, pmid = {28857164}, issn = {1469-8137}, support = {BB/I013164/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Anthozoa/*physiology ; *Biological Evolution ; Chromatophores ; Dinoflagellida/physiology ; Eutrophication ; Host-Pathogen Interactions ; Phaeophyta/*physiology ; Photosynthesis ; Phycodnaviridae/pathogenicity ; Phylogeny ; Plastids ; Symbiosis ; }, abstract = {Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.}, }
@article {pmid28839925, year = {2017}, author = {Hurst, GDD}, title = {Extended genomes: symbiosis and evolution.}, journal = {Interface focus}, volume = {7}, number = {5}, pages = {20170001}, pmid = {28839925}, issn = {2042-8898}, abstract = {Many aspects of an individual's biology derive from its interaction with symbiotic microbes, which further define many aspects of the ecology and evolution of the host species. The centrality of microbes in the function of individual organisms has given rise to the concept of the holobiont-that an individual's biology is best understood as a composite of the 'host organism' and symbionts within. This concept has been further elaborated to posit the holobiont as a unit of selection. In this review, I critically examine whether it is useful to consider holobionts as a unit of selection. I argue that microbial heredity-the direct passage of microbes from parent to offspring-is a key factor determining the degree to which the holobiont can usefully be considered a level of selection. Where direct vertical transmission (VT) is common, microbes form part of extended genomes whose dynamics can be modelled with simple population genetics, but that nevertheless have subtle quantitative distinctions from the classic mutation/selection model for nuclear genes. Without direct VT, the correlation between microbial fitness and host individual fitness erodes, and microbe fitness becomes associated with host survival only (rather than reproduction). Furthermore, turnover of microbes within a host may lessen associations between microbial fitness with host survival, and in polymicrobial communities, microbial fitness may derive largely from the ability to outcompete other microbes, to avoid host immune clearance and to minimize mortality through phage infection. These competing selection pressures make holobiont fitness a very minor consideration in determining symbiont evolution. Nevertheless, the importance of non-heritable microbes in organismal function is undoubted-and as such the evolutionary and ecological processes giving rise to variation and evolution of the microbes within and between host individuals represent a key research area in biology.}, }
@article {pmid28835914, year = {2017}, author = {Ochsenkühn, MA and Röthig, T and D'Angelo, C and Wiedenmann, J and Voolstra, CR}, title = {The role of floridoside in osmoadaptation of coral-associated algal endosymbionts to high-salinity conditions.}, journal = {Science advances}, volume = {3}, number = {8}, pages = {e1602047}, pmid = {28835914}, issn = {2375-2548}, support = {//European Research Council/International ; }, mesh = {Adaptation, Physiological/*drug effects ; Animals ; Anthozoa/*physiology ; Carbohydrates/analysis ; Chromatography, Gas ; Coral Reefs ; Dinoflagellida/*physiology ; Glycerol/*analogs &amp; derivatives/pharmacology ; Metabolomics/methods ; *Osmolar Concentration ; *Salinity ; *Symbiosis ; }, abstract = {The endosymbiosis between Symbiodinium dinoflagellates and stony corals provides the foundation of coral reef ecosystems. The survival of these ecosystems is under threat at a global scale, and better knowledge is needed to conceive strategies for mitigating future reef loss. Environmental disturbance imposing temperature, salinity, and nutrient stress can lead to the loss of the Symbiodinium partner, causing so-called coral bleaching. Some of the most thermotolerant coral-Symbiodinium associations occur in the Persian/Arabian Gulf and the Red Sea, which also represent the most saline coral habitats. We studied whether Symbiodinium alter their metabolite content in response to high-salinity environments. We found that Symbiodinium cells exposed to high salinity produced high levels of the osmolyte 2-O-glycerol-α-d-galactopyranoside (floridoside), both in vitro and in their coral host animals, thereby increasing their capacity and, putatively, the capacity of the holobiont to cope with the effects of osmotic stress in extreme environments. Given that floridoside has been previously shown to also act as an antioxidant, this osmolyte may serve a dual function: first, to serve as a compatible organic osmolyte accumulated by Symbiodinium in response to elevated salinities and, second, to counter reactive oxygen species produced as a consequence of potential salinity and heat stress.}, }
@article {pmid28826642, year = {2018}, author = {Moissl-Eichinger, C and Pausan, M and Taffner, J and Berg, G and Bang, C and Schmitz, RA}, title = {Archaea Are Interactive Components of Complex Microbiomes.}, journal = {Trends in microbiology}, volume = {26}, number = {1}, pages = {70-85}, doi = {10.1016/j.tim.2017.07.004}, pmid = {28826642}, issn = {1878-4380}, mesh = {Animals ; Archaea/classification/*physiology ; Biodiversity ; Biofilms ; Ecology ; Ecosystem ; Eukaryota ; Euryarchaeota ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Halobacteriales ; Health ; Humans ; Microbial Consortia ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Mouth/microbiology ; Phylogeny ; Plants/microbiology ; Ruminants/microbiology ; Soil Microbiology ; Symbiosis ; Viruses ; }, abstract = {Recent findings have shaken our picture of the biology of the archaea and revealed novel traits beyond archaeal extremophily and supposed 'primitiveness'. The archaea constitute a considerable fraction of the Earth's ecosystems, and their potential to shape their surroundings by a profound interaction with their biotic and abiotic environment has been recognized. Moreover, archaea have been identified as a substantial component, or even as keystone species, in complex microbiomes - in the environment or accompanying a holobiont. Species of the Euryarchaeota (methanogens, halophiles) and Thaumarchaeota, in particular, have the capacity to coexist in plant, animal, and human microbiomes, where syntrophy allows them to thrive under energy-deficiency stress. Due to methodological limitations, the archaeome remains mysterious, and many questions with respect to potential pathogenicity, function, and structural interactions with their host and other microorganisms remain.}, }
@article {pmid28824625, year = {2017}, author = {Rader, BA}, title = {Alkaline Phosphatase, an Unconventional Immune Protein.}, journal = {Frontiers in immunology}, volume = {8}, number = {}, pages = {897}, pmid = {28824625}, issn = {1664-3224}, support = {R15 GM119100/GM/NIGMS NIH HHS/United States ; }, abstract = {Recent years have seen an increase in the number of studies focusing on alkaline phosphatases (APs), revealing an expanding complexity of function of these enzymes. Of the four human AP (hAP) proteins, most is known about tissue non-specific AP (TNAP) and intestinal AP (IAP). This review highlights current understanding of TNAP and IAP in relation to human health and disease. TNAP plays a role in multiple processes, including bone mineralization, vitamin B6 metabolism, and neurogenesis, is the genetic cause of hypophosphatasia, influences inflammation through regulation of purinergic signaling, and has been implicated in Alzheimer's disease. IAP regulates fatty acid absorption and has been implicated in the regulation of diet-induced obesity and metabolic syndrome. IAP and TNAP can dephosphorylate bacterial-derived lipopolysaccharide, and IAP has been identified as a potential regulator of the composition of the intestinal microbiome, an evolutionarily conserved function. Endogenous and recombinant bovine APs and recombinant hAPs are currently being explored for their potential as pharmacological agents to treat AP-associated diseases and mitigate multiple sources of inflammation. Continued research on these versatile proteins will undoubtedly provide insight into human pathophysiology, biochemistry, and the human holobiont.}, }
@article {pmid28818037, year = {2017}, author = {Brüwer, JD and Agrawal, S and Liew, YJ and Aranda, M and Voolstra, CR}, title = {Association of coral algal symbionts with a diverse viral community responsive to heat shock.}, journal = {BMC microbiology}, volume = {17}, number = {1}, pages = {174}, pmid = {28818037}, issn = {1471-2180}, mesh = {Animals ; Anthozoa/*physiology/*virology ; Climate Change ; Cold Temperature ; Coral Reefs ; Darkness ; Dinoflagellida/physiology/virology ; Ecosystem ; Gene Expression Regulation, Viral ; Genes, Viral ; Hot Temperature ; Phylogeny ; Sequence Analysis, RNA ; *Symbiosis ; Viral Proteins/genetics/metabolism ; *Virus Physiological Phenomena ; Viruses/*classification/genetics ; }, abstract = {BACKGROUND: Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin.<br><br>RESULTS: Here, we re-analyzed an RNA-Seq dataset from a cultured coral symbiont (Symbiodinium microadriaticum, Clade A1) across four experimental treatments (control, cold shock, heat shock, dark shock) to characterize associated viral diversity, abundance, and gene expression. Our approach comprised the filtering and removal of host sequence reads, subsequent phylogenetic assignment of sequence reads of putative viral origin, and the assembly and analysis of differentially expressed viral genes. About 15.46% (123 million) of all sequence reads were non-host-related, of which <1% could be classified as archaea, bacteria, or virus. Of these, 18.78% were annotated as virus and comprised a diverse community consistent across experimental treatments. Further, non-host related sequence reads assembled into 56,064 contigs, including 4856 contigs of putative viral origin that featured 43 differentially expressed genes during heat shock. The differentially expressed genes included viral kinases, ubiquitin, and ankyrin repeat proteins (amongst others), which are suggested to help the virus proliferate and inhibit the algal host's antiviral response.<br><br>CONCLUSION: Our results suggest that a diverse viral community is associated with coral algal endosymbionts of the genus Symbiodinium, which prompts further research on their ecological role in coral health and resilience.}, }
@article {pmid28799900, year = {2017}, author = {Vorholt, JA and Vogel, C and Carlström, CI and Müller, DB}, title = {Establishing Causality: Opportunities of Synthetic Communities for Plant Microbiome Research.}, journal = {Cell host &amp; microbe}, volume = {22}, number = {2}, pages = {142-155}, doi = {10.1016/j.chom.2017.07.004}, pmid = {28799900}, issn = {1934-6069}, mesh = {Bacteria/genetics ; Bacterial Physiological Phenomena ; Ecosystem ; Host-Pathogen Interactions ; Metagenome ; Microbial Consortia/physiology ; Microbial Interactions ; *Microbiota/genetics/physiology ; Plant Roots/microbiology ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plant microbiome research highlights the importance of indigenous microbial communities for host phenotypes such as growth and health. It aims to discover the molecular basis by which host-microbe and microbe-microbe interactions shape and maintain microbial communities and to understand the role of individual microorganisms, as well as their collective ecosystem function. Here, we discuss reductionist approaches to disentangle the inherent complexity of interactions in situ. Experimentally tractable, synthetic communities enable testing of hypotheses by targeted manipulation in gnotobiotic systems. Modifications of microbial, host, and environmental parameters allow for the quantitative assessment of host and microbe characteristics with dynamic and spatial resolution. We summarize first insights from this emerging field and discuss current challenges and limitations. Using multifaceted approaches to detect interactions and functions will provide new insights into the fundamental biology of plant-microbe interactions and help to harness the power of the microbiome.}, }
@article {pmid28787582, year = {2017}, author = {Roossinck, MJ and Bazán, ER}, title = {Symbiosis: Viruses as Intimate Partners.}, journal = {Annual review of virology}, volume = {4}, number = {1}, pages = {123-139}, doi = {10.1146/annurev-virology-110615-042323}, pmid = {28787582}, issn = {2327-0578}, mesh = {Animals ; Bacteria/genetics ; DNA, Viral/*genetics ; Evolution, Molecular ; Genome ; *Host-Pathogen Interactions ; Humans ; Phylogeny ; *Symbiosis ; *Virus Physiological Phenomena ; }, abstract = {Viruses must establish an intimate relationship with their hosts and vectors in order to infect, replicate, and disseminate; hence, viruses can be considered as symbionts with their hosts. Symbiotic relationships encompass different lifestyles, including antagonistic (or pathogenic, the most well-studied lifestyle for viruses), commensal (probably the most common lifestyle), and mutualistic (important beneficial partners). Symbiotic relationships can shape the evolution of the partners in a holobiont, and placing viruses in this context provides an important framework for understanding virus-host relationships and virus ecology. Although antagonistic relationships are thought to lead to coevolution, this is not always clear in virus-host interactions, and impacts on evolution may be complex. Commensalism implies a hitchhiking role for viruses-selfish elements just along for the ride. Mutualistic relationships have been described in detail in the past decade, and they reveal how important viruses are in considering host ecology. Ultimately, symbiosis can lead to symbiogenesis, or speciation through fusion, and the presence of large amounts of viral sequence in the genomes of everything from bacteria to humans, including some important functional genes, illustrates the significance of viral symbiogenesis in the evolution of all life on Earth.}, }
@article {pmid28785524, year = {2017}, author = {Conlan, JA and Rocker, MM and Francis, DS}, title = {A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3645}, pmid = {28785524}, issn = {2167-8359}, abstract = {Lipids are involved in a host of biochemical and physiological processes in corals. Therefore, changes in lipid composition reflect changes in the ecology, nutrition, and health of corals. As such, accurate lipid extraction, quantification, and identification is critical to obtain comprehensive insight into a coral's condition. However, discrepancies exist in sample preparation methodology globally, and it is currently unknown whether these techniques generate analogous results. This study compared the two most common sample preparation techniques for lipid analysis in corals: (1) tissue isolation by air-spraying and (2) crushing the coral in toto. Samples derived from each preparation technique were subsequently analysed to quantify lipids and their constituent classes and fatty acids in four common, scleractinian coral species representing three distinct morphotypes (Acropora millepora, Montipora crassotuberculata, Porites cylindrica, and Pocillopora damicornis). Results revealed substantial amounts of organic material, including lipids, retained in the skeletons of all species following air-spraying, causing a marked underestimation of total lipid concentration using this method. Moreover, lipid class and fatty acid compositions between the denuded skeleton and sprayed tissue were substantially different. In particular, the majority of the total triacylglycerol and total fatty acid concentrations were retained in the skeleton (55-69% and 56-64%, respectively). As such, the isolated, sprayed tissue cannot serve as a reliable proxy for lipid quantification or identification in the coral holobiont. The in toto crushing method is therefore recommended for coral sample preparation prior to lipid analysis to capture the lipid profile of the entire holobiont, permitting accurate diagnoses of coral condition.}, }
@article {pmid28766142, year = {2017}, author = {Leite, L and Jude-Lemeilleur, F and Raymond, N and Henriques, I and Garabetian, F and Alves, A}, title = {Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach.}, journal = {Environmental science and pollution research international}, volume = {24}, number = {27}, pages = {21721-21732}, pmid = {28766142}, issn = {1614-7499}, support = {UID/AMB/50017/2013//Fundação para a Ciência e a Tecnologia/ ; IF/00835/2013//Fundação para a Ciência e a Tecnologia/ ; IF/00492/2013//Fundação para a Ciência e a Tecnologia/ ; SFRH/BD/86879/2012//Fundação para a Ciência e a Tecnologia/ ; TC-08_12//Programa de Ações Universitárias Integradas 
Luso-Francesas (PAULIF)/ ; }, mesh = {Actinomycetales ; Animals ; Aquaculture ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Bivalvia/chemistry/*microbiology ; DNA, Ribosomal ; France ; Gills/microbiology ; Hemolymph/microbiology ; *Microbiota ; Molecular Typing ; Phylogeny ; Portugal ; }, abstract = {According to the hologenome theory, the microbiota contributes to the fitness of the holobiont having an important role in its adaptation, survival, development, health, and evolution. Environmental stress also affects the microbiota and its capability to assist the holobiont in coping with stress factors. Here, we analyzed the diversity of cultivable bacteria associated with Manila clam tissues (mantle, gills, hemolymph) in two non-contaminated sites (Portugal and France) and one metal-contaminated site (Portugal). A total of 240 isolates were obtained. Representative isolates (n = 198) of the overall diversity were identified by 16S rDNA sequencing and subjected to functional characterization. Isolates affiliated with Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. Proteobacteria (mostly Pseudoalteromonadaceae and Vibrionaceae) were dominant in non-contaminated sites while Actinobacteria (mostly Microbacteriaceae) dominated in the metal-contaminated site. The main factor affecting the microbiota composition was contamination. No significant differences were observed between clam tissues and geographic regions. Several isolates tested positive for antibacterial activity, biofilm formation, protease, and siderophore production. The results show that the Manila clam harbors a diverse microbiota that may contribute to clam protection and overall fitness, as well as to its adaptation to stressful environments. In addition, the Manila clam microbiota is revealed as a promising source of novel probiotics with potential application in aquaculture.}, }
@article {pmid28732267, year = {2017}, author = {Sánchez-Cañizares, C and Jorrín, B and Poole, PS and Tkacz, A}, title = {Understanding the holobiont: the interdependence of plants and their microbiome.}, journal = {Current opinion in microbiology}, volume = {38}, number = {}, pages = {188-196}, doi = {10.1016/j.mib.2017.07.001}, pmid = {28732267}, issn = {1879-0364}, mesh = {*Ecosystem ; *Microbiota ; Plants/*microbiology ; }, abstract = {The holobiont is composed by the plant and its microbiome. In a similar way to ecological systems of higher organisms, the holobiont shows interdependent and complex dynamics [1,2]. While plants originate from seeds, the microbiome has a multitude of sources. The assemblage of these communities depends on the interaction between the emerging seedling and its surrounding environment, with soil being the main source. These microbial communities are controlled by the plant through different strategies, such as the specific profile of root exudates and its immune system. Despite this control, the microbiome is still able to adapt and thrive. The molecular knowledge behind these interactions and microbial '-omic' technologies are developing to the point of enabling holobiont engineering. For a long time microorganisms were in the background of plant biology but new multidisciplinary approaches have led to an appreciation of the importance of the holobiont, where plants and microbes are interdependent.}, }
@article {pmid28729652, year = {2017}, author = {Johnston, EC and Forsman, ZH and Flot, JF and Schmidt-Roach, S and Pinzón, JH and Knapp, ISS and Toonen, RJ}, title = {A genomic glance through the fog of plasticity and diversification in Pocillopora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5991}, pmid = {28729652}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics ; Bayes Theorem ; *Biodiversity ; Genome, Mitochondrial ; *Genomics ; Likelihood Functions ; Open Reading Frames/genetics ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Time Factors ; }, abstract = {Scleractinian corals of the genus Pocillopora (Lamarck, 1816) are notoriously difficult to identify morphologically with considerable debate on the degree to which phenotypic plasticity, introgressive hybridization and incomplete lineage sorting obscure well-defined taxonomic lineages. Here, we used RAD-seq to resolve the phylogenetic relationships among seven species of Pocillopora represented by 15 coral holobiont metagenomic libraries. We found strong concordance between the coral holobiont datasets, reads that mapped to the Pocillopora damicornis (Linnaeus, 1758) transcriptome, nearly complete mitochondrial genomes, 430 unlinked high-quality SNPs shared across all Pocillopora taxa, and a conspecificity matrix of the holobiont dataset. These datasets also show strong concordance with previously published clustering of the mitochondrial clades based on the mtDNA open reading frame (ORF). We resolve seven clear monophyletic groups, with no evidence for introgressive hybridization among any but the most recently derived sister species. In contrast, ribosomal and histone datasets, which are most commonly used in coral phylogenies to date, were less informative and contradictory to these other datasets. These data indicate that extant Pocillopora species diversified from a common ancestral lineage within the last ~3 million years. Key to this evolutionary success story may be the high phenotypic plasticity exhibited by Pocillopora species.}, }
@article {pmid28724687, year = {2017}, author = {Morimoto, J and Simpson, SJ and Ponton, F}, title = {Direct and trans-generational effects of male and female gut microbiota in Drosophila melanogaster.}, journal = {Biology letters}, volume = {13}, number = {7}, pages = {}, pmid = {28724687}, issn = {1744-957X}, mesh = {Acetobacter ; Animals ; Drosophila melanogaster ; Female ; *Gastrointestinal Microbiome ; Male ; Reproduction ; Sexual Behavior, Animal ; }, abstract = {There is increasing evidence of the far-reaching effects of gut bacteria on physiological and behavioural traits, yet the fitness-related consequences of changes in the gut bacteria composition of sexually interacting individuals remain unknown. To address this question, we manipulated the gut microbiota of fruit flies, Drosophila melanogaster, by monoinfecting flies with either Acetobacter pomorum (AP) or Lactobacillus plantarum (LP). Re-inoculated individuals were paired in all treatment combinations. LP-infected males had longer mating duration and induced higher short-term offspring production in females compared with AP-infected males. Furthermore, females of either re-inoculation state mated with AP-infected males were more likely to have zero offspring after mating, suggesting a negative effect of AP on male fertility. Finally, we found that the effects of male and female gut bacteria interacted to modulate their daughters', but not sons' body mass, revealing a new trans-generational effect of parental gut microbiota. In conclusion, this study shows direct and trans-generational effects of the gut microbiota on mating and reproduction.}, }
@article {pmid28717593, year = {2017}, author = {Gerth, M and Hurst, GDD}, title = {Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e3529}, pmid = {28717593}, issn = {2167-8359}, abstract = {High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these 'contaminations' provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee (Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo. We conclude that 'contamination' in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses.}, }
@article {pmid28710460, year = {2017}, author = {Pineda, MC and Strehlow, B and Sternel, M and Duckworth, A and Haan, JD and Jones, R and Webster, NS}, title = {Effects of sediment smothering on the sponge holobiont with implications for dredging management.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {5156}, pmid = {28710460}, issn = {2045-2322}, abstract = {One of the ways dredging can affect benthic habitats is through high levels of sediment deposition, which has the potential to smother sessile organisms such as sponges. In order to provide pressure-response values to sedimentation and tease apart the different cause-effect pathways of high turbidity, 5 sponge species, including heterotrophic and phototrophic nutritional modes, were exposed for up to 30 d to multiple sediment deposition events, each of which resulted in an initial covering of 80-100% of the surface of the sponges in a layer ~0.5 mm thick. The response of the sponges was examined using a suite of different response variables including growth, respiration, lipid content, community composition of the microbial symbionts, and maximum quantum yield and chlorophyll content of the phototrophic symbionts. Different species showed different mechanisms of sediment rejection and different patterns of sediment clearance. All species survived the treatments, were able to tolerate high levels of partial covering of their surfaces, and for most species the treatment did not alter the health of the sponge holobiont. Results from this study will guide interpretation of experiments examining the combined effects of all three dredging-related pressures, and aid the development of water quality thresholds for impact prediction purposes.}, }
@article {pmid28694508, year = {2017}, author = {Pineda, MC and Strehlow, B and Sternel, M and Duckworth, A and Jones, R and Webster, NS}, title = {Effects of suspended sediments on the sponge holobiont with implications for dredging management.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {4925}, pmid = {28694508}, issn = {2045-2322}, mesh = {Analysis of Variance ; Animals ; Biomarkers ; *Geologic Sediments ; Microbiota ; Porifera/microbiology/*physiology ; }, abstract = {Dredging can cause high suspended sediment concentrations (SSC) in the water column, posing a hazard to filter feeding organisms like sponges as sediment may clog their aquiferous systems and reduce feeding. In order to provide pressure-response values for sponges to SSC and tease apart the cause:effect pathways of dredging pressures, five heterotrophic and phototrophic species were experimentally exposed to a range of dredging-relevant SSC of up to 100 mg L-1, with light compensation across treatments to ensure that SSC was the primary physical parameter. This study shows that some sponge species exposed to high SSC (≥23 mg L-1) for extended periods (28 d) have lower survival, increased necrosis and depletion of energy reserves. In contrast, SSC of ≤10 mg L-1 caused few, if any, negative effects and is thus suggested as a prudent sub-lethal threshold for sponges. Microbial communities did not change significantly among SSC treatments, although a nutritional shift from mixotrophy towards increased phototrophy was detected for some sponge species exposed to high SSC. Importantly however, it is expected that the combined effect of SSC with low light availability and sediment smothering as occurs during dredging operations will increase the negative effects on sponges.}, }
@article {pmid28682223, year = {2017}, author = {Burcelin, R}, title = {[Gut microbiota and immune crosstalk in metabolic disease].}, journal = {Biologie aujourd'hui}, volume = {211}, number = {1}, pages = {1-18}, doi = {10.1051/jbio/2017008}, pmid = {28682223}, issn = {2105-0686}, mesh = {Animals ; Dysbiosis/complications/immunology/microbiology/prevention &amp; control ; Gastrointestinal Microbiome/immunology/*physiology ; Gastrointestinal Tract/immunology/metabolism ; Humans ; Immune System/*physiology ; Inflammation/etiology/microbiology ; Metabolic Diseases/*immunology/metabolism/*microbiology ; Signal Transduction/immunology ; }, abstract = {The aim of the review is to discuss about the role played by the defence crosstalk between the gut microbiota and the intestinal immune system, in the development of metabolic disease focusing on obesity and diabetes. Starting from physiological and pathological stand points and based on the latest published data, this review is addressing how the concept of the hologenome theory of evolution can drive the fate of metabolic disease. The notion of &quot;metabolic infection&quot; to explain the &quot;metabolic inflammation&quot; is discussed. This imply comments about the process of bacterial translocation and impaired intestinal immune defense against commensals. Eventually this review sets the soil for personalized medicine. The monthly increase in the number of publications on the gut microbiota to intestinal immune defense and the control of metabolism demonstrate the importance of this field of investigation. The notion of commensal as &quot;self or non-self&quot; has to be reevaluated in the light of the current data. Furthermore, data demonstrate the major role played by short chain fatty acids, secondary bile acids, LPS, peptidoglycans, indole derivatives, and other bacteria-related molecules on the shaping of cells involved in the intestinal protection against commensals is now becoming a central player in the incidence of metabolic diseases. The literature demonstrates that the onset of metabolic diseases and some specific co-morbidities can be explained by a gut microbiota to intestinal immune system crosstalk. Therefore, one should now consider this avenue of investigation as a putative source of biomarkers and therapeutic targets to personalize the treatment of metabolic disease and its co-morbidities. Gut microbiota is considered as a major regulator of metabolic disease. This reconciles the notion of metabolic inflammation and the epidemic development of the disease. In addition to evidence showing that a specific gut microbiota characterizes patients with obesity, type 2 diabetes, and hepatic steatosis, the mechanisms causal to the disease could be related to the translocation of microbiota from the gut to the tissues, which induces inflammation. The mechanisms regulating such a process are based on the crosstalk between the gut microbiota and the host immune system. The hologenome theory of evolution supports this concept and implies that therapeutic strategies aiming to control glycemia should take into account both the gut microbiota and the host immune system. This review discusses the latest evidence regarding the bidirectional impact of the gut microbiota on host immune system crosstalk for the control of metabolic disease, hyperglycemia, and obesity. To avoid redundancies with the literature, we will focus our attention on the intestinal immune system, identifying evidence for the generation of novel therapeutic strategies, which could be based on the control of the translocation of gut bacteria to tissues. Such novel strategies should hamper the role played by gut microbiota dysbiosis on the development of metabolic inflammation. Recent evidence in rodents allows us to conclude that an impaired intestinal immune system characterizes and could be causal in the development of metabolic disease. The fine understanding of the molecular mechanisms should allow for the development of a first line of treatment for metabolic disease and its co-morbidities.}, }
@article {pmid28681143, year = {2018}, author = {van de Water, JAJM and Voolstra, CR and Rottier, C and Cocito, S and Peirano, A and Allemand, D and Ferrier-Pagès, C}, title = {Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea.}, journal = {Microbial ecology}, volume = {75}, number = {1}, pages = {274-288}, pmid = {28681143}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; High-Throughput Nucleotide Sequencing ; Mediterranean Sea ; *Microbiota ; Phylogeny ; Seasons ; Seawater ; Symbiosis ; }, abstract = {Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.}, }
@article {pmid28679724, year = {2017}, author = {Smith, EG and D'Angelo, C and Sharon, Y and Tchernov, D and Wiedenmann, J}, title = {Acclimatization of symbiotic corals to mesophotic light environments through wavelength transformation by fluorescent protein pigments.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1858}, pages = {}, pmid = {28679724}, issn = {1471-2954}, support = {311179//European Research Council/International ; }, mesh = {*Acclimatization ; Animals ; Anthozoa/physiology/*radiation effects ; Coral Reefs ; Dinoflagellida/physiology/*radiation effects ; Fluorescence ; *Light ; *Pigmentation ; Symbiosis ; }, abstract = {The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate that host pigments, specifically photoconvertible red fluorescent proteins (pcRFPs), can promote coral adaptation/acclimatization to deeper-water light environments by transforming the prevalent blue light into orange-red light, which can penetrate deeper within zooxanthellae-containing tissues; this facilitates a more homogeneous distribution of photons across symbiont communities. The ecological importance of pcRFPs in deeper reefs is supported by the increasing proportion of red fluorescent corals with depth (measured down to 45 m) and increased survival of colour morphs with strong expression of pcRFPs in long-term light manipulation experiments. In addition to screening by host pigments from high light intensities in shallow water, the spectral transformation observed in deeper-water corals highlights the importance of GFP-like protein expression as an ecological mechanism to support the functioning of the coral-Symbiodinium association across steep environmental gradients.}, }
@article {pmid28659968, year = {2017}, author = {Sandoval-Motta, S and Aldana, M and Martínez-Romero, E and Frank, A}, title = {The Human Microbiome and the Missing Heritability Problem.}, journal = {Frontiers in genetics}, volume = {8}, number = {}, pages = {80}, pmid = {28659968}, issn = {1664-8021}, abstract = {The &quot;missing heritability&quot; problem states that genetic variants in Genome-Wide Association Studies (GWAS) cannot completely explain the heritability of complex traits. Traditionally, the heritability of a phenotype is measured through familial studies using twins, siblings and other close relatives, making assumptions on the genetic similarities between them. When this heritability is compared to the one obtained through GWAS for the same traits, a substantial gap between both measurements arise with genome wide studies reporting significantly smaller values. Several mechanisms for this &quot;missing heritability&quot; have been proposed, such as epigenetics, epistasis, and sequencing depth. However, none of them are able to fully account for this gap in heritability. In this paper we provide evidence that suggests that in order for the phenotypic heritability of human traits to be broadly understood and accounted for, the compositional and functional diversity of the human microbiome must be taken into account. This hypothesis is based on several observations: (A) The composition of the human microbiome is associated with many important traits, including obesity, cancer, and neurological disorders. (B) Our microbiome encodes a second genome with nearly a 100 times more genes than the human genome, and this second genome may act as a rich source of genetic variation and phenotypic plasticity. (C) Human genotypes interact with the composition and structure of our microbiome, but cannot by themselves explain microbial variation. (D) Microbial genetic composition can be strongly influenced by the host's behavior, its environment or by vertical and horizontal transmissions from other hosts. Therefore, genetic similarities assumed in familial studies may cause overestimations of heritability values. We also propose a method that allows the compositional and functional diversity of our microbiome to be incorporated to genome wide association studies.}, }
@article {pmid28659905, year = {2017}, author = {Yang, SH and Tseng, CH and Huang, CR and Chen, CP and Tandon, K and Lee, STM and Chiang, PW and Shiu, JH and Chen, CA and Tang, SL}, title = {Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {1094}, pmid = {28659905}, issn = {1664-302X}, abstract = {The coral holobiont is the assemblage of coral host and its microbial symbionts, which functions as a unit and is responsive to host species and environmental factors. Although monitoring surveys have been done to determine bacteria associated with coral, none have persisted for >1 year. Therefore, potential variations in minor or dominant community members that occur over extended intervals have not been characterized. In this study, 16S rRNA gene amplicon pyrosequencing was used to investigate the relationship between bacterial communities in healthy Stylophora pistillata in tropical and subtropical Taiwan over 2 years, apparently one of the longest surveys of coral-associated microbes. Dominant bacterial genera in S. pistillata had disparate changes in different geographical setups, whereas the constitution of minor bacteria fluctuated in abundance over time. We concluded that dominant bacteria (Acinetobacter, Propionibacterium, and Pseudomonas) were stable in composition, regardless of seasonal and geographical variations, whereas Endozoicomonas had a geographical preference. In addition, by combining current data with previous studies, we concluded that a minor bacteria symbiont, Ralstonia, was a keystone species in coral. Finally, we concluded that long-term surveys for coral microbial communities were necessary to detect compositional shifts, especially for minor bacterial members in corals.}, }
@article {pmid28654220, year = {2017}, author = {Campisano, A and Albanese, D and Yousaf, S and Pancher, M and Donati, C and Pertot, I}, title = {Temperature drives the assembly of endophytic communities' seasonal succession.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {3353-3364}, doi = {10.1111/1462-2920.13843}, pmid = {28654220}, issn = {1462-2920}, mesh = {Bradyrhizobium/classification/growth &amp; development/isolation &amp; purification ; Burkholderia/classification/growth &amp; development/isolation &amp; purification ; Endophytes/*classification/*growth &amp; development/isolation &amp; purification ; Mesorhizobium/classification/growth &amp; development/isolation &amp; purification ; *Microbiota ; Plant Roots/*microbiology ; Propionibacterium/classification/growth &amp; development/isolation &amp; purification ; Ralstonia/classification/growth &amp; development/isolation &amp; purification ; Seasons ; Temperature ; Vitis/*microbiology ; }, abstract = {Endophytic microorganisms asymptomatically colonise plant tissues. Exploring the assembly dynamics of bacterial endophytic communities is essential to understand the functioning of the plant holobiont and to optimise their possible use as biopesticides or plant biostimulants. The variation in endophytic communities in above and below-ground organs in Vitis vinifera in the field were studied. To understand the specific effect of temperature on endophytic communities, a separate experiment was set up where grapevine cuttings were grown under controlled conditions at three different temperatures. The findings revealed the succession of endophytic communities over the year. Endophytic communities of roots and stems differ in terms of composition and dynamic response to temperature. Noticeably, compositional differences during the seasons affected bacterial taxa more in stems than in roots, suggesting that roots offer a more stable and less easily perturbed environment. Correlation abundance networks showed that the presence of several taxa (including Bradyrhizobium, Burkholderia, Dyella, Mesorhizobium, Propionibacterium and Ralstonia) is linked in both the field and the greenhouse.}, }
@article {pmid28646902, year = {2017}, author = {Pitlik, SD and Koren, O}, title = {How holobionts get sick-toward a unifying scheme of disease.}, journal = {Microbiome}, volume = {5}, number = {1}, pages = {64}, pmid = {28646902}, issn = {2049-2618}, support = {//CIHR/Canada ; }, mesh = {Animals ; Bacteria/pathogenicity ; Biological Evolution ; *Disease ; Genome ; Host-Pathogen Interactions ; Humans ; *Microbiota ; Plants ; Symbiosis ; }, abstract = {All humans, animals, and plants are holobionts. Holobionts comprise the host and a myriad of interacting microorganisms-the microbiota. The hologenome encompasses the genome of the host plus the composite of all microbial genomes (the microbiome). In health, there is a fine-tuned and resilient equilibrium within the members of the microbiota and between them and the host. This relative stability is maintained by a high level of microbial diversity, a delicate bio-geographic distribution of microorganisms, and a sophisticated and intricate molecular crosstalk among the multiple components of the holobiont. Pathobionts are temporarily benign microbes with the potential, under modified ecosystem conditions, to become key players in disease. Pathobionts may be endogenous, living for prolonged periods of time inside or on the host, or exogenous, invading the host during opportunistic situations. In both cases, the end result is the transformation of the beneficial microbiome into a health-perturbing pathobiome. We hypothesize that probably all diseases of holobionts, acute or chronic, infectious or non-infectious, and regional or systemic, are characterized by a perturbation of the healthy microbiome into a diseased pathobiome.}, }
@article {pmid28625867, year = {2017}, author = {Postler, TS and Ghosh, S}, title = {Understanding the Holobiont: How Microbial Metabolites Affect Human Health and Shape the Immune System.}, journal = {Cell metabolism}, volume = {26}, number = {1}, pages = {110-130}, pmid = {28625867}, issn = {1932-7420}, support = {R01 DK102180/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Immune System/*metabolism/microbiology ; Inflammation/*metabolism/microbiology ; Inflammatory Bowel Diseases/metabolism/microbiology ; Metabolic Diseases/*metabolism/microbiology ; *Metabolome ; }, abstract = {The human gastrointestinal tract is populated by a diverse, highly mutualistic microbial flora, which is known as the microbiome. Disruptions to the microbiome have been shown to be associated with severe pathologies of the host, including metabolic disease, cancer, and inflammatory bowel disease. Mood and behavior are also susceptible to alterations in the gut microbiota. A particularly striking example of the symbiotic effects of the microbiome is the immune system, whose cells depend critically on a diverse array of microbial metabolites for normal development and behavior. This includes metabolites that are produced by bacteria from dietary components, metabolites that are produced by the host and biochemically modified by gut bacteria, and metabolites that are synthesized de novo by gut microbes. In this review, we highlight the role of the intestinal microbiome in human metabolic and inflammatory diseases and focus in particular on the molecular mechanisms that govern the gut-immune axis.}, }
@article {pmid28624904, year = {2017}, author = {Coelho-Souza, SA and Jenkins, SR and Casarin, A and Baeta-Neves, MH and Salgado, LT and Guimaraes, JRD and Coutinho, R}, title = {The Effect of Light on Bacterial Activity in a Seaweed Holobiont.}, journal = {Microbial ecology}, volume = {74}, number = {4}, pages = {868-876}, pmid = {28624904}, issn = {1432-184X}, mesh = {Anti-Bacterial Agents/*pharmacology ; *Autotrophic Processes ; *Bacterial Physiological Phenomena/drug effects ; *Biofilms/drug effects/growth &amp; development/radiation effects ; Brazil ; Circadian Rhythm ; *Light ; Sargassum/microbiology ; Seasons ; }, abstract = {Holobionts are characterized by the relationship between host and their associated organisms such as the biofilm associated with macroalgae. Considering that light is essential to macroalgae survival, the aim of this study was to verify the effect of light on the heterotrophic activity in biofilms of the brown macroalgae Sargassum furcatum during its growth cycle. Measurements of heterotrophic activity were done under natural light levels at different times during a daily cycle and under an artificial extinction of natural light during the afternoon. We also measured Sargassum primary production under these light levels in the afternoon. Both measurements were done with and without photosynthesis inhibitor and antibiotics. Biofilm composition was mainly represented by bacteria but diatoms, cyanobacteria, and other organisms were also common. When a peak of diatom genera was recorded, the heterotrophic activity of the biofilm was higher. Heterotrophic activity was usually highest during the afternoon and the presence of a photosynthesis inhibitor caused an average reduction of 17% but there was no relationship with Sargassum primary production. These results indicate that autotrophic production in the biofilm was reduced by the inhibitor with consequences on bacterial activity. Heterotrophic activity was mainly bacterial and the antibiotics chloramphenicol and penicillin were more effective than streptomycin. We suggest primary producers in the biofilm are more important to increase bacterial activity than the macroalgae itself because of coherence of the peaks of heterotrophic and autotrophic activity in biofilm during the afternoon and the effects of autotrophic inhibitors on heterotrophic activity.}, }
@article {pmid28601483, year = {2017}, author = {Tripp, EA and Zhang, N and Schneider, H and Huang, Y and Mueller, GM and Hu, Z and Häggblom, M and Bhattacharya, D}, title = {Reshaping Darwin's Tree: Impact of the Symbiome.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {8}, pages = {552-555}, doi = {10.1016/j.tree.2017.05.002}, pmid = {28601483}, issn = {1872-8383}, mesh = {*Biodiversity ; Humans ; *Phylogeny ; }, abstract = {Much of the undescribed biodiversity on Earth is microbial, often in mutualistic or pathogenic associations. Physically associated and coevolving life forms comprise a symbiome. We propose that systematics research can accelerate progress in science by introducing a new framework for phylogenetic analysis of symbiomes, here termed SYMPHY (symbiome phylogenetics).}, }
@article {pmid28572677, year = {2017}, author = {Wright, RM and Kenkel, CD and Dunn, CE and Shilling, EN and Bay, LK and Matz, MV}, title = {Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2609}, pmid = {28572677}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*genetics/immunology ; Disease Resistance ; Gene Expression Profiling ; Genetic Markers/genetics ; *Genotype ; Hydrobiology ; Species Specificity ; Stress, Physiological/*genetics/immunology ; Transcriptome ; Vibrio/*physiology ; Vibrio Infections/*immunology ; }, abstract = {Disease causes significant coral mortality worldwide; however, factors responsible for intraspecific variation in disease resistance remain unclear. We exposed fragments of eight Acropora millepora colonies (genotypes) to putatively pathogenic bacteria (Vibrio spp.). Genotypes varied from zero to >90% mortality, with bacterial challenge increasing average mortality rates 4-6 fold and shifting the microbiome in favor of stress-associated taxa. Constitutive immunity and subsequent immune and transcriptomic responses to the challenge were more prominent in high-mortality individuals, whereas low-mortality corals remained largely unaffected and maintained expression signatures of a healthier condition (i.e., did not launch a large stress response). Our results suggest that lesions appeared due to changes in the coral pathobiome (multiple bacterial species associated with disease) and general health deterioration after the biotic disturbance, rather than the direct activity of any specific pathogen. If diseases in nature arise because of weaknesses in holobiont physiology, instead of the virulence of any single etiological agent, environmental stressors compromising coral condition might play a larger role in disease outbreaks than is currently thought. To facilitate the diagnosis of compromised individuals, we developed and independently cross-validated a biomarker assay to predict mortality based on genes whose expression in asymptomatic individuals coincides with mortality rates.}, }
@article {pmid28553264, year = {2017}, author = {Carrier, TJ and Reitzel, AM}, title = {The Hologenome Across Environments and the Implications of a Host-Associated Microbial Repertoire.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {802}, pmid = {28553264}, issn = {1664-302X}, abstract = {Our understanding of the diverse interactions between hosts and microbes has grown profoundly over the past two decades and, as a product, has revolutionized our knowledge of the life sciences. Through primarily laboratory experiments, the current framework for holobionts and their respective hologenomes aims to decipher the underpinnings and implications of symbioses between host and microbiome. However, the laboratory setting restricts the full spectrum of host-associated symbionts as compared to those found in nature; thus, limiting the potential for a holistic interpretation of the functional roles the microbiome plays in host biology. When holobionts are studied in nature, associated microbial communities vary considerably between conditions, resulting in more microbial associates as part of the &quot;hologenome&quot; across environments than in either environment alone. We review and synthesize empirical evidence suggesting that hosts may associate with a larger microbial network that, in part, corresponds to experiencing diverse environmental conditions. To conceptualize the interactions between host and microbiome in an ecological context, we suggest the &quot;host-associated microbial repertoire,&quot; which is the sum of microbial species a host may associate with over the course of its life-history under all encountered environmental circumstances. Furthermore, using examples from both terrestrial and marine ecosystems, we discuss how this concept may be used as a framework to compare the ability of the holobiont to acclimate and adapt to environmental variation, and propose three &quot;signatures&quot; of the concept.}, }
@article {pmid28549621, year = {2017}, author = {Lemanceau, P and Blouin, M and Muller, D and Moënne-Loccoz, Y}, title = {Let the Core Microbiota Be Functional.}, journal = {Trends in plant science}, volume = {22}, number = {7}, pages = {583-595}, doi = {10.1016/j.tplants.2017.04.008}, pmid = {28549621}, issn = {1878-4372}, mesh = {Plants/*microbiology ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The microbial community that is systematically associated with a given host plant is called the core microbiota. The definition of the core microbiota was so far based on its taxonomic composition, but we argue that it should also be based on its functions. This so-called functional core microbiota encompasses microbial vehicles carrying replicators (genes) with essential functions for holobiont (i.e., plant plus microbiota) fitness. It builds up from enhanced horizontal transfers of replicators as well as from ecological enrichment of their vehicles. The transmission pathways of this functional core microbiota vary over plant generations according to environmental constraints and its added value for holobiont fitness.}, }
@article {pmid28546553, year = {2017}, author = {Smith, EG and Vaughan, GO and Ketchum, RN and McParland, D and Burt, JA}, title = {Symbiont community stability through severe coral bleaching in a thermally extreme lagoon.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {2428}, pmid = {28546553}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; DNA, Intergenic ; Dinoflagellida/*physiology ; Environment ; *Symbiosis ; Temperature ; }, abstract = {Coral reefs are threatened by climate change as coral-algal symbioses are currently living close to their upper thermal limits. The resilience of the algal partner plays a key role in determining the thermal tolerance of the coral holobiont and therefore, understanding the acclimatory limits of present day coral-algal symbioses is fundamental to forecasting corals' responses to climate change. This study characterised the symbiont community in a highly variable and thermally extreme (Max = 37.5 °C, Min = 16.8 °C) lagoon located in the southern Persian/Arabian Gulf using next generation sequencing of ITS2 amplicons. Despite experiencing extreme temperatures, severe bleaching and many factors that would be expected to promote the presence of, or transition to clade D dominance, the symbiont communities of the lagoon remain dominated by the C3 variant, Symbiodinium thermophilum. The stability of this symbiosis across multiple genera with different means of symbiont transmission highlights the importance of Symbiodinium thermophilum for corals living at the acclimatory limits of modern day corals. Corals in this extreme environment did not undergo adaptive bleaching, suggesting they are living at the edge of their acclimatory potential and that this valuable source of thermally tolerant genotypes may be lost in the near future under climate change.}, }
@article {pmid28534879, year = {2017}, author = {Frischkorn, KR and Rouco, M and Van Mooy, BAS and Dyhrman, ST}, title = {Epibionts dominate metabolic functional potential of Trichodesmium colonies from the oligotrophic ocean.}, journal = {The ISME journal}, volume = {11}, number = {9}, pages = {2090-2101}, pmid = {28534879}, issn = {1751-7370}, mesh = {Nitrogen/metabolism ; Nitrogen Fixation ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Trichodesmium/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Trichodesmium is a genus of marine diazotrophic colonial cyanobacteria that exerts a profound influence on global biogeochemistry, by injecting 'new' nitrogen into the low nutrient systems where it occurs. Colonies of Trichodesmium ubiquitously contain a diverse assemblage of epibiotic microorganisms, constituting a microbiome on the Trichodesmium host. Metagenome sequences from Trichodesmium colonies were analyzed along a resource gradient in the western North Atlantic to examine microbiome community structure, functional diversity and metabolic contributions to the holobiont. Here we demonstrate the presence of a core Trichodesmium microbiome that is modulated to suit different ocean regions, and contributes over 10 times the metabolic potential of Trichodesmium to the holobiont. Given the ubiquitous nature of epibionts on colonies, the substantial functional diversity within the microbiome is likely an integral facet of Trichodesmium physiological ecology across the oligotrophic oceans where this biogeochemically significant diazotroph thrives.}, }
@article {pmid28533520, year = {2017}, author = {Strand, R and Whalan, S and Webster, NS and Kutti, T and Fang, JKH and Luter, HM and Bannister, RJ}, title = {The response of a boreal deep-sea sponge holobiont to acute thermal stress.}, journal = {Scientific reports}, volume = {7}, number = {1}, pages = {1660}, pmid = {28533520}, issn = {2045-2322}, mesh = {*Adaptation, Biological ; Animals ; *Aquatic Organisms ; Energy Metabolism ; Intracellular Membranes/metabolism ; Lysosomes/metabolism ; Microbiota ; Nutritional Physiological Phenomena ; Oxygen Consumption ; Porifera/microbiology/*physiology ; *Seawater ; *Stress, Physiological ; *Temperature ; }, abstract = {Effects of elevated seawater temperatures on deep-water benthos has been poorly studied, despite reports of increased seawater temperature (up to 4 °C over 24 hrs) coinciding with mass mortality events of the sponge Geodia barretti at Tisler Reef, Norway. While the mechanisms driving these mortality events are unclear, manipulative laboratory experiments were conducted to quantify the effects of elevated temperature (up to 5 °C, above ambient levels) on the ecophysiology (respiration rate, nutrient uptake, cellular integrity and sponge microbiome) of G. barretti. No visible signs of stress (tissue necrosis or discolouration) were evident across experimental treatments; however, significant interactive effects of time and treatment on respiration, nutrient production and cellular stress were detected. Respiration rates and nitrogen effluxes doubled in responses to elevated temperatures (11 °C &amp; 12 °C) compared to control temperatures (7 °C). Cellular stress, as measured through lysosomal destabilisation, was 2-5 times higher at elevated temperatures than for control temperatures. However, the microbiome of G. barretti remained stable throughout the experiment, irrespective of temperature treatment. Mortality was not evident and respiration rates returned to pre-experimental levels during recovery. These results suggest other environmental processes, either alone or in combination with elevated temperature, contributed to the mortality of G. barretti at Tisler reef.}, }
@article {pmid28509908, year = {2017}, author = {Webster, NS and Reusch, TBH}, title = {Microbial contributions to the persistence of coral reefs.}, journal = {The ISME journal}, volume = {11}, number = {10}, pages = {2167-2174}, pmid = {28509908}, issn = {1751-7370}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology/physiology ; *Coral Reefs ; Evolution, Molecular ; Gene Transfer, Horizontal ; *Microbiota/genetics ; }, abstract = {On contemplating the adaptive capacity of reef organisms to a rapidly changing environment, the microbiome offers significant and greatly unrecognised potential. Microbial symbionts contribute to the physiology, development, immunity and behaviour of their hosts, and can respond very rapidly to changing environmental conditions, providing a powerful mechanism for acclimatisation and also possibly rapid evolution of coral reef holobionts. Environmentally acquired fluctuations in the microbiome can have significant functional consequences for the holobiont phenotype upon which selection can act. Environmentally induced changes in microbial abundance may be analogous to host gene duplication, symbiont switching / shuffling as a result of environmental change can either remove or introduce raw genetic material into the holobiont; and horizontal gene transfer can facilitate rapid evolution within microbial strains. Vertical transmission of symbionts is a key feature of many reef holobionts and this would enable environmentally acquired microbial traits to be faithfully passed to future generations, ultimately facilitating microbiome-mediated transgenerational acclimatisation (MMTA) and potentially even adaptation of reef species in a rapidly changing climate. In this commentary, we highlight the capacity and mechanisms for MMTA in reef species, propose a modified Price equation as a framework for assessing MMTA and recommend future areas of research to better understand how microorganisms contribute to the transgenerational acclimatisation of reef organisms, which is essential if we are to reliably predict the consequences of global change for reef ecosystems.}, }
@article {pmid28491055, year = {2017}, author = {Xia, X and Gurr, GM and Vasseur, L and Zheng, D and Zhong, H and Qin, B and Lin, J and Wang, Y and Song, F and Li, Y and Lin, H and You, M}, title = {Metagenomic Sequencing of Diamondback Moth Gut Microbiome Unveils Key Holobiont Adaptations for Herbivory.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {663}, pmid = {28491055}, issn = {1664-302X}, abstract = {Herbivore specialists adapt to feed on a specific group of host plants by evolving various mechanisms to respond to plant defenses. Insects also possess complex gut microbiotas but their potential role in adaptation is poorly understood. Our previous study of the genome of diamondback moth, Plutella xylostella, revealed an intrinsic capacity to detoxify plant defense compounds, which is an important factor in its success as a pest. Here we expand on that work with a complete taxonomic and functional profile of the P. xylostella gut microbiota obtained by metagenomic sequencing. Gene enrichment in the metagenome, accompanied by functional identification, revealed an important role of specific gut bacteria in the breakdown of plant cell walls, detoxification of plant phenolics, and synthesis of amino acids. Microbes participating in these pathways mainly belonged to three highly abundant bacteria: Enterobacter cloacae, Enterobacter asburiae, and Carnobacterium maltaromaticum. Results show that while the gut microbial community may be complex, a small number of functionally active species can be disproportionally important. The presence of specific enzymes in the microbiota community, such as supporting amino acid synthesis, digestion and detoxification functions, demonstrates the beneficial interactions between P. xylostella and its gut microbiota. These interactions can be potential targets for manipulation to provide novel pest management approaches.}, }
@article {pmid28486655, year = {2017}, author = {Silveira, CB and Cavalcanti, GS and Walter, JM and Silva-Lima, AW and Dinsdale, EA and Bourne, DG and Thompson, CC and Thompson, FL}, title = {Microbial processes driving coral reef organic carbon flow.}, journal = {FEMS microbiology reviews}, volume = {41}, number = {4}, pages = {575-595}, doi = {10.1093/femsre/fux018}, pmid = {28486655}, issn = {1574-6976}, mesh = {Biodiversity ; Carbon/*metabolism ; *Coral Reefs ; Ecosystem ; Microbiota/*physiology ; Mucus/microbiology ; *Water Microbiology ; }, abstract = {Coral reefs are one of the most productive ecosystems on the planet, with primary production rates compared to that of rain forests. Benthic organisms release 10-50% of their gross organic production as mucus that stimulates heterotrophic microbial metabolism in the water column. As a result, coral reef microbes grow up to 50 times faster than open ocean communities. Anthropogenic disturbances cause once coral-dominated reefs to become dominated by fleshy organisms, with several outcomes for trophic relationships. Here we review microbial processes implicated in organic carbon flux in coral reefs displaying species phase shifts. The first section presents microbial players and interactions within the coral holobiont that contribute to reef carbon flow. In the second section, we identify four ecosystem-level microbial features that directly respond to benthic species phase shifts: community composition, biomass, metabolism and viral predation. The third section discusses the significance of microbial consumption of benthic organic matter to reef trophic relationships. In the fourth section, we propose that the 'microbial phase shifts' discussed here are conducive to lower resilience, facilitating the transition to new degradation states in coral reefs.}, }
@article {pmid28484479, year = {2017}, author = {Smith, DL and Gravel, V and Yergeau, E}, title = {Editorial: Signaling in the Phytomicrobiome.}, journal = {Frontiers in plant science}, volume = {8}, number = {}, pages = {611}, pmid = {28484479}, issn = {1664-462X}, }
@article {pmid28473829, year = {2017}, author = {Romano, M}, title = {Gut Microbiota as a Trigger of Accelerated Directional Adaptive Evolution: Acquisition of Herbivory in the Context of Extracellular Vesicles, MicroRNAs and Inter-Kingdom Crosstalk.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {721}, pmid = {28473829}, issn = {1664-302X}, abstract = {According to a traditional view, the specific diet in vertebrates is one of the key factors structuring the composition of the gut microbiota. In this interpretation, the microbiota assumes a subordinate position, where the larger host shapes, through evolution and its fitness, the taxonomical composition of the hosted microbiota. The present contribution shows how the evolution of herbivory, framed within the new concept of holobiont, the possibility of inter-kingdom crosstalk and its epigenetic effects, could pave the way to a completely reversed interpretation: instead of being passively shaped, the microbiota can mold and shape the general host body structure to increase its fitness. Central elements to consider in this context are the inter-kingdom crosstalk, the possibility of transporting RNAs through nanovesicles in feces from parents to offspring, and the activation of epigenetic processes passed on vertically from generation to generation. The new hypothesis is that the gut microbiota could play a great role in the macroevolutionary dynamics of herbivorous vertebrates, causing directly through host-microbiota dialog of epigenetic nature (i.e., methylation, histone acetylation, etc.), major changes in the organisms phenotype. The vertical exchange of the same microbial communities from parents to offspring, the interaction of these microbes with fairly uniform genotypes, and the socially restricted groups where these processes take place, could all explain the reasons why herbivory has appeared several time (and independently) during the evolution of vertebrates. The new interpretation could also represent a key factor in understanding the convergent evolution of analogous body structures in very distant lineages.}, }
@article {pmid28464532, year = {2017}, author = {Sogin, EM and Putnam, HM and Nelson, CE and Anderson, P and Gates, RD}, title = {Correspondence of coral holobiont metabolome with symbiotic bacteria, archaea and Symbiodinium communities.}, journal = {Environmental microbiology reports}, volume = {9}, number = {3}, pages = {310-315}, doi = {10.1111/1758-2229.12541}, pmid = {28464532}, issn = {1758-2229}, mesh = {Alveolata/*growth &amp; development/metabolism ; Animals ; Anthozoa/*microbiology/*parasitology ; Archaea/classification/*growth &amp; development/metabolism ; Biodiversity ; Coral Reefs ; Gammaproteobacteria/*growth &amp; development/metabolism ; Metabolome/physiology ; Symbiosis/*physiology ; Vibrionaceae/*growth &amp; development/metabolism ; }, abstract = {Microbial symbiotic partners, such as those associated with Scleractinian corals, mediate biochemical transformations that influence host performance and survival. While evidence suggests microbial community composition partly accounts for differences in coral physiology, how these symbionts affect metabolic pathways remains underexplored. We aimed to assess functional implications of variation among coral-associated microbial partners in hospite. To this end, we characterized and compared metabolomic profiles and microbial community composition from nine reef-building coral species. These data demonstrate metabolite profiles and microbial communities are species-specific and are correlated to one another. Using Porites spp. as a case study, we present evidence that the relative abundance of different sub-clades of Symbiodinium and bacterial/archaeal families are linked to positive and negative metabolomic signatures. Our data suggest that while some microbial partners benefit the union, others are more opportunistic with potential detriment to the host. Consequently, coral partner choice likely influences cellular metabolic activities and, therefore, holobiont nutrition.}, }
@article {pmid28447372, year = {2017}, author = {Chakravarti, LJ and Beltran, VH and van Oppen, MJH}, title = {Rapid thermal adaptation in photosymbionts of reef-building corals.}, journal = {Global change biology}, volume = {23}, number = {11}, pages = {4675-4688}, doi = {10.1111/gcb.13702}, pmid = {28447372}, issn = {1365-2486}, mesh = {*Acclimatization/physiology ; Animals ; Anthozoa/*physiology ; Climate ; Coral Reefs ; Dinoflagellida/*physiology ; Genotype ; Photosynthesis ; *Symbiosis ; Temperature ; }, abstract = {Climate warming is occurring at a rate not experienced by life on Earth for 10 s of millions of years, and it is unknown whether the coral-dinoflagellate (Symbiodinium spp.) symbiosis can evolve fast enough to ensure coral reef persistence. Coral thermal tolerance is partly dependent on the Symbiodinium hosted. Therefore, directed laboratory evolution in Symbiodinium has been proposed as a strategy to enhance coral holobiont thermal tolerance. Using a reciprocal transplant design, we show that the upper temperature tolerance and temperature tolerance range of Symbiodinium C1 increased after ~80 asexual generations (2.5 years) of laboratory thermal selection. Relative to wild-type cells, selected cells showed superior photophysiological performance and growth rate at 31°C in vitro, and performed no worse at 27°C; they also had lower levels of extracellular reactive oxygen species (exROS). In contrast, wild-type cells were unable to photosynthesise or grow at 31°C and produced up to 17 times more exROS. In symbiosis, the increased thermal tolerance acquired ex hospite was less apparent. In recruits of two of three species tested, those harbouring selected cells showed no difference in growth between the 27 and 31°C treatments, and a trend of positive growth at both temperatures. Recruits that were inoculated with wild-type cells, however, showed a significant difference in growth rates between the 27 and 31°C treatments, with a negative growth trend at 31°C. There were no significant differences in the rate and severity of bleaching in coral recruits harbouring wild-type or selected cells. Our findings highlight the need for additional Symbiodinium genotypes to be tested with this assisted evolution approach. Deciphering the genetic basis of enhanced thermal tolerance in Symbiodinium and the cause behind its limited transference to the coral holobiont in this genotype of Symbiodinium C1 are important next steps for developing methods that aim to increase coral bleaching tolerance.}, }
@article {pmid28446691, year = {2017}, author = {Enríquez, S and Méndez, ER and Hoegh-Guldberg, O and Iglesias-Prieto, R}, title = {Key functional role of the optical properties of coral skeletons in coral ecology and evolution.}, journal = {Proceedings. Biological sciences}, volume = {284}, number = {1853}, pages = {}, pmid = {28446691}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/*physiology ; *Coral Reefs ; Ecology ; *Light ; Optical Phenomena ; Symbiosis ; }, abstract = {Multiple scattering of light on coral skeleton enhances light absorption efficiency of coral symbionts and plays a key role in the regulation of their internal diffuse light field. To understand the dependence of this enhancement on skeleton meso- and macrostructure, we analysed the scattering abilities of naked coral skeletons for 74 Indo-Pacific species. Sensitive morphotypes to thermal and light stress, flat-extraplanate and branching corals, showed the most efficient structures, while massive-robust species were less efficient. The lowest light-enhancing scattering abilities were found for the most primitive colonial growth form: phaceloid. Accordingly, the development of highly efficient light-collecting structures versus the selection of less efficient but more robust holobionts to cope with light stress may constitute a trade-off in the evolution of modern symbiotic scleractinian corals, characterizing two successful adaptive solutions. The coincidence of the most important structural modifications with epitheca decline supports the importance of the enhancement of light transmission across coral skeleton in modern scleractinian diversification, and the central role of these symbioses in the design and optimization of coral skeleton. Furthermore, the same ability that lies at the heart of the success of symbiotic corals as coral-reef-builders can also explain the 'Achilles's heel' of these symbioses in a warming ocean.}, }
@article {pmid28437665, year = {2017}, author = {Carvalhais, LC and Schenk, PM and Dennis, PG}, title = {Jasmonic acid signalling and the plant holobiont.}, journal = {Current opinion in microbiology}, volume = {37}, number = {}, pages = {42-47}, doi = {10.1016/j.mib.2017.03.009}, pmid = {28437665}, issn = {1879-0364}, mesh = {Cyclopentanes/*metabolism ; *Microbiota ; Oxylipins/*metabolism ; Plant Growth Regulators/*metabolism ; Plants/*metabolism/*microbiology ; *Signal Transduction ; }, abstract = {The plant holobiont - which is the plant and its associated microbiome - is increasingly viewed as an evolving entity. Some interacting microbes that compose the microbiome assist plants in combating pathogens and herbivorous insects. However, knowledge of the factors that influence the microbiome in the context of defence signalling pathways is still in its infancy. Recent research reported that changes in jasmonic acid (JA) and salicylic acid signalling affects the root microbiome of Arabidopsis thaliana. This review aims to present the hypothesis that the JA pathway represents a novel mechanism for microbiome engineering for improved holobiont fitness in agricultural systems.}, }
@article {pmid28431245, year = {2017}, author = {Scott, TA and Quintaneiro, LM and Norvaisas, P and Lui, PP and Wilson, MP and Leung, KY and Herrera-Dominguez, L and Sudiwala, S and Pessia, A and Clayton, PT and Bryson, K and Velagapudi, V and Mills, PB and Typas, A and Greene, NDE and Cabreiro, F}, title = {Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans.}, journal = {Cell}, volume = {169}, number = {3}, pages = {442-456.e18}, pmid = {28431245}, issn = {1097-4172}, support = {102532/Z/12/Z//Wellcome Trust/United Kingdom ; MR/N003713/1//Medical Research Council/United Kingdom ; }, mesh = {Animals ; Antineoplastic Agents/*metabolism ; Autophagy ; Caenorhabditis elegans ; Cell Death ; Colorectal Neoplasms/drug therapy ; Diet ; Escherichia coli/enzymology/genetics/*metabolism ; Fluorouracil/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Models, Animal ; Pentosyltransferases/genetics ; }, abstract = {Fluoropyrimidines are the first-line treatment for colorectal cancer, but their efficacy is highly variable between patients. We queried whether gut microbes, a known source of inter-individual variability, impacted drug efficacy. Combining two tractable genetic models, the bacterium E. coli and the nematode C. elegans, we performed three-way high-throughput screens that unraveled the complexity underlying host-microbe-drug interactions. We report that microbes can bolster or suppress the effects of fluoropyrimidines through metabolic drug interconversion involving bacterial vitamin B6, B9, and ribonucleotide metabolism. Also, disturbances in bacterial deoxynucleotide pools amplify 5-FU-induced autophagy and cell death in host cells, an effect regulated by the nucleoside diphosphate kinase ndk-1. Our data suggest a two-way bacterial mediation of fluoropyrimidine effects on host metabolism, which contributes to drug efficacy. These findings highlight the potential therapeutic power of manipulating intestinal microbiota to ensure host metabolic health and treat disease.}, }
@article {pmid28430944, year = {2017}, author = {Berg, G and Köberl, M and Rybakova, D and Müller, H and Grosch, R and Smalla, K}, title = {Plant microbial diversity is suggested as the key to future biocontrol and health trends.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {5}, pages = {}, doi = {10.1093/femsec/fix050}, pmid = {28430944}, issn = {1574-6941}, support = {J 3638//Austrian Science Fund FWF/Austria ; T 847//Austrian Science Fund FWF/Austria ; }, mesh = {Biodiversity ; Biological Control Agents ; Ecosystem ; Microbiota/*physiology ; Plant Development ; Plant Diseases/*microbiology ; Plants/*microbiology ; Symbiosis/*physiology ; Volatile Organic Compounds/metabolism ; }, abstract = {The microbiome of plants plays a crucial role in both plant and ecosystem health. Rapid advances in multi-omics tools are dramatically increasing access to the plant microbiome and consequently to the identification of its links with diseases and to the control of those diseases. Recent insights reveal a close, often symbiotic relationship between microorganisms and plants. Microorganisms can stimulate germination and plant growth, prevent diseases, and promote stress resistance and general fitness. Plants and their associated microorganisms form a holobiont and have to be considered as co-evolved species assemblages consisting of bacterial, archaeal and diverse eukaryotic species. The beneficial interplay of the host and its microbiome is responsible for maintaining the health of the holobiont, while diseases are often correlated with microbial dysbioses. Microbial diversity was identified as a key factor in preventing diseases and can be implemented as a biomarker in plant protection strategies. Targeted and predictive biocontrol approaches are possible by developing microbiome-based solutions. Moreover, combined breeding and biocontrol strategies maintaining diversity and ecosystem health are required. The analysis of plant microbiome data has brought about a paradigm shift in our understanding of its role in health and disease and has substantial consequences for biocontrol and health issues.}, }
@article {pmid28429531, year = {2017}, author = {Pogoreutz, C and Rädecker, N and Cárdenas, A and Gärdes, A and Voolstra, CR and Wild, C}, title = {Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching.}, journal = {Global change biology}, volume = {23}, number = {9}, pages = {3838-3848}, doi = {10.1111/gcb.13695}, pmid = {28429531}, issn = {1365-2486}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Dinoflagellida ; *Nitrogen Fixation ; Symbiosis ; }, abstract = {The disruption of the coral-algae symbiosis (coral bleaching) due to rising sea surface temperatures has become an unprecedented global threat to coral reefs. Despite decades of research, our ability to manage mass bleaching events remains hampered by an incomplete mechanistic understanding of the processes involved. In this study, we induced a coral bleaching phenotype in the absence of heat and light stress by adding sugars. The sugar addition resulted in coral symbiotic breakdown accompanied by a fourfold increase of coral-associated microbial nitrogen fixation. Concomitantly, increased N:P ratios by the coral host and algal symbionts suggest excess availability of nitrogen and a disruption of the nitrogen limitation within the coral holobiont. As nitrogen fixation is similarly stimulated in ocean warming scenarios, here we propose a refined coral bleaching model integrating the cascading effects of stimulated microbial nitrogen fixation. This model highlights the putative role of nitrogen-fixing microbes in coral holobiont functioning and breakdown.}, }
@article {pmid28425179, year = {2017}, author = {Gajigan, AP and Diaz, LA and Conaco, C}, title = {Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.}, journal = {MicrobiologyOpen}, volume = {6}, number = {4}, pages = {}, pmid = {28425179}, issn = {2045-8827}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/*radiation effects ; Biota/*radiation effects ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Temperature ; }, abstract = {The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont.}, }
@article {pmid28410570, year = {2017}, author = {Valadez-Cano, C and Olivares-Hernández, R and Resendis-Antonio, O and DeLuna, A and Delaye, L}, title = {Natural selection drove metabolic specialization of the chromatophore in Paulinella chromatophora.}, journal = {BMC evolutionary biology}, volume = {17}, number = {1}, pages = {99}, pmid = {28410570}, issn = {1471-2148}, mesh = {Biological Evolution ; Cercozoa/*cytology/genetics/*physiology ; Computer Simulation ; Cyanobacteria/genetics/*physiology ; Hexoses/metabolism ; Selection, Genetic ; Symbiosis ; Synechococcus/cytology/metabolism ; }, abstract = {BACKGROUND: Genome degradation of host-restricted mutualistic endosymbionts has been attributed to inactivating mutations and genetic drift while genes coding for host-relevant functions are conserved by purifying selection. Unlike their free-living relatives, the metabolism of mutualistic endosymbionts and endosymbiont-originated organelles is specialized in the production of metabolites which are released to the host. This specialization suggests that natural selection crafted these metabolic adaptations. In this work, we analyzed the evolution of the metabolism of the chromatophore of Paulinella chromatophora by in silico modeling. We asked whether genome reduction is driven by metabolic engineering strategies resulted from the interaction with the host. As its widely known, the loss of enzyme coding genes leads to metabolic network restructuring sometimes improving the production rates. In this case, the production rate of reduced-carbon in the metabolism of the chromatophore.<br><br>RESULTS: We reconstructed the metabolic networks of the chromatophore of P. chromatophora CCAC 0185 and a close free-living relative, the cyanobacterium Synechococcus sp. WH 5701. We found that the evolution of free-living to host-restricted lifestyle rendered a fragile metabolic network where >80% of genes in the chromatophore are essential for metabolic functionality. Despite the lack of experimental information, the metabolic reconstruction of the chromatophore suggests that the host provides several metabolites to the endosymbiont. By using these metabolites as intracellular conditions, in silico simulations of genome evolution by gene lose recover with 77% accuracy the actual metabolic gene content of the chromatophore. Also, the metabolic model of the chromatophore allowed us to predict by flux balance analysis a maximum rate of reduced-carbon released by the endosymbiont to the host. By inspecting the central metabolism of the chromatophore and the free-living cyanobacteria we found that by improvements in the gluconeogenic pathway the metabolism of the endosymbiont uses more efficiently the carbon source for reduced-carbon production. In addition, our in silico simulations of the evolutionary process leading to the reduced metabolic network of the chromatophore showed that the predicted rate of released reduced-carbon is obtained in less than 5% of the times under a process guided by random gene deletion and genetic drift. We interpret previous findings as evidence that natural selection at holobiont level shaped the rate at which reduced-carbon is exported to the host. Finally, our model also predicts that the ABC phosphate transporter (pstSACB) which is conserved in the genome of the chromatophore of P. chromatophora strain CCAC 0185 is a necessary component to release reduced-carbon molecules to the host.<br><br>CONCLUSION: Our evolutionary analysis suggests that in the case of Paulinella chromatophora natural selection at the holobiont level played a prominent role in shaping the metabolic specialization of the chromatophore. We propose that natural selection acted as a &quot;metabolic engineer&quot; by favoring metabolic restructurings that led to an increased release of reduced-carbon to the host.}, }
@article {pmid28404738, year = {2017}, author = {Galla, S and Chakraborty, S and Mell, B and Vijay-Kumar, M and Joe, B}, title = {Microbiotal-Host Interactions and Hypertension.}, journal = {Physiology (Bethesda, Md.)}, volume = {32}, number = {3}, pages = {224-233}, doi = {10.1152/physiol.00003.2017}, pmid = {28404738}, issn = {1548-9221}, support = {R01 HL020176/HL/NHLBI NIH HHS/United States ; R37 HL020176/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Hypertension/*genetics/*microbiology ; *Metagenome ; Mice ; *Microbiota ; }, abstract = {Hypertension, or elevated blood pressure (BP), has been extensively researched over decades and clearly demonstrated to be caused due to a combination of host genetic and environmental factors. Although much research remains to be conducted to pin-point the precise genetic elements on the host genome that control BP, new lines of evidence are emerging to indicate that, besides the host genome, the genomes of all indigenous commensal micro-organisms, collectively referred to as the microbial metagenome or microbiome, are important, but largely understudied, determinants of BP. Unlike the rigid host genome, the microbiome or the &quot;second genome&quot; can be altered by diet or microbiotal transplantation in the host. This possibility is attractive from the perspective of exploiting the microbiotal composition for clinical management of inherited hypertension. Thus, focusing on the limited current literature supporting a role for the microbiome in BP regulation, this review highlights the need to further explore the role of the co-existence of host and the microbiota as an organized biological unit called the &quot;holobiont&quot; in the context of BP regulation.}, }
@article {pmid28366817, year = {2017}, author = {Forsman, ZH and Knapp, ISS and Tisthammer, K and Eaton, DAR and Belcaid, M and Toonen, RJ}, title = {Coral hybridization or phenotypic variation? Genomic data reveal gene flow between Porites lobata and P. Compressa.}, journal = {Molecular phylogenetics and evolution}, volume = {111}, number = {}, pages = {132-148}, doi = {10.1016/j.ympev.2017.03.023}, pmid = {28366817}, issn = {1095-9513}, mesh = {Animals ; Anthozoa/*genetics ; Gene Flow/*genetics ; Genome, Mitochondrial ; Genomics/*methods ; Geography ; Hawaii ; *Hybridization, Genetic ; Likelihood Functions ; Phenotype ; Phylogeny ; Polymorphism, Single Nucleotide/genetics ; Principal Component Analysis ; Sequence Alignment ; Species Specificity ; }, abstract = {Major gaps remain in our understanding of the ecology, evolution, biodiversity, biogeography, extinction risk, and adaptive potential of reef building corals. One of the central challenges remains that there are few informative genetic markers for studying boundaries between species, and variation within species. Reduced representation sequencing approaches, such as RADseq (Restriction site Associated DNA sequencing) have great potential for resolving such relationships. However, it is necessary to identify loci in order to make inferences for endosymbiotic organisms such as corals. Here, we examined twenty-one coral holobiont ezRAD libraries from Hawai'i, focusing on P. lobata and P. compressa, two species with contrasting morphology and habitat preference that previous studies have not resolved. We used a combination of de novo assembly and reference mapping approaches to identify and compare loci: we used reference mapping to extract and compare nearly complete mitochondrial genomes, ribosomal arrays, and histone genes. We used de novo clustering and phylogenomic methods to compare the complete holobiont data set with coral and symbiont subsets that map to transcriptomic data. In addition, we used reference assemblies to examine genetic structure from SNPs (Single Nucleotide Polymorphisms). All approaches resolved outgroup taxa but failed to resolve P. lobata and P. compressa as distinct, with mito-nuclear discordance and shared mitochondrial haplotypes within the species complex. The holobiont and 'coral transcriptomic' datasets were highly concordant, revealing stronger genetic structure between sites than between coral morphospecies. These results suggest that either branching morphology is a polymorphic trait, or that these species frequently hybridize. This study provides examples of several approaches to acquire, identify, and compare loci across metagenomic samples such as the coral holobiont while providing insights into the nature of coral variability.}, }
@article {pmid28326066, year = {2017}, author = {Peixoto, RS and Rosado, PM and Leite, DC and Rosado, AS and Bourne, DG}, title = {Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {341}, pmid = {28326066}, issn = {1664-302X}, abstract = {The symbiotic association between the coral animal and its endosymbiotic dinoflagellate partner Symbiodinium is central to the success of corals. However, an array of other microorganisms associated with coral (i.e., Bacteria, Archaea, Fungi, and viruses) have a complex and intricate role in maintaining homeostasis between corals and Symbiodinium. Corals are sensitive to shifts in the surrounding environmental conditions. One of the most widely reported responses of coral to stressful environmental conditions is bleaching. During this event, corals expel Symbiodinium cells from their gastrodermal tissues upon experiencing extended seawater temperatures above their thermal threshold. An array of other environmental stressors can also destabilize the coral microbiome, resulting in compromised health of the host, which may include disease and mortality in the worst scenario. However, the exact mechanisms by which the coral microbiome supports coral health and increases resilience are poorly understood. Earlier studies of coral microbiology proposed a coral probiotic hypothesis, wherein a dynamic relationship exists between corals and their symbiotic microorganisms, selecting for the coral holobiont that is best suited for the prevailing environmental conditions. Here, we discuss the microbial-host relationships within the coral holobiont, along with their potential roles in maintaining coral health. We propose the term BMC (Beneficial Microorganisms for Corals) to define (specific) symbionts that promote coral health. This term and concept are analogous to the term Plant Growth Promoting Rhizosphere (PGPR), which has been widely explored and manipulated in the agricultural industry for microorganisms that inhabit the rhizosphere and directly or indirectly promote plant growth and development through the production of regulatory signals, antibiotics and nutrients. Additionally, we propose and discuss the potential mechanisms of the effects of BMC on corals, suggesting strategies for the use of this knowledge to manipulate the microbiome, reversing dysbiosis to restore and protect coral reefs. This may include developing and using BMC consortia as environmental &quot;probiotics&quot; to improve coral resistance after bleaching events and/or the use of BMC with other strategies such as human-assisted acclimation/adaption to shifting environmental conditions.}, }
@article {pmid28302492, year = {2017}, author = {O'Malley, MA}, title = {From endosymbiosis to holobionts: Evaluating a conceptual legacy.}, journal = {Journal of theoretical biology}, volume = {434}, number = {}, pages = {34-41}, doi = {10.1016/j.jtbi.2017.03.008}, pmid = {28302492}, issn = {1095-8541}, mesh = {*Biological Evolution ; *Microbiota ; Research ; *Symbiosis ; Terminology as Topic ; }, abstract = {In her influential 1967 paper, Lynn Margulis synthesized a range of data to support the idea of endosymbiosis. Building on the success of this work, she applied the same methodology to promote the role of symbiosis more generally in evolution. As part of this broader project, she coined the term 'holobiont' to refer to a unified entity of symbiont and host. This concept is now applied with great gusto in microbiome research, and often implies not just a physiological unit but also various senses of an evolving system. My analysis will track how Margulis came to propose the term, its current use in microbiome research, and how those applications link back to Margulis. I then evaluate what contemporary use says about Margulis's legacy for microbiome research.}, }
@article {pmid28296889, year = {2017}, author = {Cowart, DA and Durand, L and Cambon-Bonavita, MA and Arnaud-Haond, S}, title = {Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering.}, journal = {PloS one}, volume = {12}, number = {3}, pages = {e0172543}, pmid = {28296889}, issn = {1932-6203}, mesh = {Animals ; Crustacea/*microbiology ; Gastrointestinal Tract/*microbiology ; *Geography ; }, abstract = {Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.}, }
@article {pmid28295957, year = {2017}, author = {Partida-Martínez, LP}, title = {The fungal holobiont: Evidence from early diverging fungi.}, journal = {Environmental microbiology}, volume = {19}, number = {8}, pages = {2919-2923}, doi = {10.1111/1462-2920.13731}, pmid = {28295957}, issn = {1462-2920}, mesh = {*Fungi ; *Phylogeny ; }, }
@article {pmid28290203, year = {2017}, author = {Eymann, C and Lassek, C and Wegner, U and Bernhardt, J and Fritsch, OA and Fuchs, S and Otto, A and Albrecht, D and Schiefelbein, U and Cernava, T and Aschenbrenner, I and Berg, G and Grube, M and Riedel, K}, title = {Symbiotic Interplay of Fungi, Algae, and Bacteria within the Lung Lichen Lobaria pulmonaria L. Hoffm. as Assessed by State-of-the-Art Metaproteomics.}, journal = {Journal of proteome research}, volume = {16}, number = {6}, pages = {2160-2173}, doi = {10.1021/acs.jproteome.6b00974}, pmid = {28290203}, issn = {1535-3907}, mesh = {*Ascomycota ; Biodiversity ; *Chlorophyta ; *Cyanobacteria ; *Lichens ; Metabolomics ; Microbial Interactions ; Proteomics ; Pulmonaria ; *Symbiosis ; }, abstract = {Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed the structure and functionality of the entire lung lichen Lobaria pulmonaria L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to the green algae and the ascomycetous fungus, a lichenicolous fungus as well as a complex prokaryotic community (different from the cyanobacteria) was found, the latter dominated by methanotrophic Rhizobiales. Various partner-specific proteins could be assigned to the different lichen symbionts, for example, fungal proteins involved in vesicle transport, algal proteins functioning in photosynthesis, cyanobacterial nitrogenase and GOGAT involved in nitrogen fixation, and bacterial enzymes responsible for methanol/C1-compound metabolism as well as CO-detoxification. Structural and functional information on proteins expressed by the lichen community complemented and extended our recent symbiosis model depicting the functional multiplayer network of single holobiont partners.1 Our new metaproteome analysis strongly supports the hypothesis (i) that interactions within the self-supporting association are multifaceted and (ii) that the strategy of functional diversification within the single lichen partners may support the longevity of L. pulmonaria under certain ecological conditions.}, }
@article {pmid28245221, year = {2017}, author = {Richardson, LA}, title = {Evolving as a holobiont.}, journal = {PLoS biology}, volume = {15}, number = {2}, pages = {e2002168}, pmid = {28245221}, issn = {1545-7885}, mesh = {Animals ; Biological Evolution ; Evolution, Molecular ; Humans ; Microbiota/*physiology ; Phylogeny ; Symbiosis/physiology ; }, }
@article {pmid28233813, year = {2017}, author = {Weigel, BL and Erwin, PM}, title = {Effects of reciprocal transplantation on the microbiome and putative nitrogen cycling functions of the intertidal sponge, Hymeniacidon heliophila.}, journal = {Scientific reports}, volume = {7}, number = {}, pages = {43247}, pmid = {28233813}, issn = {2045-2322}, mesh = {Animals ; Biodiversity ; *Microbiota ; *Nitrogen Cycle ; Porifera/*metabolism/*microbiology ; Symbiosis ; }, abstract = {Microbial symbionts in sponges are ubiquitous, forming complex and highly diverse host-specific communities. Conspecific sponges display remarkable stability in their symbiont communities, both spatially and temporally, yet extreme fluctuations in environmental factors can cause shifts in host-symbiont associations. We previously demonstrated that the marine sponge Hymeniacidon heliophila displayed significant community-level differences in microbial symbiont diversity, structure and composition when sampled from intertidal and subtidal environments. Here, we conducted a 70-day reciprocal transplant experiment to directly test the effect of tidal exposure on the microbiome of H. heliophila, using next-generation Illumina sequencing of 16S rRNA gene sequences to characterize symbiont communities. While sponges transplanted between habitats displayed shifts in microbial communities after 70 days, temporal variation was the dominant factor affecting microbial community composition. Further, we identified core symbionts that persisted across these spatio-temporal scales and used a metagenomic approach to show that these dominant members of the microbiome of H. heliophila represent nitrogen cycling taxa that have the potential to contribute to a diverse array of nitrogen transformations in the sponge holobiont. Together, these results indicate that despite moderate spatio-temporal shifts in symbiont composition, core symbiont functions (e.g. nitrogen cycling) can be maintained in sponge microbiomes through functional redundancy.}, }
@article {pmid28223979, year = {2017}, author = {Leite, DC and Leão, P and Garrido, AG and Lins, U and Santos, HF and Pires, DO and Castro, CB and van Elsas, JD and Zilberberg, C and Rosado, AS and Peixoto, RS}, title = {Broadcast Spawning Coral Mussismilia hispida Can Vertically Transfer its Associated Bacterial Core.}, journal = {Frontiers in microbiology}, volume = {8}, number = {}, pages = {176}, pmid = {28223979}, issn = {1664-302X}, abstract = {The hologenome theory of evolution (HTE), which is under fierce debate, presupposes that parts of the microbiome are transmitted from one generation to the next [vertical transmission (VT)], which may also influence the evolution of the holobiont. Even though bacteria have previously been described in early life stages of corals, these early life stages (larvae) could have been inoculated in the water and not inside the parental colony (through gametes) carrying the parental microbiome. How Symbiodinium is transmitted to offspring is also not clear, as only one study has described this mechanism in spawners. All other studies refer to incubators. To explore the VT hypothesis and the key components being transferred, colonies of the broadcast spawner species Mussismilia hispida were kept in nurseries until spawning. Gamete bundles, larvae and adult corals were analyzed to identify their associated microbiota with respect to composition and location. Symbiodinium and bacteria were detected by sequencing in gametes and coral planula larvae. However, no cells were detected using microscopy at the gamete stage, which could be related to the absence of those cells inside the oocytes/dispersed in the mucus or to a low resolution of our approach. A preliminary survey of Symbiodinium diversity indicated that parental colonies harbored Symbiodinium clades B, C and G, whereas only clade B was found in oocytes and planula larvae [5 days after fertilization (a.f.)]. The core bacterial populations found in the bundles, planula larvae and parental colonies were identified as members of the genera Burkholderia, Pseudomonas, Acinetobacter, Ralstonia, Inquilinus and Bacillus, suggesting that these populations could be vertically transferred through the mucus. The collective data suggest that spawner corals, such as M. hispida, can transmit Symbiodinium cells and the bacterial core to their offspring by a coral gamete (and that this gamete, with its bacterial load, is released into the water), supporting the HTE. However, more data are required to indicate the stability of the transmitted populations to indicate whether the holobiont can be considered a unit of natural selection or a symbiotic assemblage of independently evolving organisms.}, }
@article {pmid28152002, year = {2017}, author = {Goulet, TL and Shirur, KP and Ramsby, BD and Iglesias-Prieto, R}, title = {The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp.}, journal = {PloS one}, volume = {12}, number = {2}, pages = {e0171032}, pmid = {28152002}, issn = {1932-6203}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/chemistry/*physiology ; Caribbean Region ; Chlorophyll/analysis/metabolism ; Chlorophyll A ; Dinoflagellida/genetics/*physiology ; Enzymes/metabolism ; Genotype ; Mexico ; Seawater ; Symbiosis/physiology ; Temperature ; }, abstract = {Global climate change not only leads to elevated seawater temperatures but also to episodic anomalously high or low temperatures lasting for several hours to days. Scleractinian corals are detrimentally affected by thermal fluctuations, which often lead to an uncoupling of their mutualism with Symbiodinium spp. (coral bleaching) and potentially coral death. Consequently, on many Caribbean reefs scleractinian coral cover has plummeted. Conversely, gorgonian corals persist, with their abundance even increasing. How gorgonians react to thermal anomalies has been investigated utilizing limited parameters of either the gorgonian, Symbiodinium or the combined symbiosis (holobiont). We employed a holistic approach to examine the effect of an experimental five-day elevated temperature episode on parameters of the host, symbiont, and the holobiont in Eunicea tourneforti, E. flexuosa and Pseudoplexaura porosa. These gorgonian corals reacted and coped with 32°C seawater temperatures. Neither Symbiodinium genotypes nor densities differed between the ambient 29.5°C and 32°C. Chlorophyll a and c2 per Symbiodinium cell, however, were lower at 32°C leading to a reduction in chlorophyll content in the branches and an associated reduction in estimated absorbance and increase in the chlorophyll a specific absorption coefficient. The adjustments in the photochemical parameters led to changes in photochemical efficiencies, although these too showed that the gorgonians were coping. For example, the maximum excitation pressure, Qm, was significantly lower at 32°C than at 29.5°C. In addition, although per dry weight the amount of protein and lipids were lower at 32°C, the overall energy content in the tissues did not differ between the temperatures. Antioxidant activity either remained the same or increased following exposure to 32°C further reiterating a response that dealt with the stressor. Taken together, the capability of Caribbean gorgonian corals to modify symbiont, host and consequently holobiont parameters may partially explain their persistence on reefs faced with climate change.}, }
@article {pmid28133884, year = {2017}, author = {Arnaud-Haond, S and Aires, T and Candeias, R and Teixeira, SJL and Duarte, CM and Valero, M and Serrão, EA}, title = {Entangled fates of holobiont genomes during invasion: nested bacterial and host diversities in Caulerpa taxifolia.}, journal = {Molecular ecology}, volume = {26}, number = {8}, pages = {2379-2391}, doi = {10.1111/mec.14030}, pmid = {28133884}, issn = {1365-294X}, mesh = {Bacteria/classification ; Caulerpa/*genetics/*microbiology ; DNA, Bacterial/genetics ; *Genetic Variation ; Genetics, Population ; Genotype ; *Introduced Species ; Mediterranean Sea ; *Microbiota ; Microsatellite Repeats ; RNA, Ribosomal, 16S/genetics ; South Australia ; *Symbiosis ; }, abstract = {Successful prevention and mitigation of biological invasions requires retracing the initial steps of introduction, as well as understanding key elements enhancing the adaptability of invasive species. We studied the genetic diversity of the green alga Caulerpa taxifolia and its associated bacterial communities in several areas around the world. The striking congruence of α and β diversity of the algal genome and endophytic communities reveals a tight association, supporting the holobiont concept as best describing the unit of spreading and invasion. Both genomic compartments support the hypotheses of a unique accidental introduction in the Mediterranean and of multiple invasion events in southern Australia. In addition to helping with tracing the origin of invasion, bacterial communities exhibit metabolic functions that can potentially enhance adaptability and competitiveness of the consortium they form with their host. We thus hypothesize that low genetic diversities of both host and symbiont communities may contribute to the recent regression in the Mediterranean, in contrast with the persistence of highly diverse assemblages in southern Australia. This study supports the importance of scaling up from the host to the holobiont for a comprehensive understanding of invasions.}, }
@article {pmid28119709, year = {2016}, author = {Rotini, A and Mejia, AY and Costa, R and Migliore, L and Winters, G}, title = {Ecophysiological Plasticity and Bacteriome Shift in the Seagrass Halophila stipulacea along a Depth Gradient in the Northern Red Sea.}, journal = {Frontiers in plant science}, volume = {7}, number = {}, pages = {2015}, pmid = {28119709}, issn = {1664-462X}, abstract = {Halophila stipulacea is a small tropical seagrass species. It is the dominant seagrass species in the Gulf of Aqaba (GoA; northern Red Sea), where it grows in both shallow and deep environments (1-50 m depth). Native to the Red Sea, Persian Gulf, and Indian Ocean, this species has invaded the Mediterranean and has recently established itself in the Caribbean Sea. Due to its invasive nature, there is growing interest to understand this species' capacity to adapt to new conditions, which might be attributed to its ability to thrive in a broad range of ecological niches. In this study, a multidisciplinary approach was used to depict variations in morphology, biochemistry (pigment and phenol content) and epiphytic bacterial communities along a depth gradient (4-28 m) in the GoA. Along this gradient, H. stipulacea increased leaf area and pigment contents (Chlorophyll a and b, total Carotenoids), while total phenol contents were mostly uniform. H. stipulacea displayed a well conserved core bacteriome, as assessed by 454-pyrosequencing of 16S rRNA gene reads amplified from metagenomic DNA. The core bacteriome aboveground (leaves) and belowground (roots and rhizomes), was composed of more than 100 Operational Taxonomic Units (OTUs) representing 63 and 52% of the total community in each plant compartment, respectively, with a high incidence of the classes Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria across all depths. Above and belowground communities were different and showed higher within-depth variability at the intermediate depths (9 and 18 m) than at the edges. Plant parts showed a clear influence in shaping the communities while depth showed a greater influence on the belowground communities. Overall, results highlighted a different ecological status of H. stipulacea at the edges of the gradient (4-28 m), where plants showed not only marked differences in morphology and biochemistry, but also the most distinct associated bacterial consortium. We demonstrated the pivotal role of morphology, biochemistry (pigment and phenol content), and epiphytic bacterial communities in helping plants to cope with environmental and ecological variations. The plant/holobiont capability to persist and adapt to environmental changes probably has an important role in its ecological resilience and invasiveness.}, }
@article {pmid28115399, year = {2017}, author = {Esteves, AI and Cullen, A and Thomas, T}, title = {Competitive interactions between sponge-associated bacteria.}, journal = {FEMS microbiology ecology}, volume = {93}, number = {3}, pages = {}, doi = {10.1093/femsec/fix008}, pmid = {28115399}, issn = {1574-6941}, mesh = {Animals ; Bacillus/genetics ; Bacteria/genetics/*metabolism ; Biotechnology ; Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics/physiology ; }, abstract = {The diversity of the microbial communities associated with marine sponges has been extensively studied, but their functioning and interactions within the sponge holobiont are only recently being appreciated. Sponge-associated microorganisms are known for the production of a range of inhibitory metabolites with biotechnological application, but the ecological role that these compounds remains elusive. In this work, we explore the competitive interactions between cultivated sponge-associated bacteria to inspect whether bacteria that produce antimicrobial activities are able to inhibit potentially pathogenic bacteria. We isolated a Bacillus sp. bacterium with sponge-degrading activity, which likely has a negative impact on the host. This bacterium, along with other sponge isolates from the same genus, was found to be inhibited by a subpopulation of closely related sponge-derived Pseudovibrio spp. In some Pseudovibrio strains, these inhibitory activities were correlated with the genetic capacity to produce polyketides, such as erythronolide. Our observations suggest that antagonistic activities likely influence the composition of the sponge microbiome, including the abundance of bacteria that can be harmful to the host.}, }
@article {pmid28103686, year = {2017}, author = {Alcolombri, U and Lei, L and Meltzer, D and Vardi, A and Tawfik, DS}, title = {Assigning the Algal Source of Dimethylsulfide Using a Selective Lyase Inhibitor.}, journal = {ACS chemical biology}, volume = {12}, number = {1}, pages = {41-46}, doi = {10.1021/acschembio.6b00844}, pmid = {28103686}, issn = {1554-8937}, mesh = {Animals ; Anthozoa/drug effects/enzymology/*metabolism ; Bacteria/drug effects/enzymology/metabolism ; Carbon-Sulfur Lyases/antagonists &amp; inhibitors/metabolism ; Enzyme Inhibitors/metabolism ; Haptophyta/drug effects/enzymology/*metabolism ; Oceans and Seas ; Sulfides/*metabolism ; }, abstract = {Atmospheric dimethylsulfide (DMS) is massively produced in the oceans by bacteria, algae, and corals. To enable identification of DMS sources, we developed a potent mechanism-based inhibitor of the algal Alma dimethylsulfoniopropionate lyase family that does not inhibit known bacterial lyases. Its application to coral holobiont indicates that DMS originates from Alma lyase(s). This biochemical profiling may complement meta-genomics and transcriptomics to provide better understanding of the marine sulfur cycle.}, }
@article {pmid28097070, year = {2017}, author = {Fiore, CL and Freeman, CJ and Kujawinski, EB}, title = {Sponge exhalent seawater contains a unique chemical profile of dissolved organic matter.}, journal = {PeerJ}, volume = {5}, number = {}, pages = {e2870}, pmid = {28097070}, issn = {2167-8359}, abstract = {Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater). Samples were collected from two sponge species, Ircinia campana and Spheciospongia vesparium, on a near-shore hard bottom reef in the Florida Keys. Metabolic profiles generated from untargeted metabolomics analysis indicated that many more compounds were enhanced in the exhalent samples than in the inhalant samples. Targeted metabolomics analysis revealed differences in diversity and concentration of metabolites between exhalent and off reef seawater. For example, most of the nucleosides were enriched in the exhalent seawater, while the aromatic amino acids, caffeine and the nucleoside xanthosine were elevated in the off reef water samples. Although the metabolic profile of the exhalent seawater was unique, the impact of sponge metabolism on the overall reef DOM profile was spatially limited in our study. There were also no significant differences in the metabolic profiles of exhalent water between the two sponge species, potentially indicating that there is a characteristic DOM profile in the exhalent seawater of Caribbean sponges. Additional work is needed to determine whether the impact of sponge DOM is greater in habitats with higher sponge cover and diversity. This work provides the first insight into the molecular-level impact of sponge holobiont metabolism on reef DOM and establishes a foundation for future experimental studies addressing the influence of sponge-derived DOM on chemical and ecological processes in coral reef ecosystems.}, }
@article {pmid28088765, year = {2017}, author = {Karlin, EF and Smouse, PE}, title = {Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.}, journal = {Annals of botany}, volume = {120}, number = {2}, pages = {221-231}, pmid = {28088765}, issn = {1095-8290}, mesh = {Alleles ; Argentina ; Australia ; *Biological Evolution ; Chile ; Genetic Variation ; Genome, Plant ; *Hybridization, Genetic ; Microsatellite Repeats ; New Zealand ; Sphagnopsida/*genetics ; Tasmania ; *Triploidy ; }, abstract = {Background and Aims: Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations.<br><br>Methods: Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures.<br><br>Key Results: The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information.<br><br>Conclusions: Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation, rather than by subsequent evolutionary radiation. However, some post-hybridization genetic diversification has become fixed in at least one regional population. Methodology allowing statistical analysis of any ploidy level is presented.}, }
@article {pmid28066403, year = {2016}, author = {Pita, L and Fraune, S and Hentschel, U}, title = {Emerging Sponge Models of Animal-Microbe Symbioses.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {2102}, pmid = {28066403}, issn = {1664-302X}, abstract = {Sponges have a significant impact on marine benthic communities, they are of biotechnological interest owing to their production of bioactive natural compounds, and they promise to provide insights into conserved mechanisms of host-microbe interactions in basal metazoans. The natural variability of sponge-microbe associations across species and environments provides a meaningful ecological and evolutionary framework to investigate animal-microbial symbiosis through experimentation in the field and also in aquaria. In addition, next-generation sequencing technologies have shed light on the genomic repertoire of the sponge host and revealed metabolic capacities and symbiotic lifestyle features of their microbiota. However, our understanding of symbiotic mechanisms is still in its infancy. Here, we discuss the potential and limitations of the sponge-microbe symbiosis as emerging models for animal-associated microbiota.}, }
@article {pmid28050778, year = {2017}, author = {Miller, WB and Torday, JS}, title = {A systematic approach to cancer: evolution beyond selection.}, journal = {Clinical and translational medicine}, volume = {6}, number = {1}, pages = {2}, pmid = {28050778}, issn = {2001-1326}, abstract = {Cancer is typically scrutinized as a pathological process characterized by chromosomal aberrations and clonal expansion subject to stochastic Darwinian selection within adaptive cellular ecosystems. Cognition based evolution is suggested as an alternative approach to cancer development and progression in which neoplastic cells of differing karyotypes and cellular lineages are assessed as self-referential agencies with purposive participation within tissue microenvironments. As distinct self-aware entities, neoplastic cells occupy unique participant/observer status within tissue ecologies. In consequence, neoplastic proliferation by clonal lineages is enhanced by the advantaged utilization of ecological resources through flexible re-connection with progenitor evolutionary stages.}, }
@article {pmid28003808, year = {2016}, author = {Gopal, M and Gupta, A}, title = {Microbiome Selection Could Spur Next-Generation Plant Breeding Strategies.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1971}, pmid = {28003808}, issn = {1664-302X}, abstract = {&quot;No plant is an island too…&quot; Plants, though sessile, have developed a unique strategy to counter biotic and abiotic stresses by symbiotically co-evolving with microorganisms and tapping into their genome for this purpose. Soil is the bank of microbial diversity from which a plant selectively sources its microbiome to suit its needs. Besides soil, seeds, which carry the genetic blueprint of plants during trans-generational propagation, are home to diverse microbiota that acts as the principal source of microbial inoculum in crop cultivation. Overall, a plant is ensconced both on the outside and inside with a diverse assemblage of microbiota. Together, the plant genome and the genes of the microbiota that the plant harbors in different plant tissues, i.e., the 'plant microbiome,' form the holobiome which is now considered as unit of selection: 'the holobiont.' The 'plant microbiome' not only helps plants to remain fit but also offers critical genetic variability, hitherto, not employed in the breeding strategy by plant breeders, who traditionally have exploited the genetic variability of the host for developing high yielding or disease tolerant or drought resistant varieties. This fresh knowledge of the microbiome, particularly of the rhizosphere, offering genetic variability to plants, opens up new horizons for breeding that could usher in cultivation of next-generation crops depending less on inorganic inputs, resistant to insect pest and diseases and resilient to climatic perturbations. We surmise, from ever increasing evidences, that plants and their microbial symbionts need to be co-propagated as life-long partners in future strategies for plant breeding. In this perspective, we propose bottom-up approach to co-propagate the co-evolved, the plant along with the target microbiome, through - (i) reciprocal soil transplantation method, or (ii) artificial ecosystem selection method of synthetic microbiome inocula, or (iii) by exploration of microRNA transfer method - for realizing this next-generation plant breeding approach. Our aim, thus, is to bring closer the information accrued through the advanced nucleotide sequencing and bioinformatics in conjunction with conventional culture-dependent isolation method for practical application in plant breeding and overall agriculture.}, }
@article {pmid27995440, year = {2017}, author = {Catania, F and Krohs, U and Chittò, M and Ferro, D and Ferro, K and Lepennetier, G and Görtz, HD and Schreiber, RS and Kurtz, J and Gadau, J}, title = {The hologenome concept: we need to incorporate function.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {136}, number = {3-4}, pages = {89-98}, pmid = {27995440}, issn = {1611-7530}, mesh = {*Adaptation, Biological ; Animals ; Anthozoa ; *Biological Evolution ; Biology/*methods ; Drosophila ; Ecology/*methods ; Fungi ; Humans ; Paramecium ; Phenotype ; Plants ; Rickettsia ; Symbiosis ; }, abstract = {Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called 'typical' organisms no longer organisms in their own right? Is the study of the holobiont-host plus its symbiotic microorganisms-no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host's environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.}, }
@article {pmid27980125, year = {2017}, author = {Hawkins, TD and Warner, ME}, title = {Warm preconditioning protects against acute heat-induced respiratory dysfunction and delays bleaching in a symbiotic sea anemone.}, journal = {The Journal of experimental biology}, volume = {220}, number = {Pt 6}, pages = {969-983}, doi = {10.1242/jeb.150391}, pmid = {27980125}, issn = {1477-9145}, mesh = {*Acclimatization ; Animals ; Dinoflagellida/enzymology/*physiology ; Heat-Shock Response ; Hot Temperature ; Mitochondria/enzymology/metabolism ; Oxygen Consumption ; Photosynthesis ; Sea Anemones/enzymology/*physiology ; *Symbiosis ; }, abstract = {Preconditioning to non-stressful warming can protect some symbiotic cnidarians against the high temperature-induced collapse of their mutualistic endosymbiosis with photosynthetic dinoflagellates (Symbiodinium spp.), a process known as bleaching. Here, we sought to determine whether such preconditioning is underpinned by differential regulation of aerobic respiration. We quantified in vivo metabolism and mitochondrial respiratory enzyme activity in the naturally symbiotic sea anemone Exaiptasia pallida preconditioned to 30°C for >7 weeks as well as anemones kept at 26°C. Preconditioning resulted in increased Symbiodinium photosynthetic activity and holobiont (host+symbiont) respiration rates. Biomass-normalised activities of host respiratory enzymes [citrate synthase and the mitochondrial electron transport chain (mETC) complexes I and IV] were higher in preconditioned animals, suggesting that increased holobiont respiration may have been due to host mitochondrial biogenesis and/or enlargement. Subsequent acute heating of preconditioned and 'thermally naive' animals to 33°C induced dramatic increases in host mETC complex I and Symbiodinium mETC complex II activities only in thermally naive E. pallida These changes were not reflected in the activities of other respiratory enzymes. Furthermore, bleaching in preconditioned E. pallida (defined as the significant loss of symbionts) was delayed by several days relative to the thermally naive group. These findings suggest that changes to mitochondrial biogenesis and/or function in symbiotic cnidarians during warm preconditioning might play a protective role during periods of exposure to stressful heating.}, }
@article {pmid27958345, year = {2016}, author = {Pineda, MC and Strehlow, B and Duckworth, A and Doyle, J and Jones, R and Webster, NS}, title = {Effects of light attenuation on the sponge holobiont- implications for dredging management.}, journal = {Scientific reports}, volume = {6}, number = {}, pages = {39038}, pmid = {27958345}, issn = {2045-2322}, mesh = {Animals ; Biota/*physiology ; *Light ; Porifera/*physiology ; Symbiosis/*physiology ; }, abstract = {Dredging and natural sediment resuspension events can cause high levels of turbidity, reducing the amount of light available for photosynthetic benthic biota. To determine how marine sponges respond to light attenuation, five species were experimentally exposed to a range of light treatments. Tolerance thresholds and capacity for recovery varied markedly amongst species. Whilst light attenuation had no effect on the heterotrophic species Stylissa flabelliformis and Ianthella basta, the phototrophic species Cliona orientalis and Carteriospongia foliascens discoloured (bleached) over a 28 day exposure period to very low light (<0.8 mol photons m-2 d-1). In darkness, both species discoloured within a few days, concomitant with reduced fluorescence yields, chlorophyll concentrations and shifts in their associated microbiomes. The phototrophic species Cymbastela coralliophila was less impacted by light reduction. C. orientalis and C. coralliophila exhibited full recovery under normal light conditions, whilst C. foliascens did not recover and showed high levels of mortality. The light treatments used in the study are directly relevant to conditions that can occur in situ during dredging projects, indicating that light attenuation poses a risk to photosynthetic marine sponges. Examining benthic light levels over temporal scales would enable dredging proponents to be aware of conditions that could impact on sponge physiology.}, }
@article {pmid27924868, year = {2016}, author = {Diaz, JM and Hansel, CM and Apprill, A and Brighi, C and Zhang, T and Weber, L and McNally, S and Xun, L}, title = {Species-specific control of external superoxide levels by the coral holobiont during a natural bleaching event.}, journal = {Nature communications}, volume = {7}, number = {}, pages = {13801}, pmid = {27924868}, issn = {2041-1723}, mesh = {Animals ; Anthozoa/*metabolism/microbiology ; Circadian Rhythm ; Dinoflagellida/*metabolism ; Larva/physiology ; Microbiota ; *Pigmentation ; Species Specificity ; Superoxides/*metabolism ; *Symbiosis ; }, abstract = {The reactive oxygen species superoxide (O2·-) is both beneficial and detrimental to life. Within corals, superoxide may contribute to pathogen resistance but also bleaching, the loss of essential algal symbionts. Yet, the role of superoxide in coral health and physiology is not completely understood owing to a lack of direct in situ observations. By conducting field measurements of superoxide produced by corals during a bleaching event, we show substantial species-specific variation in external superoxide levels, which reflect the balance of production and degradation processes. Extracellular superoxide concentrations are independent of light, algal symbiont abundance and bleaching status, but depend on coral species and bacterial community composition. Furthermore, coral-derived superoxide concentrations ranged from levels below bulk seawater up to ∼120 nM, some of the highest superoxide concentrations observed in marine systems. Overall, these results unveil the ability of corals and/or their microbiomes to regulate superoxide in their immediate surroundings, which suggests species-specific roles of superoxide in coral health and physiology.}, }
@article {pmid27920768, year = {2016}, author = {Zhang, Y and Yang, Q and Ling, J and Van Nostrand, JD and Shi, Z and Zhou, J and Dong, J}, title = {The Shifts of Diazotrophic Communities in Spring and Summer Associated with Coral Galaxea astreata, Pavona decussata, and Porites lutea.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1870}, pmid = {27920768}, issn = {1664-302X}, abstract = {The coral holobiont often resides in oligotrophic waters; both coral cells and their symbiotic dinoflagellates possess ammonium assimilation enzymes and potentially benefit from the nitrogen fixation of coral-associated diazotrophs. However, the seasonal dynamics of coral-associated diazotrophs are not well characterized. Here, the seasonal variations of diazotrophic communities associated with three corals, Galaxea astreata, Pavona decussata, and Porites lutea, were studied using nifH gene amplicon pyrosequencing techniques. Our results revealed a great diversity of coral-associated diazotrophs. nifH sequences related to Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria were ubiquitous and dominant in all corals in two seasons. In contrast with the coral P. decussata, both G. astreata and P. lutea showed significant seasonal changes in the diazotrophic communities and nifH gene abundance. Variable diazotroph groups accounted for a range from 11 to 49% within individual coral samples. Most of the variable diazotrophic groups from P. decussata were species-specific, however, the majority of overlapping variable groups in G. astreata and P. lutea showed the same seasonal variation characteristics. Rhodopseudomonas palustris- and Gluconacetobacter diazotrophicus-affiliated sequences were relatively abundant in the summer, whereas a nifH sequence related to Halorhodospira halophila was relatively abundant in spring G. astreata and P. lutea. The seasonal variations of all diazotrophic communities were significantly correlated with the seasonal shifts of ammonium and nitrate, suggesting that diazotrophs play an important role in the nitrogen cycle of the coral holobiont.}, }
@article {pmid27919551, year = {2017}, author = {Hernandez-Agreda, A and Gates, RD and Ainsworth, TD}, title = {Defining the Core Microbiome in Corals' Microbial Soup.}, journal = {Trends in microbiology}, volume = {25}, number = {2}, pages = {125-140}, doi = {10.1016/j.tim.2016.11.003}, pmid = {27919551}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*microbiology/*parasitology ; Bacteria/*isolation &amp; purification ; *Coral Reefs ; Dinoflagellida/*isolation &amp; purification ; Dysbiosis/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis/physiology ; }, abstract = {Corals are considered one of the most complex microbial biospheres studied to date, hosting thousands of bacterial phylotypes in species-specific associations. There are, however, substantial knowledge gaps and challenges in understanding the functional significance of bacterial communities and bacterial symbioses of corals. The ubiquitous nature of some bacterial interactions has only recently been investigated and an accurate differentiation between the healthy (symbiotic) and unhealthy (dysbiotic) microbial state has not yet been determined. Here we review the complexity of the coral holobiont, coral microbiome diversity, and recently proposed bacterial symbioses of corals. We provide insight into coupling the core microbiome framework with community ecology principals, and draw on the theoretical insights from other complex systems, to build a framework to aid in deciphering ecologically significant microbes within a corals' microbial soup.}, }
@article {pmid27908589, year = {2017}, author = {Shapira, M}, title = {Adaptation from Within or from Without: A Reply to Rodrigo et al.}, journal = {Trends in ecology &amp; evolution}, volume = {32}, number = {2}, pages = {85}, doi = {10.1016/j.tree.2016.11.003}, pmid = {27908589}, issn = {1872-8383}, mesh = {*Adaptation, Physiological ; Humans ; *Symbiosis ; }, }
@article {pmid27907979, year = {2017}, author = {Webster, NS}, title = {Conceptual and methodological advances for holobiont research.}, journal = {Environmental microbiology reports}, volume = {9}, number = {1}, pages = {30-32}, doi = {10.1111/1758-2229.12500}, pmid = {27907979}, issn = {1758-2229}, mesh = {Animals ; Aquatic Organisms/*microbiology/physiology ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Physiological Phenomena ; Biodiversity ; Seawater/*microbiology ; *Symbiosis ; }, }
@article {pmid27877161, year = {2016}, author = {Horn, H and Slaby, BM and Jahn, MT and Bayer, K and Moitinho-Silva, L and Förster, F and Abdelmohsen, UR and Hentschel, U}, title = {An Enrichment of CRISPR and Other Defense-Related Features in Marine Sponge-Associated Microbial Metagenomes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1751}, pmid = {27877161}, issn = {1664-302X}, abstract = {Many marine sponges are populated by dense and taxonomically diverse microbial consortia. We employed a metagenomics approach to unravel the differences in the functional gene repertoire among three Mediterranean sponge species, Petrosia ficiformis, Sarcotragus foetidus, Aplysina aerophoba and seawater. Different signatures were observed between sponge and seawater metagenomes with regard to microbial community composition, GC content, and estimated bacterial genome size. Our analysis showed further a pronounced repertoire for defense systems in sponge metagenomes. Specifically, clustered regularly interspaced short palindromic repeats, restriction modification, DNA phosphorothioation and phage growth limitation systems were enriched in sponge metagenomes. These data suggest that defense is an important functional trait for an existence within sponges that requires mechanisms to defend against foreign DNA from microorganisms and viruses. This study contributes to an understanding of the evolutionary arms race between viruses/phages and bacterial genomes and it sheds light on the bacterial defenses that have evolved in the context of the sponge holobiont.}, }
@article {pmid27858116, year = {2017}, author = {Lee, HU and McPherson, ZE and Tan, B and Korecka, A and Pettersson, S}, title = {Host-microbiome interactions: the aryl hydrocarbon receptor and the central nervous system.}, journal = {Journal of molecular medicine (Berlin, Germany)}, volume = {95}, number = {1}, pages = {29-39}, pmid = {27858116}, issn = {1432-1440}, mesh = {Animals ; Central Nervous System/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Host-Pathogen Interactions ; Humans ; Ligands ; *Microbiota ; Neurodegenerative Diseases/etiology/metabolism/pathology ; Neurogenesis ; Receptors, Aryl Hydrocarbon/*metabolism ; *Signal Transduction ; }, abstract = {The microbiome located within a given host and its organs forms a holobiont, an intimate functional entity with evolutionarily designed interactions to support nutritional intake and reproduction. Thus, all organs in a holobiont respond to changes within the microbiome. The development and function of the central nervous system and its homeostatic mechanisms are no exception and are also subject to regulation by the gut microbiome. In order for the holobiont to function effectively, the microbiome and host must communicate. The aryl hydrocarbon receptor is an evolutionarily conserved receptor recognizing environmental compounds, including a number of ligands produced directly and indirectly by the microbiome. This review focuses on the microbiome-gut-brain axis in regard to the aryl hydrocarbon receptor signaling pathway and its impact on underlying mechanisms in neurodegeneration.}, }
@article {pmid27857087, year = {2016}, author = {Kilian, M and Chapple, IL and Hannig, M and Marsh, PD and Meuric, V and Pedersen, AM and Tonetti, MS and Wade, WG and Zaura, E}, title = {The oral microbiome - an update for oral healthcare professionals.}, journal = {British dental journal}, volume = {221}, number = {10}, pages = {657-666}, pmid = {27857087}, issn = {1476-5373}, mesh = {*Dental Caries ; Humans ; *Microbiota ; Mouth/*microbiology ; *Oral Health ; Periodontitis ; }, abstract = {For millions of years, our resident microbes have coevolved and coexisted with us in a mostly harmonious symbiotic relationship. We are not distinct entities from our microbiome, but together we form a 'superorganism' or holobiont, with the microbiome playing a significant role in our physiology and health. The mouth houses the second most diverse microbial community in the body, harbouring over 700 species of bacteria that colonise the hard surfaces of teeth and the soft tissues of the oral mucosa. Through recent advances in technology, we have started to unravel the complexities of the oral microbiome and gained new insights into its role during both health and disease. Perturbations of the oral microbiome through modern-day lifestyles can have detrimental consequences for our general and oral health. In dysbiosis, the finely-tuned equilibrium of the oral ecosystem is disrupted, allowing disease-promoting bacteria to manifest and cause conditions such as caries, gingivitis and periodontitis. For practitioners and patients alike, promoting a balanced microbiome is therefore important to effectively maintain or restore oral health. This article aims to give an update on our current knowledge of the oral microbiome in health and disease and to discuss implications for modern-day oral healthcare.}, }
@article {pmid27833995, year = {2017}, author = {Thomas, P and Sekhar, AC}, title = {Cultivation Versus Molecular Analysis of Banana (Musa sp.) Shoot-Tip Tissue Reveals Enormous Diversity of Normally Uncultivable Endophytic Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {4}, pages = {885-899}, pmid = {27833995}, issn = {1432-184X}, mesh = {Bacteria/*classification/*genetics/isolation &amp; purification ; Biodiversity ; Chloroplasts/genetics ; DNA, Bacterial/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Ecosystem ; Endophytes/*classification/*genetics/isolation &amp; purification ; India ; Metagenome ; Metagenomics/methods ; Microbiota ; Mitochondria/genetics ; Musa/*microbiology ; *Phylogeny ; Plant Shoots/*growth &amp; development/*microbiology ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; }, abstract = {The interior of plants constitutes a unique environment for microorganisms with various organisms inhabiting as endophytes. Unlike subterranean plant parts, aboveground parts are relatively less explored for endophytic microbial diversity. We employed a combination of cultivation and molecular approaches to study the endophytic bacterial diversity in banana shoot-tips. Cultivable bacteria from 20 sucker shoot-tips of cv. Grand Naine included 37 strains under 16 genera and three phyla (Proteobacteria, Actinobacteria, Firmicutes). 16S rRNA gene-ribotyping approach on 799f and 1492r PCR-amplicons to avoid plant organelle sequences was ineffective showing limited bacterial diversity. 16S rRNA metagene profiling targeting the V3-V4 hypervariable region after filtering out the chloroplast (74.2 %), mitochondrial (22.9 %), and unknown sequences (1.1 %) revealed enormous bacterial diversity. Proteobacteria formed the predominant phylum (64 %) succeeded by Firmicutes (12.1 %), Actinobacteria (9.5 %), Bacteroidetes (6.4 %), Planctomycetes, Cyanobacteria, and minor shares (<1 %) of 14 phyla including several candidate phyla besides the domain Euryarchaeota (0.2 %). Microbiome analysis of single shoot-tips through 16S rRNA V3 region profiling showed similar taxonomic richness and diversity and was less affected by plant sequence interferences. DNA extraction kit ominously influenced the phylogenetic diversity. The study has revealed vast diversity of normally uncultivable endophytic bacteria prevailing in banana shoot-tips (20 phyla, 46 classes) with about 2.6 % of the deciphered 269 genera and 1.5 % of the 656 observed species from the same source of shoot-tips attained through cultivation. The predominant genera included several agriculturally important bacteria. The study reveals an immense ecosystem of endophytic bacteria in banana shoot tissues endorsing the earlier documentation of intracellular &quot;Cytobacts&quot; and &quot;Peribacts&quot; with possible roles in plant holobiome and hologenome.}, }
@article {pmid27822559, year = {2016}, author = {Apprill, A and Weber, LG and Santoro, AE}, title = {Distinguishing between Microbial Habitats Unravels Ecological Complexity in Coral Microbiomes.}, journal = {mSystems}, volume = {1}, number = {5}, pages = {}, pmid = {27822559}, issn = {2379-5077}, abstract = {The diverse prokaryotic communities associated with reef-building corals may provide important ecological advantages to their threatened hosts. The consistency of relationships between corals and specific prokaryotes, however, is debated, and the locations where microbially mediated processes occur in the host are not resolved. Here, we examined how the prokaryotic associates of five common Caribbean corals with different evolutionary and ecological traits differ across mucus and tissue habitats. We used physical and chemical separation of coral mucus and tissue and sequencing of partial small-subunit rRNA genes of bacteria and archaea from these samples to demonstrate that coral tissue and mucus harbor unique reservoirs of prokaryotes, with 23 to 49% and 31 to 56% of sequences exclusive to the tissue and mucus habitats, respectively. Across all coral species, we found that 46 tissue- and 22 mucus-specific microbial members consistently associated with the different habitats. Sequences classifying as &quot;Candidatus Amoebophilus,&quot; Bacteroidetes-affiliated intracellular symbionts of amoebae, emerged as previously unrecognized tissue associates of three coral species. This study demonstrates how coral habitat differentiation enables highly resolved examination of ecological interactions between corals and their associated microorganisms and identifies previously unrecognized tissue and mucus associates of Caribbean corals for future targeted study. IMPORTANCE This study demonstrates that coral tissue or mucus habitats structure the microbiome of corals and that separation of these habitats facilitates identification of consistent microbial associates. Using this approach, we demonstrated that sequences related to &quot;Candidatus Amoebophilus,&quot; recognized intracellular symbionts of amoebae, were highly associated with the tissues of Caribbean corals and possibly endosymbionts of a protistan host within corals, adding a further degree of intricacy to coral holobiont symbioses. Examining specific habitats within complex hosts such as corals is useful for targeting important microbial associations that may otherwise be masked by the sheer microbial diversity associated with all host habitats.}, }
@article {pmid27822520, year = {2016}, author = {Theis, KR and Dheilly, NM and Klassen, JL and Brucker, RM and Baines, JF and Bosch, TC and Cryan, JF and Gilbert, SF and Goodnight, CJ and Lloyd, EA and Sapp, J and Vandenkoornhuyse, P and Zilber-Rosenberg, I and Rosenberg, E and Bordenstein, SR}, title = {Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.}, journal = {mSystems}, volume = {1}, number = {2}, pages = {}, pmid = {27822520}, issn = {2379-5077}, abstract = {Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.}, }
@article {pmid27819120, year = {2016}, author = {Li, Z and Wang, Y and Li, J and Liu, F and He, L and He, Y and Wang, S}, title = {Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {18}, number = {6}, pages = {659-671}, pmid = {27819120}, issn = {1436-2236}, mesh = {Animals ; Archaea/classification/*genetics/metabolism ; Bacteria/classification/*genetics/metabolism ; Biological Evolution ; Carbon/metabolism ; Fungi/classification/*genetics/metabolism ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Microbiota/genetics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; Porifera/classification/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; RNA, Ribosomal, 28S/genetics ; Stramenopiles/classification/*genetics/metabolism ; Sulfur/metabolism ; Symbiosis/physiology ; }, abstract = {Sponges host complex symbiotic communities, but to date, the whole picture of the metabolic potential of sponge microbiota remains unclear, particularly the difference between the shallow-water and deep-sea sponge holobionts. In this study, two completely different sponges, shallow-water sponge Theonella swinhoei from the South China Sea and deep-sea sponge Neamphius huxleyi from the Indian Ocean, were selected to compare their whole symbiotic communities and metabolic potential, particularly in element transformation. Phylogenetically diverse bacteria, archaea, fungi, and algae were detected in both shallow-water sponge T. swinhoei and deep-sea sponge N. huxleyi, and different microbial community structures were indicated between these two sponges. Metagenome-based gene abundance analysis indicated that, though the two sponge microbiota have similar core functions, they showed different potential strategies in detailed metabolic processes, e.g., in the transformation and utilization of carbon, nitrogen, phosphorus, and sulfur by corresponding microbial symbionts. This study provides insight into the putative metabolic potentials of the microbiota associated with the shallow-water and deep-sea sponges at the whole community level, extending our knowledge of the sponge microbiota's functions, the association of sponge- microbes, as well as the adaption of sponge microbiota to the marine environment.}, }
@article {pmid27818648, year = {2016}, author = {Kopac, SM and Klassen, JL}, title = {Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1647}, pmid = {27818648}, issn = {1664-302X}, abstract = {Virtually all multicellular organisms host a community of symbionts composed of mutualistic, commensal, and pathogenic microbes, i.e., their microbiome. The mechanism of selection on host-microbe assemblages remains contentious, particularly regarding whether selection acts differently on hosts and their microbial symbionts. Here, we attempt to reconcile these viewpoints using a model that describes how hosts and their microbial symbionts alter each other's niche and thereby fitness. We describe how host-microbe interactions might change the shape of the host niche and/or reproductive rates within it, which are directly related to host fitness. A host may also alter the niche of a symbiotic microbe, although this depends on the extent to which that microbe is dependent on the host for reproduction. Finally, we provide a mathematical model to test whether interactions between hosts and microbes are necessary to describe the niche of either partner. Our synthesis highlights the phenotypic effects of host-microbe interactions while respecting the unique lifestyles of each partner, and thereby provides a unified framework to describe how selection might act on a host that is associated with its microbiome.}, }
@article {pmid27809267, year = {2016}, author = {Xu, L and Shi, Z and Wang, B and Lu, M and Sun, J}, title = {Pine Defensive Monoterpene α-Pinene Influences the Feeding Behavior of Dendroctonus valens and Its Gut Bacterial Community Structure.}, journal = {International journal of molecular sciences}, volume = {17}, number = {11}, pages = {}, pmid = {27809267}, issn = {1422-0067}, mesh = {Animals ; Bacteria/classification/genetics ; Bicyclic Monoterpenes ; Coleoptera/*drug effects/microbiology/physiology ; DNA, Bacterial/chemistry/genetics ; Dose-Response Relationship, Drug ; Feeding Behavior/*drug effects ; Gastrointestinal Microbiome/*drug effects/genetics/physiology ; Genetic Variation ; Host-Pathogen Interactions/drug effects ; Monoterpenes/*pharmacology ; Phloem/chemistry ; Pinus/*chemistry ; Polymerase Chain Reaction ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Time Factors ; }, abstract = {The exposure to plant defense chemicals has negative effects on insect feeding activity and modifies insect gut microbial community composition. Dendroctonus valens is a very destructive forest pest in China, and harbors a large diversity and abundance of gut microorganisms. Host pine defensive chemicals can protect the pines from attack by the holobiont. In this study, boring length of D. valens feeding on 0 mg/g α-pinene and 9 mg/g α-pinene concentration in phloem media for 6 and 48 h were recorded, and their gut bacterial communities were analyzed in parallel. Nine milligram per gram α-pinene concentration significantly inhibited boring length of D. valens and altered its gut microbial community structure after 6 h. The inhibition of boring length from 9 mg/g α-pinene in diets ceased after 48 h. No significant differences of the bacterial communities were observed between the beetles in 0 and 9 mg/g α-pinene concentration in phloem media after 48 h. Our results showed that the inhibition of the feeding behavior of D. valens and the disturbance to its gut bacterial communities in 9 mg/g α-pinene concentration in phloem media after 6 h were eliminated after 48 h. The resilience of gut bacterial community of D. valens may help the beetle catabolize pine defense chemical.}, }
@article {pmid27803185, year = {2016}, author = {Schröder, K and Bosch, TC}, title = {The Origin of Mucosal Immunity: Lessons from the Holobiont Hydra.}, journal = {mBio}, volume = {7}, number = {6}, pages = {}, pmid = {27803185}, issn = {2150-7511}, mesh = {Animals ; *Biological Evolution ; Hydra/*immunology ; *Immunity, Innate ; *Immunity, Mucosal ; Models, Animal ; Vertebrates/*immunology ; }, abstract = {Historically, mucosal immunity-i.e., the portion of the immune system that protects an organism's various mucous membranes from invasion by potentially pathogenic microbes-has been studied in single-cell epithelia in the gastrointestinal and upper respiratory tracts of vertebrates. Phylogenetically, mucosal surfaces appeared for the first time about 560 million years ago in members of the phylum Cnidaria. There are remarkable similarities and shared functions of mucosal immunity in vertebrates and innate immunity in cnidarians, such as Hydra species. Here, we propose a common origin for both systems and review observations that indicate that the ultimately simple holobiont Hydra provides both a new perspective on the relationship between bacteria and animal cells and a new prism for viewing the emergence and evolution of epithelial tissue-based innate immunity. In addition, recent breakthroughs in our understanding of immune responses in Hydra polyps reared under defined short-term gnotobiotic conditions open up the potential of Hydra as an animal research model for the study of common mucosal disorders.}, }
@article {pmid27799924, year = {2016}, author = {Berg, M and Zhou, XY and Shapira, M}, title = {Host-Specific Functional Significance of Caenorhabditis Gut Commensals.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1622}, pmid = {27799924}, issn = {1664-302X}, support = {S10 RR027303/RR/NCRR NIH HHS/United States ; S10 RR029668/RR/NCRR NIH HHS/United States ; }, abstract = {The gut microbiota is an important contributor to host health and fitness. Given its importance, microbiota composition should not be left to chance. However, what determines this composition is far from clear, with results supporting contributions of both environmental factors and host genetics. To gauge the relative contributions of host genetics and environment, specifically the microbial diversity, we characterized the gut microbiotas of Caenorhabditis species spanning 200-300 million years of evolution, and raised on different composted soil environments. Comparisons were based on 16S rDNA deep sequencing data, as well as on functional evaluation of gut isolates. Worm microbiotas were distinct from those in their respective soil environment, and included bacteria previously identified as part of the C. elegans core microbiota. Microbiotas differed between experiments initiated with different soil communities, but within each experiment, worm microbiotas clustered according to host identity, demonstrating a dominant contribution of environmental diversity, but also a significant contribution of host genetics. The dominance of environmental contributions hindered identification of host-associated microbial taxa from 16S data. Characterization of gut isolates from C. elegans and C. briggsae, focusing on the core family Enterobacteriaceae, were also unable to expose phylogenetic distinctions between microbiotas of the two species. However, functional evaluation of the isolates revealed host-specific contributions, wherein gut commensals protected their own host from infection, but not a non-host. Identification of commensal host-specificity at the functional level, otherwise overlooked in standard sequence-based analyses, suggests that the contribution of host genetics to shaping of gut microbiotas may be greater than previously realized.}, }
@article {pmid27795310, year = {2017}, author = {Morrow, KM and Bromhall, K and Motti, CA and Munn, CB and Bourne, DG}, title = {Allelochemicals Produced by Brown Macroalgae of the Lobophora Genus Are Active against Coral Larvae and Associated Bacteria, Supporting Pathogenic Shifts to Vibrio Dominance.}, journal = {Applied and environmental microbiology}, volume = {83}, number = {1}, pages = {}, pmid = {27795310}, issn = {1098-5336}, mesh = {Animals ; Anthozoa/drug effects/*microbiology ; Archaea/drug effects/genetics/growth &amp; development/isolation &amp; purification ; Bacteria/drug effects/genetics/growth &amp; development/pathogenicity ; Coral Reefs ; Ecosystem ; Larva/drug effects ; Metagenomics ; Microbial Consortia/drug effects/genetics ; Microbiota/*drug effects/genetics ; Phaeophyta/*chemistry/physiology ; Pheromones/biosynthesis/chemistry/*pharmacology ; Population Dynamics ; RNA, Ribosomal, 16S ; Seaweed/chemistry/growth &amp; development/*physiology ; Vibrio/*isolation &amp; purification/pathogenicity/physiology ; }, abstract = {Pervasive environmental stressors on coral reefs are attributed with shifting the competitive balance in favor of alternative dominants, such as macroalgae. Previous studies have demonstrated that macroalgae compete with corals via a number of mechanisms, including the production of potent primary and secondary metabolites that can influence coral-associated microbial communities. The present study investigates the effects of the Pacific brown macroalga Lobophora sp. (due to the shifting nature of the Lobophora species complex, it will be referred to here as Lobophora sp.) on coral bacterial isolates, coral larvae, and the microbiome associated with the coral Porites cylindrica. Crude aqueous and organic macroalgal extracts were found to inhibit the growth of coral-associated bacteria. Extracts and fractions were also shown to inhibit coral larval settlement and cause mortality at concentrations lower (<0.3 mg · ml-1) than calculated natural concentrations (4.4 mg · ml-1). Microbial communities associated with coral tissues exposed to aqueous (e.g., hydrophilic) crude extracts demonstrated a significant shift to Vibrio dominance and a loss of sequences related to the putative coral bacterial symbiont, Endozoicomonas sp., based on 16S rRNA amplicon sequencing. This study contributes to growing evidence that macroalgal allelochemicals, dissolved organic material, and native macroalgal microbial assemblages all play a role in shifting the microbial equilibrium of the coral holobiont away from a beneficial state, contributing to a decline in coral fitness and a shift in ecosystem structure.<br><br>IMPORTANCE: Diverse microbial communities associate with coral tissues and mucus, providing important protective and nutritional services, but once disturbed, the microbial equilibrium may shift from a beneficial state to one that is detrimental or pathogenic. Macroalgae (e.g., seaweeds) can physically and chemically interact with corals, causing abrasion, bleaching, and overall stress. This study contributes to a growing body of evidence suggesting that macroalgae play a critical role in shifting the coral holobiont equilibrium, which may promote the invasion of opportunistic pathogens and cause coral mortality, facilitating additional macroalgal growth and invasion in the reef. Thus, macroalgae not only contribute to a decline in coral fitness but also influence coral reef ecosystem structure.}, }
@article {pmid27594308, year = {2016}, author = {Root-Bernstein, R}, title = {Autoimmunity and the microbiome: T-cell receptor mimicry of &quot;self&quot; and microbial antigens mediates self tolerance in holobionts: The concepts of &quot;holoimmunity&quot; (TcR-mediated tolerance for the holobiont) and &quot;holoautoimmunity&quot; (loss of tolerance for the holobiont) are introduced.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {11}, pages = {1068-1083}, doi = {10.1002/bies.201600083}, pmid = {27594308}, issn = {1521-1878}, mesh = {*Autoimmunity ; Humans ; Immune Tolerance ; Microbiota/*immunology ; Receptors, Antigen, T-Cell/*immunology ; }, abstract = {I propose a T-cell receptor (TcR)-based mechanism by which immunity mediates both &quot;genetic self&quot; and &quot;microbial self&quot; thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross-reactivity with &quot;self,&quot; resulting in selection for a TcR repertoire mimicking &quot;genetic self.&quot; Second, evolution has selected for a &quot;microbial self&quot; that mimics &quot;genetic self&quot; so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR-microbiome mimicry &quot;holoimmunity&quot; to denote immune tolerance to the &quot;holobiont self.&quot; Logically, microbiome-host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross-react with host antigens producing &quot;holoautoimmunity.&quot;}, }
@article {pmid27777745, year = {2016}, author = {Aichelman, HE and Townsend, JE and Courtney, TA and Baumann, JH and Davies, SW and Castillo, KD}, title = {Heterotrophy mitigates the response of the temperate coral Oculina arbuscula to temperature stress.}, journal = {Ecology and evolution}, volume = {6}, number = {18}, pages = {6758-6769}, pmid = {27777745}, issn = {2045-7758}, abstract = {Anthropogenic increases in atmospheric carbon dioxide concentration have caused global average sea surface temperature (SST) to increase by approximately 0.11°C per decade between 1971 and 2010 - a trend that is projected to continue through the 21st century. A multitude of research studies have demonstrated that increased SSTs compromise the coral holobiont (cnidarian host and its symbiotic algae) by reducing both host calcification and symbiont density, among other variables. However, we still do not fully understand the role of heterotrophy in the response of the coral holobiont to elevated temperature, particularly for temperate corals. Here, we conducted a pair of independent experiments to investigate the influence of heterotrophy on the response of the temperate scleractinian coral Oculina arbuscula to thermal stress. Colonies of O. arbuscula from Radio Island, North Carolina, were exposed to four feeding treatments (zero, low, moderate, and high concentrations of newly hatched Artemia sp. nauplii) across two independent temperature experiments (average annual SST (20°C) and average summer temperature (28°C) for the interval 2005-2012) to quantify the effects of heterotrophy on coral skeletal growth and symbiont density. Results suggest that heterotrophy mitigated both reduced skeletal growth and decreased symbiont density observed for unfed corals reared at 28°C. This study highlights the importance of heterotrophy in maintaining coral holobiont fitness under thermal stress and has important implications for the interpretation of coral response to climate change.}, }
@article {pmid27726033, year = {2017}, author = {van de Water, JA and Melkonian, R and Voolstra, CR and Junca, H and Beraud, E and Allemand, D and Ferrier-Pagès, C}, title = {Comparative Assessment of Mediterranean Gorgonian-Associated Microbial Communities Reveals Conserved Core and Locally Variant Bacteria.}, journal = {Microbial ecology}, volume = {73}, number = {2}, pages = {466-478}, pmid = {27726033}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/genetics/isolation &amp; purification ; Base Sequence ; Biodiversity ; Classification ; Coral Reefs ; DNA, Bacterial/genetics ; Gene Library ; Mediterranean Sea ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/microbiology ; Species Specificity ; Temperature ; }, abstract = {Gorgonians are key habitat-forming species of Mediterranean benthic communities, but their populations have suffered from mass mortality events linked to high summer seawater temperatures and microbial disease. However, our knowledge on the diversity, dynamics and function of gorgonian-associated microbial communities is limited. Here, we analysed the spatial variability of the microbiomes of five sympatric gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa, Leptogorgia sarmentosa and Paramuricea clavata), collected from the Mediterranean Sea over a scale of ∼1100 km, using next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all gorgonian species were generally dominated by members of the genus Endozoicomonas, which were at very low abundance in the surrounding seawater. Although the composition of the core microbiome (operational taxonomic units consistently present in a species) was found to be unique for each host species, significant overlap was observed. These spatially consistent associations between gorgonians and their core bacteria suggest intricate symbiotic relationships and regulation of the microbiome composition by the host. At the same time, local variations in microbiome composition were observed. Functional predictive profiling indicated that these differences could be attributed to seawater pollution. Taken together, our data indicate that gorgonian-associated microbiomes are composed of spatially conserved bacteria (core microbiome members) and locally variant members, and that local pollution may influence these local associations, potentially impacting gorgonian health.}, }
@article {pmid27721807, year = {2016}, author = {Dittmer, J and van Opstal, EJ and Shropshire, JD and Bordenstein, SR and Hurst, GD and Brucker, RM}, title = {Disentangling a Holobiont - Recent Advances and Perspectives in Nasonia Wasps.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1478}, pmid = {27721807}, issn = {1664-302X}, abstract = {The parasitoid wasp genus Nasonia (Hymenoptera: Chalcidoidea) is a well-established model organism for insect development, evolutionary genetics, speciation, and symbiosis. The host-microbiota assemblage which constitutes the Nasonia holobiont (a host together with all of its associated microbes) consists of viruses, two heritable bacterial symbionts and a bacterial community dominated in abundance by a few taxa in the gut. In the wild, all four Nasonia species are systematically infected with the obligate intracellular bacterium Wolbachia and can additionally be co-infected with Arsenophonus nasoniae. These two reproductive parasites have different transmission modes and host manipulations (cytoplasmic incompatibility vs. male-killing, respectively). Pioneering studies on Wolbachia in Nasonia demonstrated that closely related Nasonia species harbor multiple and mutually incompatible Wolbachia strains, resulting in strong symbiont-mediated reproductive barriers that evolved early in the speciation process. Moreover, research on host-symbiont interactions and speciation has recently broadened from its historical focus on heritable symbionts to the entire microbial community. In this context, each Nasonia species hosts a distinguishable community of gut bacteria that experiences a temporal succession during host development and members of this bacterial community cause strong hybrid lethality during larval development. In this review, we present the Nasonia species complex as a model system to experimentally investigate questions regarding: (i) the impact of different microbes, including (but not limited to) heritable endosymbionts, on the extended phenotype of the holobiont, (ii) the establishment and regulation of a species-specific microbiota, (iii) the role of the microbiota in speciation, and (iv) the resilience and adaptability of the microbiota in wild populations subjected to different environmental pressures. We discuss the potential for easy microbiota manipulations in Nasonia as a promising experimental approach to address these fundamental aspects.}, }
@article {pmid27716053, year = {2016}, author = {Peterson, BF and Scharf, ME}, title = {Metatranscriptome analysis reveals bacterial symbiont contributions to lower termite physiology and potential immune functions.}, journal = {BMC genomics}, volume = {17}, number = {1}, pages = {772}, pmid = {27716053}, issn = {1471-2164}, mesh = {Amidohydrolases/genetics/metabolism ; Animals ; Antibiosis ; Bacteria/*genetics ; Computational Biology/methods ; Fungi/physiology ; Gene Expression Profiling ; Genes, rRNA ; Glutathione Transferase/metabolism ; Isoptera/*immunology/metabolism/*microbiology ; *Metagenome ; *Metagenomics/methods ; Oxidative Stress ; Reactive Oxygen Species/metabolism ; Reproducibility of Results ; *Symbiosis ; *Transcriptome ; }, abstract = {BACKGROUND: Symbioses throughout the animal kingdom are known to extend physiological and ecological capabilities to hosts. Insect-microbe associations are extremely common and are often related to novel niche exploitation, fitness advantages, and even speciation events. These phenomena include expansions in host diet, detoxification of insecticides and toxins, and increased defense against pathogens. However, dissecting the contributions of individual groups of symbionts at the molecular level is often underexplored due to methodological and analytical limitations. Termites are one of the best studied systems for physiological collaborations between host and symbiota; however, most work in lower termites (those with bacterial and protist symbionts) focuses on the eukaryotic members of this symbiotic consortium. Here we present a metatranscriptomic analysis which provides novel insights into bacterial contributions to the holobiont of the eastern subterranean termite, Reticulitermes flavipes, in the presence and absence of a fungal pathogen.<br><br>RESULTS: Using a customized ribodepletion strategy, a metatranscriptome assembly was obtained representing the host termite as well as bacterial and protist symbiota. Sequence data provide new insights into biosynthesis, catabolism, and transport of major organic molecules and ions by the gut consortium, and corroborate previous findings suggesting that bacteria play direct roles in nitrogen fixation, amino acid biosynthesis, and lignocellulose digestion. With regard to fungal pathogen challenge, a total of 563 differentially expressed candidate host and symbiont contigs were identified (162 up- and 401 downregulated; α/FDR = 0.05) including an upregulated bacterial amidohydrolase.<br><br>CONCLUSIONS: This study presents the most complete bacterial metatranscriptome from a lower termite and provides a framework on which to build a more complete model of termite-symbiont interactions including, but not limited to, digestion and pathogen defense.}, }
@article {pmid27708547, year = {2016}, author = {Torday, JS and Miller, WB}, title = {Life is determined by its environment.}, journal = {International journal of astrobiology}, volume = {15}, number = {4}, pages = {345-350}, pmid = {27708547}, issn = {1473-5504}, support = {R01 HL055268/HL/NHLBI NIH HHS/United States ; //United States NHLBI/ ; }, abstract = {A well-developed theory of evolutionary biology requires understanding of the origins of life on Earth. However, the initial conditions (ontology) and causal (epistemology) bases on which physiology proceeded have more recently been called into question, given the teleologic nature of Darwinian evolutionary thinking. When evolutionary development is focused on cellular communication, a distinctly different perspective unfolds. The cellular communicative-molecular approach affords a logical progression for the evolutionary narrative based on the basic physiologic properties of the cell. Critical to this appraisal is recognition of the cell as a fundamental reiterative unit of reciprocating communication that receives information from and reacts to epiphenomena to solve problems. Following the course of vertebrate physiology from its unicellular origins instead of its overt phenotypic appearances and functional associations provides a robust, predictive picture for the means by which complex physiology evolved from unicellular organisms. With this foreknowledge of physiologic principles, we can determine the fundamentals of Physiology based on cellular first principles using a logical, predictable method. Thus, evolutionary creativity on our planet can be viewed as a paradoxical product of boundary conditions that permit homeostatic moments of varying length and amplitude that can productively absorb a variety of epigenetic impacts to meet environmental challenges.}, }
@article {pmid27690269, year = {2016}, author = {McIlroy, SE and Gillette, P and Cunning, R and Klueter, A and Capo, T and Baker, AC and Coffroth, MA}, title = {The effects of Symbiodinium (Pyrrhophyta) identity on growth, survivorship, and thermal tolerance of newly settled coral recruits.}, journal = {Journal of phycology}, volume = {52}, number = {6}, pages = {1114-1124}, doi = {10.1111/jpy.12471}, pmid = {27690269}, issn = {1529-8817}, mesh = {Animals ; Anthozoa/growth &amp; development/*physiology ; Dinoflagellida/*physiology ; Florida ; Species Specificity ; *Symbiosis ; *Thermotolerance ; }, abstract = {For many coral species, the obligate association with phylogenetically diverse algal endosymbiont species is dynamic in time and space. Here, we used controlled laboratory inoculations of newly settled, aposymbiotic corals (Orbicella faveolata) with two cultured species of algal symbiont (Symbiodinium microadriaticum and S. minutum) to examine the role of symbiont identity on growth, survivorship, and thermal tolerance of the coral holobiont. We evaluated these data in the context of Symbiodinium photophysiology for 9 months post-settlement and also during a 5-d period of elevated temperatures Our data show that recruits that were inoculated with S. minutum grew significantly slower than those inoculated with S. microadriaticum (occasionally co-occurring with S. minutum), but that there was no difference in survivorship of O. faveolata polyps infected with Symbiodinium. However, photophysiological metrics (∆Fv/F'm, the efficiency with which available light is used to drive photosynthesis and α, the maximum light utilization coefficient) were higher in those slower growing recruits containing S. minutum. These findings suggest that light use (i.e., photophysiology) and carbon acquisition by the coral host (i.e., host growth) are decoupled, but did not distinguish the source of this difference. Neither Symbiodinium treatment demonstrated a significant negative effect of a 5-d exposure to temperatures as high as 32°C under low light conditions similar to those measured at settlement habitats.}, }
@article {pmid27690185, year = {2016}, author = {Rubio-Portillo, E and Santos, F and Martínez-García, M and de Los Ríos, A and Ascaso, C and Souza-Egipsy, V and Ramos-Esplá, AA and Anton, J}, title = {Structure and temporal dynamics of the bacterial communities associated to microhabitats of the coral Oculina patagonica.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {4564-4578}, doi = {10.1111/1462-2920.13548}, pmid = {27690185}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/*microbiology ; Denaturing Gradient Gel Electrophoresis ; Ecosystem ; Mediterranean Sea ; Vibrio/isolation &amp; purification/physiology ; }, abstract = {Corals are known to contain a diverse microbiota that plays a paramount role in the physiology and health of holobiont. However, few studies have addressed the variability of bacterial communities within the coral host. In this study, bacterial community composition from the mucus, tissue and skeleton of the scleractinian coral Oculina patagonica were investigated seasonally at two locations in the Western Mediterranean Sea, to further understand how environmental conditions and the coral microbiome structure are related. We used denaturing gradient gel electrophoresis in combination with next-generation sequencing and electron microscopy to characterize the bacterial community. The bacterial communities were significantly different among coral compartments, and coral tissue displayed the greatest changes related to environmental conditions and coral health status. Species belonging to the Rhodobacteraceae and Vibrionaceae families form part of O. patagonica tissues core microbiome and may play significant roles in the nitrogen cycle. Furthermore, sequences related to the coral pathogens, Vibrio mediterranei and Vibrio coralliilyticus, were detected not only in bleached corals but also in healthy ones, even during cold months. This fact opens a new view onto unveiling the role of pathogens in the development of coral diseases in the future.}, }
@article {pmid27688961, year = {2016}, author = {Wada, N and Pollock, FJ and Willis, BL and Ainsworth, T and Mano, N and Bourne, DG}, title = {In situ visualization of bacterial populations in coral tissues: pitfalls and solutions.}, journal = {PeerJ}, volume = {4}, number = {}, pages = {e2424}, pmid = {27688961}, issn = {2167-8359}, abstract = {In situ visualization of microbial communities within their natural habitats provides a powerful approach to explore complex interactions between microorganisms and their macroscopic hosts. Specifically, the application of fluorescence in situ hybridization (FISH) to simultaneously identify and visualize diverse microbial taxa associated with coral hosts, including symbiotic algae (Symbiodinium), Bacteria, Archaea, Fungi and protists, could help untangle the structure and function of these diverse taxa within the coral holobiont. However, the application of FISH approaches to coral samples is constrained by non-specific binding of targeted rRNA probes to cellular structures within the coral animal tissues (including nematocysts, spirocysts, granular gland cells within the gastrodermis and cnidoglandular bands of mesenterial filaments). This issue, combined with high auto-fluorescence of both host tissues and endosymbiotic dinoflagellates (Symbiodinium), make FISH approaches for analyses of coral tissues challenging. Here we outline the major pitfalls associated with applying FISH to coral samples and describe approaches to overcome these challenges.}, }
@article {pmid27668211, year = {2016}, author = {Miller, WB}, title = {The Eukaryotic Microbiome: Origins and Implications for Fetal and Neonatal Life.}, journal = {Frontiers in pediatrics}, volume = {4}, number = {}, pages = {96}, pmid = {27668211}, issn = {2296-2360}, abstract = {All eukaryotic organisms are holobionts representing complex collaborations between the entire microbiome of each eukaryote and its innate cells. These linked constituencies form complex localized and interlocking ecologies in which the specific microbial constituents and their relative abundance differ substantially according to age and environmental exposures. Rapid advances in microbiology and genetic research techniques have uncovered a significant previous underestimate of the extent of that microbial contribution and its metabolic and developmental impact on holobionts. Therefore, a re-calibration of the neonatal period is suggested as a transitional phase in development that includes the acquisition of consequential collaborative microbial life from extensive environmental influences. These co-dependent, symbiotic relationships formed in the fetal and neonatal stages extend into adulthood and even across generations.}, }
@article {pmid27643794, year = {2016}, author = {Ueda, Y and Frindte, K and Knief, C and Ashrafuzzaman, M and Frei, M}, title = {Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice.}, journal = {PloS one}, volume = {11}, number = {9}, pages = {e0163178}, pmid = {27643794}, issn = {1932-6203}, mesh = {Bacteria/genetics/*metabolism ; Oryza/*metabolism/microbiology ; Ozone/*metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Microbes constitute a vital part of the plant holobiont. They establish plant-microbe or microbe-microbe associations, forming a unique microbiota with each plant species and under different environmental conditions. These microbial communities have to adapt to diverse environmental conditions, such as geographical location, climate conditions and soil types, and are subjected to changes in their surrounding environment. Elevated ozone concentration is one of the most important aspects of global change, but its effect on microbial communities living on plant surfaces has barely been investigated. In the current study, we aimed at elucidating the potential effect of elevated ozone concentrations on the phyllosphere (aerial part of the plant) and rhizoplane (surface of the root) microbiota by adopting next-generation 16S rRNA amplicon sequencing. A standard japonica rice cultivar Nipponbare and an ozone-tolerant breeding line L81 (Nipponbare background) were pre-grown in a greenhouse for 10 weeks and then exposed to ozone at 85 ppb for 7 h daily for 30 days in open top chambers. Microbial cells were collected from the phyllosphere and rhizoplane separately. The treatment or different genotypes did not affect various diversity indices. On the other hand, the relative abundance of some bacterial taxa were significantly affected in the rhizoplane community of ozone-treated plants. A significant effect of ozone was detected by homogeneity of molecular variance analysis in the phyllosphere, meaning that the community from ozone-treated phyllosphere samples was more variable than those from control plants. In addition, a weak treatment effect was observed by clustering samples based on the Yue and Clayton and weighted UniFrac distance matrices among samples. We therefore conclude that the elevated ozone concentrations affected the bacterial community structure of the phyllosphere and the rhizosplane as a whole, even though this effect was rather weak and did not lead to changes of the function of the communities.}, }
@article {pmid27630618, year = {2016}, author = {Francino, MP and Medina, M}, title = {Editorial: Recent Advances in Symbiosis Research: Integrative Approaches.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1331}, doi = {10.3389/fmicb.2016.01331}, pmid = {27630618}, issn = {1664-302X}, }
@article {pmid27617200, year = {2016}, author = {Burcelin, R}, title = {Gut microbiota and immune crosstalk in metabolic disease.}, journal = {Molecular metabolism}, volume = {5}, number = {9}, pages = {771-781}, pmid = {27617200}, issn = {2212-8778}, abstract = {BACKGROUND: Gut microbiota is considered as a major regulator of metabolic disease. This reconciles the notion of metabolic inflammation and the epidemic development of the disease. In addition to evidence showing that a specific gut microbiota characterizes patients with obesity, type 2 diabetes, and hepatic steatosis, the mechanisms causal to the disease could be related to the translocation of microbiota from the gut to the tissues, inducing inflammation. The mechanisms regulating such a process are based on the crosstalk between the gut microbiota and the host immune system. The hologenome theory of evolution supports this concept and implies that therapeutic strategies aiming to control glycemia should take into account both the gut microbiota and the host immune system.<br><br>SCOPE OF REVIEW: This review discusses the latest evidence regarding the bidirectional impact of the gut microbiota on host immune system crosstalk for the control of metabolic disease, hyperglycemia, and obesity. To avoid redundancies with the literature, we will focus our attention on the intestinal immune system, identifying evidence for the generation of novel therapeutic strategies, which could be based on the control of the translocation of gut bacteria to tissues. Such novel strategies should hamper the role played by gut microbiota dysbiosis on the development of metabolic inflammation.<br><br>MAJOR CONCLUSIONS: Recent evidence in rodents allows us to conclude that an impaired intestinal immune system characterizes and could be causal in the development of metabolic disease. The fine understanding of the molecular mechanisms should allow for the development of a first line of treatment for metabolic disease and its co-morbidities. This article is part of a special issue on microbiota.}, }
@article {pmid27602023, year = {2016}, author = {Hahn, MA and Dheilly, NM}, title = {Experimental Models to Study the Role of Microbes in Host-Parasite Interactions.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1300}, pmid = {27602023}, issn = {1664-302X}, abstract = {Until recently, parasitic infections have been primarily studied as interactions between the parasite and the host, leaving out crucial players: microbes. The recent realization that microbes play key roles in the biology of all living organisms is not only challenging our understanding of host-parasite evolution, but it also provides new clues to develop new therapies and remediation strategies. In this paper we provide a review of promising and advanced experimental organismal systems to examine the dynamic of host-parasite-microbe interactions. We address the benefits of developing new experimental models appropriate to this new research area and identify systems that offer the best promises considering the nature of the interactions among hosts, parasites, and microbes. Based on these systems, we identify key criteria for selecting experimental models to elucidate the fundamental principles of these complex webs of interactions. It appears that no model is ideal and that complementary studies should be performed on different systems in order to understand the driving roles of microbes in host and parasite evolution.}, }
@article {pmid27581522, year = {2016}, author = {Rouco, M and Haley, ST and Dyhrman, ST}, title = {Microbial diversity within the Trichodesmium holobiont.}, journal = {Environmental microbiology}, volume = {18}, number = {12}, pages = {5151-5160}, doi = {10.1111/1462-2920.13513}, pmid = {27581522}, issn = {1462-2920}, mesh = {*Biodiversity ; Nitrogen/metabolism ; Nitrogen Fixation ; Oceans and Seas ; Phylogeny ; Seawater/*microbiology ; Trichodesmium/classification/genetics/*isolation &amp; purification/metabolism ; }, abstract = {Nitrogen-fixing cyanobacteria in the genus Trichodesmium play a critical role in the productivity of the tropical and subtropical oligotrophic oceans. The ecological success of these populations is likely associated with the diverse microbial interactions occurring within the Trichodesmium holobiont, especially between Trichodesmium and heterotrophic bacterial epibionts. Yet, the composition of the Trichodesmium holobiont and the processes governing microbial assemblage are not well documented. Here, we used high-resolution 16S rDNA amplicon sequencing to examine the diversity of Trichodesmium and associated epibionts across different ocean regions and colony morphologies (puffs and rafts). Trichodesmium Clade I (i.e., T. thiebautii-like) dominated the colonies in all ocean basins regardless of morphology, although the Trichodesmium community structure significantly varied between morphologies in some regions. On average, Alphaproteobacteria (i.e., Thalassobius), Gammaproteobacteria (i.e., Pseudoalteromonas), Sphingobacteria (i.e., Microscilla and Vibrio) and Flavobacteria dominated the epibiont communities, but community composition and structure significantly differed between regions. Epibionts from the two colony morphologies were taxonomically and functionally distinct in the North Atlantic and North Pacific. These findings suggest that the colony types might define two distinct niches and that epibiont assemblage might be driven in part by selective processes, where epibionts are selected according to their influence on colony metabolism.}, }
@article {pmid27507098, year = {2016}, author = {Schnorr, SL and Sankaranarayanan, K and Lewis, CM and Warinner, C}, title = {Insights into human evolution from ancient and contemporary microbiome studies.}, journal = {Current opinion in genetics &amp; development}, volume = {41}, number = {}, pages = {14-26}, pmid = {27507098}, issn = {1879-0380}, support = {R01 GM089886/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Ecology ; *Evolution, Molecular ; Humans ; Microbiota/*genetics ; Primates/genetics/*microbiology ; }, abstract = {Over the past decade, human microbiome research has energized the study of human evolution through a complete shift in our understanding of what it means to be human. The microbiome plays a pivotal role in human biology, performing key functions in digestion, mood and behavior, development and immunity, and a range of acute and chronic diseases. It is therefore critical to understand its evolution and changing ecology through time. Here we review recent findings on the microbiota of diverse human populations, non-human primates, and past human populations and discuss the implications of this research in formulating a deeper evolutionary understanding of the human holobiont.}, }
@article {pmid27492757, year = {2016}, author = {Garcia, GD and Santos, Ede O and Sousa, GV and Zingali, RB and Thompson, CC and Thompson, FL}, title = {Metaproteomics reveals metabolic transitions between healthy and diseased stony coral Mussismilia braziliensis.}, journal = {Molecular ecology}, volume = {25}, number = {18}, pages = {4632-4644}, doi = {10.1111/mec.13775}, pmid = {27492757}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*genetics/*microbiology ; Bacteria/*classification ; Brazil ; Proteomics ; Symbiosis ; Tandem Mass Spectrometry ; }, abstract = {Infectious diseases such as white plague syndrome (WPS) and black band disease (BBD) have caused massive coral loss worldwide. We performed a metaproteomic study on the Abrolhos coral Mussismilia braziliensis to define the types of proteins expressed in healthy corals compared to WPS- and BBD-affected corals. A total of 6363 MS/MS spectra were identified as 361 different proteins. Healthy corals had a set of proteins that may be considered markers of holobiont homoeostasis, including tubulin, histone, Rab family, ribosomal, peridinin-chlorophyll a-binding protein, F0F1-type ATP synthase, alpha-iG protein, calmodulin and ADP-ribosylation factor. Cnidaria proteins found in healthy M. braziliensis were associated with Cnidaria-Symbiodinium endosymbiosis and included chaperones (hsp70, hsp90 and calreticulin), structural and membrane modelling proteins (actin) and proteins with functions related to intracellular vesicular traffic (Rab7 and ADP-ribosylation factor 1) and signal transduction (14-3-3 protein and calmodulin). WPS resulted in a clear shift in the predominance of proteins, from those related to aerobic nitrogen-fixing bacteria (i.e. Rhizobiales, Sphingomonadales and Actinomycetales) in healthy corals to those produced by facultative/anaerobic sulphate-reducing bacteria (i.e. Enterobacteriales, Alteromonadales, Clostridiales and Bacteroidetes) in WPS corals. BBD corals developed a diverse community dominated by cyanobacteria and sulphur cycle bacteria. Hsp60, hsp90 and adenosylhomocysteinase proteins were produced mainly by cyanobacteria in BBD corals, which is consistent with elevated oxidative stress in hydrogen sulphide- and cyanotoxin-rich environments. This study demonstrates the usefulness of metaproteomics for gaining better comprehension of coral metabolic status in health and disease, especially in reef systems such as the Abrolhos that are suffering from the increase in global and local threatening events.}, }
@article {pmid27486438, year = {2016}, author = {Seston, SL and Beinart, RA and Sarode, N and Shockey, AC and Ranjan, P and Ganesh, S and Girguis, PR and Stewart, FJ}, title = {Metatranscriptional Response of Chemoautotrophic Ifremeria nautilei Endosymbionts to Differing Sulfur Regimes.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {1074}, pmid = {27486438}, issn = {1664-302X}, abstract = {Endosymbioses between animals and chemoautotrophic bacteria are ubiquitous at hydrothermal vents. These environments are distinguished by high physico-chemical variability, yet we know little about how these symbioses respond to environmental fluctuations. We therefore examined how the γ-proteobacterial symbionts of the vent snail Ifremeria nautilei respond to changes in sulfur geochemistry. Via shipboard high-pressure incubations, we subjected snails to 105 μM hydrogen sulfide (LS), 350 μM hydrogen sulfide (HS), 300 μM thiosulfate (TS) and seawater without any added inorganic electron donor (ND). While transcript levels of sulfur oxidation genes were largely consistent across treatments, HS and TS treatments stimulated genes for denitrification, nitrogen assimilation, and CO2 fixation, coincident with previously reported enhanced rates of inorganic carbon incorporation and sulfur oxidation in these treatments. Transcripts for genes mediating oxidative damage were enriched in the ND and LS treatments, potentially due to a reduction in O2 scavenging when electron donors were scarce. Oxidative TCA cycle gene transcripts were also more abundant in ND and LS treatments, suggesting that I. nautilei symbionts may be mixotrophic when inorganic electron donors are limiting. These data reveal the extent to which I. nautilei symbionts respond to changes in sulfur concentration and species, and, interpreted alongside coupled biochemical metabolic rates, identify gene targets whose expression patterns may be predictive of holobiont physiology in environmental samples.}, }
@article {pmid27485233, year = {2016}, author = {Mansour, TA and Rosenthal, JJ and Brown, CT and Roberson, LM}, title = {Transcriptome of the Caribbean stony coral Porites astreoides from three developmental stages.}, journal = {GigaScience}, volume = {5}, number = {1}, pages = {33}, pmid = {27485233}, issn = {2047-217X}, support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/genetics/*growth &amp; development/parasitology ; Caribbean Region ; Coral Reefs ; Dinoflagellida/*genetics/physiology ; Gene Expression Profiling/*methods ; Gene Expression Regulation, Developmental ; Gene Library ; Sequence Analysis, RNA/*methods ; Symbiosis ; }, abstract = {BACKGROUND: Porites astreoides is a ubiquitous species of coral on modern Caribbean reefs that is resistant to increasing temperatures, overfishing, and other anthropogenic impacts that have threatened most other coral species. We assembled and annotated a transcriptome from this coral using Illumina sequences from three different developmental stages collected over several years: free-swimming larvae, newly settled larvae, and adults (>10 cm in diameter). This resource will aid understanding of coral calcification, larval settlement, and host-symbiont interactions.<br><br>FINDINGS: A de novo transcriptome for the P. astreoides holobiont (coral plus algal symbiont) was assembled using 594 Mbp of raw Illumina sequencing data generated from five age-specific cDNA libraries. The new transcriptome consists of 867 255 transcript elements with an average length of 685 bases. The isolated P. astreoides assembly consists of 129 718 transcript elements with an average length of 811 bases, and the isolated Symbiodinium sp. assembly had 186 177 transcript elements with an average length of 1105 bases.<br><br>CONCLUSIONS: This contribution to coral transcriptome data provides a valuable resource for researchers studying the ontogeny of gene expression patterns within both the coral and its dinoflagellate symbiont.}, }
@article {pmid27482741, year = {2016}, author = {Bourne, DG and Morrow, KM and Webster, NS}, title = {Insights into the Coral Microbiome: Underpinning the Health and Resilience of Reef Ecosystems.}, journal = {Annual review of microbiology}, volume = {70}, number = {}, pages = {317-340}, doi = {10.1146/annurev-micro-102215-095440}, pmid = {27482741}, issn = {1545-3251}, mesh = {Animals ; Anthozoa/genetics/*microbiology/*physiology ; Bacteria/classification/genetics/growth &amp; development/*isolation &amp; purification ; Coral Reefs ; Ecosystem ; Fungi/classification/genetics/growth &amp; development/*isolation &amp; purification ; *Microbiota ; }, abstract = {Corals are fundamental ecosystem engineers, creating large, intricate reefs that support diverse and abundant marine life. At the core of a healthy coral animal is a dynamic relationship with microorganisms, including a mutually beneficial symbiosis with photosynthetic dinoflagellates (Symbiodinium spp.) and enduring partnerships with an array of bacterial, archaeal, fungal, protistan, and viral associates, collectively termed the coral holobiont. The combined genomes of this coral holobiont form a coral hologenome, and genomic interactions within the hologenome ultimately define the coral phenotype. Here we integrate contemporary scientific knowledge regarding the ecological, host-specific, and environmental forces shaping the diversity, specificity, and distribution of microbial symbionts within the coral holobiont, explore physiological pathways that contribute to holobiont fitness, and describe potential mechanisms for holobiont homeostasis. Understanding the role of the microbiome in coral resilience, acclimation, and environmental adaptation is a new frontier in reef science that will require large-scale collaborative research efforts.}, }
@article {pmid27468993, year = {2017}, author = {Bandyopadhyay, P and Bhuyan, SK and Yadava, PK and Varma, A and Tuteja, N}, title = {Emergence of plant and rhizospheric microbiota as stable interactomes.}, journal = {Protoplasma}, volume = {254}, number = {2}, pages = {617-626}, pmid = {27468993}, issn = {1615-6102}, mesh = {Ecosystem ; *Microbial Interactions ; *Microbiota ; Models, Biological ; Plants/*microbiology ; *Rhizosphere ; }, abstract = {The growing human population and depletion of resources have necessitated development of sustainable agriculture. Beneficial plant-microbe associations have been known for quite some time now. To maintain sustainability, one could show better reliance upon beneficial attributes of the rhizosphere microbiome. To harness the best agronomic traits, understanding the entire process of recruitment, establishment, and maintenance of microbiota as stable interactome within the rhizosphere is important. In this article, we highlight the process of recruitment and establishment of microbiota within rhizosphere. Further, we have discussed the interlinkages and the ability of multiple (microbial and plant) partners to interact with one another forming a stable plant holobiont system. Lastly, we address the possibility of exploring the knowledge gained from the holobiont system to tailor the rhizosphere microbiome for better productivity and maintenance of agroecosystems. The article provide new insights into the broad principles of stable plant-microbe interactions which could be useful for sustaining agriculture and food security.}, }
@article {pmid27446031, year = {2016}, author = {Egan, S and Gardiner, M}, title = {Microbial Dysbiosis: Rethinking Disease in Marine Ecosystems.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {991}, pmid = {27446031}, issn = {1664-302X}, abstract = {With growing environmental pressures placed on our marine habitats there is concern that the prevalence and severity of diseases affecting marine organisms will increase. Yet relative to terrestrial systems, we know little about the underlying causes of many of these diseases. Moreover, factors such as saprophytic colonizers and a lack of baseline data on healthy individuals make it difficult to accurately assess the role of specific microbial pathogens in disease states. Emerging evidence in the field of medicine suggests that a growing number of human diseases result from a microbiome imbalance (or dysbiosis), questioning the traditional view of a singular pathogenic agent. Here we discuss the possibility that many diseases seen in marine systems are, similarly, the result of microbial dysbiosis and the rise of opportunistic or polymicrobial infections. Thus, understanding and managing disease in the future will require us to also rethink definitions of disease and pathogenesis for marine systems. We suggest that a targeted, multidisciplinary approach that addresses the questions of microbial symbiosis in both healthy and diseased states, and at that the level of the holobiont, will be key to progress in this area.}, }
@article {pmid27418200, year = {2016}, author = {Mitter, B and Pfaffenbichler, N and Sessitsch, A}, title = {Plant-microbe partnerships in 2020.}, journal = {Microbial biotechnology}, volume = {9}, number = {5}, pages = {635-640}, pmid = {27418200}, issn = {1751-7915}, mesh = {Agriculture/*methods/trends ; *Ecosystem ; Plants/*microbiology ; }, abstract = {The plant holobiont comprises the plant and its associated microbiota, which interact with each other and determine holobiont functioning and plant performance. We have started to understand the complexity of the involved microorganisms and their interactions, however, we need more research on plant-microbiome interactions to understand holobiont functioning. By 2020 we expect that our knowledge on these interactions will have considerably increased facilitating crop management practices based on the interactions of the plant holobiont.}, }
@article {pmid27392086, year = {2017}, author = {Neave, MJ and Rachmawati, R and Xun, L and Michell, CT and Bourne, DG and Apprill, A and Voolstra, CR}, title = {Differential specificity between closely related corals and abundant Endozoicomonas endosymbionts across global scales.}, journal = {The ISME journal}, volume = {11}, number = {1}, pages = {186-200}, pmid = {27392086}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/classification/*microbiology ; Coral Reefs ; Gammaproteobacteria/classification/genetics/isolation &amp; purification/*physiology ; Genotype ; In Situ Hybridization, Fluorescence ; *Symbiosis ; }, abstract = {Reef-building corals are well regarded not only for their obligate association with endosymbiotic algae, but also with prokaryotic symbionts, the specificity of which remains elusive. To identify the central microbial symbionts of corals, their specificity across species and conservation over geographic regions, we sequenced partial SSU ribosomal RNA genes of Bacteria and Archaea from the common corals Stylophora pistillata and Pocillopora verrucosa across 28 reefs within seven major geographical regions. We demonstrate that both corals harbor Endozoicomonas bacteria as their prevalent symbiont. Importantly, catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with Endozoicomonas-specific probes confirmed their residence as large aggregations deep within coral tissues. Using fine-scale genotyping techniques and single-cell genomics, we demonstrate that P. verrucosa harbors the same Endozoicomonas, whereas S. pistillata associates with geographically distinct genotypes. This specificity may be shaped by the different reproductive strategies of the hosts, potentially uncovering a pattern of symbiont selection that is linked to life history. Spawning corals such as P. verrucosa acquire prokaryotes from the environment. In contrast, brooding corals such as S. pistillata release symbiont-packed planula larvae, which may explain a strong regional signature in their microbiome. Our work contributes to the factors underlying microbiome specificity and adds detail to coral holobiont functioning.}, }
@article {pmid27375564, year = {2016}, author = {Laffy, PW and Wood-Charlson, EM and Turaev, D and Weynberg, KD and Botté, ES and van Oppen, MJ and Webster, NS and Rattei, T}, title = {HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {822}, pmid = {27375564}, issn = {1664-302X}, abstract = {Abundant bioinformatics resources are available for the study of complex microbial metagenomes, however their utility in viral metagenomics is limited. HoloVir is a robust and flexible data analysis pipeline that provides an optimized and validated workflow for taxonomic and functional characterization of viral metagenomes derived from invertebrate holobionts. Simulated viral metagenomes comprising varying levels of viral diversity and abundance were used to determine the optimal assembly and gene prediction strategy, and multiple sequence assembly methods and gene prediction tools were tested in order to optimize our analysis workflow. HoloVir performs pairwise comparisons of single read and predicted gene datasets against the viral RefSeq database to assign taxonomy and additional comparison to phage-specific and cellular markers is undertaken to support the taxonomic assignments and identify potential cellular contamination. Broad functional classification of the predicted genes is provided by assignment of COG microbial functional category classifications using EggNOG and higher resolution functional analysis is achieved by searching for enrichment of specific Swiss-Prot keywords within the viral metagenome. Application of HoloVir to viral metagenomes from the coral Pocillopora damicornis and the sponge Rhopaloeides odorabile demonstrated that HoloVir provides a valuable tool to characterize holobiont viral communities across species, environments, or experiments.}, }
@article {pmid27264698, year = {2016}, author = {Ribes, M and Calvo, E and Movilla, J and Logares, R and Coma, R and Pelejero, C}, title = {Restructuring of the sponge microbiome favors tolerance to ocean acidification.}, journal = {Environmental microbiology reports}, volume = {8}, number = {4}, pages = {536-544}, doi = {10.1111/1758-2229.12430}, pmid = {27264698}, issn = {1758-2229}, mesh = {Adaptation, Physiological ; Animals ; Hydrogen-Ion Concentration ; *Microbiota ; Oceans and Seas ; Porifera/drug effects/*microbiology/*physiology ; Seawater/*chemistry ; Survival Analysis ; }, abstract = {Ocean acidification is increasing and affects many marine organisms. However, certain sponge species can withstand low-pH conditions. This may be related to their complex association with microbes. We hypothesized that species with greater microbial diversity may develop functional redundancy that could enable the holobiont to survive even if particular microbes are lost at low-pH conditions. We evaluated the effects of acidification on the growth and associated microbes of three ubiquitous Mediterranean sponges by exposing them to the present pH level and that predicted for the year 2100. We found marked differences among the species in the acquisition of new microbes, being high in Dysidea avara, moderate in Agelas oroides and null in Chondrosia reniformis; however, we did not observe variation in the overall microbiome abundance, richness or diversity. The relative abilities to alter the microbiomes contributes to survivorship in an OA scenario as demonstrated by lowered pH severely affecting the growth of C. reniformis, halving that of A. oroides, and unaffecting D. avara. Our results indicate that functional stability of the sponge holobiont to withstand future OA is species-specific and is linked to the species' ability to use horizontal transmission to modify the associated microbiome to adapt to environmental change.}, }
@article {pmid27234003, year = {2016}, author = {Cardini, U and van Hoytema, N and Bednarz, VN and Rix, L and Foster, RA and Al-Rshaidat, MM and Wild, C}, title = {Microbial dinitrogen fixation in coral holobionts exposed to thermal stress and bleaching.}, journal = {Environmental microbiology}, volume = {18}, number = {8}, pages = {2620-2633}, doi = {10.1111/1462-2920.13385}, pmid = {27234003}, issn = {1462-2920}, mesh = {Animals ; *Anthozoa/metabolism/microbiology/parasitology ; Bacteria/growth &amp; development/*metabolism ; Dinoflagellida/growth &amp; development/*metabolism ; Global Warming ; Heterotrophic Processes ; Hot Temperature ; Microbiota/physiology ; Nitrogen Fixation/*physiology ; Photosynthesis/physiology ; Stress, Physiological/physiology ; Symbiosis/physiology ; }, abstract = {Coral holobionts (i.e., coral-algal-prokaryote symbioses) exhibit dissimilar thermal sensitivities that may determine which coral species will adapt to global warming. Nonetheless, studies simultaneously investigating the effects of warming on all holobiont members are lacking. Here we show that exposure to increased temperature affects key physiological traits of all members (herein: animal host, zooxanthellae and diazotrophs) of both Stylophora pistillata and Acropora hemprichii during and after thermal stress. S. pistillata experienced severe loss of zooxanthellae (i.e., bleaching) with no net photosynthesis at the end of the experiment. Conversely, A. hemprichii was more resilient to thermal stress. Exposure to increased temperature (+ 6°C) resulted in a drastic increase in daylight dinitrogen (N2) fixation, particularly in A. hemprichii (threefold compared with controls). After the temperature was reduced again to in situ levels, diazotrophs exhibited a reversed diel pattern of activity, with increased N2 fixation rates recorded only in the dark, particularly in bleached S. pistillata (twofold compared to controls). Concurrently, both animal hosts, but particularly bleached S. pistillata, reduced both organic matter release and heterotrophic feeding on picoplankton. Our findings indicate that physiological plasticity by coral-associated diazotrophs may play an important role in determining the response of coral holobionts to ocean warming.}, }
@article {pmid27230747, year = {2016}, author = {Maistrenko, OM and Serga, SV and Vaiserman, AM and Kozeretska, IA}, title = {Longevity-modulating effects of symbiosis: insights from Drosophila-Wolbachia interaction.}, journal = {Biogerontology}, volume = {17}, number = {5-6}, pages = {785-803}, doi = {10.1007/s10522-016-9653-9}, pmid = {27230747}, issn = {1573-6768}, mesh = {Aging/*physiology ; Animals ; Bacterial Proteins/metabolism ; Drosophila/*microbiology/*physiology ; Drosophila Proteins/metabolism ; Longevity/*physiology ; Models, Biological ; Symbiosis/*physiology ; Wolbachia/*physiology ; }, abstract = {Microbial communities are known to significantly affect various fitness components and survival of their insect hosts, including Drosophila. The composition of symbiotic microbiota has been shown to change with the host's aging. It is unclear whether these changes are caused by the aging process or, vice versa, they affect the host's aging and longevity. Recent findings indicate that fitness and lifespan of Drosophila are affected by endosymbiotic bacteria Wolbachia. These effects, however, are inconsistent and have been reported both to extend and shorten longevity. The main molecular pathways underlying the lifespan-modulating effects of Wolbachia remain unclear, however insulin/insulin-like growth factor, immune deficiency, ecdysteroid synthesis and signaling and c-Jun N-terminal kinase pathways as well as heat shock protein synthesis and autophagy have been proposed to play a role. Here we revise the current evidence that elucidates the impact of Wolbachia endosymbionts on the aging processes in Drosophila.}, }
@article {pmid27213462, year = {2016}, author = {Miller, WB}, title = {Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow.}, journal = {Biology}, volume = {5}, number = {2}, pages = {}, pmid = {27213462}, issn = {2079-7737}, abstract = {As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. Immunological reactions support and reinforce self-recognition juxtaposed against external environmental stresses.}, }
@article {pmid27160191, year = {2016}, author = {Dirksen, P and Marsh, SA and Braker, I and Heitland, N and Wagner, S and Nakad, R and Mader, S and Petersen, C and Kowallik, V and Rosenstiel, P and Félix, MA and Schulenburg, H}, title = {The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model.}, journal = {BMC biology}, volume = {14}, number = {}, pages = {38}, pmid = {27160191}, issn = {1741-7007}, mesh = {Animals ; Antifungal Agents/metabolism ; Caenorhabditis elegans/growth &amp; development/*microbiology ; Life Cycle Stages ; *Microbiota ; *Models, Biological ; Phenotype ; Proteobacteria/isolation &amp; purification/metabolism ; Species Specificity ; }, abstract = {BACKGROUND: Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics.<br><br>RESULTS: Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo.<br><br>CONCLUSION: This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions.}, }
@article {pmid27148918, year = {2016}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Do microbiotas warm their hosts?.}, journal = {Gut microbes}, volume = {7}, number = {4}, pages = {283-285}, pmid = {27148918}, issn = {1949-0984}, mesh = {Animals ; Bacteria/genetics/isolation &amp; purification/*metabolism ; Energy Metabolism ; Gastrointestinal Tract/metabolism/*microbiology ; Hot Temperature ; Humans ; Insecta/microbiology ; *Microbiota ; Plants/microbiology ; }, abstract = {All natural animals and plants are holobionts, consisting of a host and abundant and diverse microbiota. During the last 20 years, numerous studies have shown that microbiotas participate in the ability of their hosts to survive and reproduce in a particular environment in many ways, including contributing to their morphology, development, behavior, physiology, resistance to disease and to their evolution. Here we posit another possible contribution of microbiotas to their hosts, which has been underexplored - the generation of heat. We estimate that microbial metabolism in the human gut, for example, produces 61 kcal/h, which corresponds to approximately 70% of the total heat production of an average person at rest.}, }
@article {pmid27148239, year = {2016}, author = {Aires, T and Serrão, EA and Engelen, AH}, title = {Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {559}, pmid = {27148239}, issn = {1664-302X}, abstract = {As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.}, }
@article {pmid27148067, year = {2016}, author = {Hawkins, TD and Hagemeyer, JC and Hoadley, KD and Marsh, AG and Warner, ME}, title = {Partitioning of Respiration in an Animal-Algal Symbiosis: Implications for Different Aerobic Capacity between Symbiodinium spp.}, journal = {Frontiers in physiology}, volume = {7}, number = {}, pages = {128}, pmid = {27148067}, issn = {1664-042X}, abstract = {Cnidarian-dinoflagellate symbioses are ecologically important and the subject of much investigation. However, our understanding of critical aspects of symbiosis physiology, such as the partitioning of total respiration between the host and symbiont, remains incomplete. Specifically, we know little about how the relationship between host and symbiont respiration varies between different holobionts (host-symbiont combinations). We applied molecular and biochemical techniques to investigate aerobic respiratory capacity in naturally symbiotic Exaiptasia pallida sea anemones, alongside animals infected with either homologous ITS2-type A4 Symbiodinium or a heterologous isolate of Symbiodinium minutum (ITS2-type B1). In naturally symbiotic anemones, host, symbiont, and total holobiont mitochondrial citrate synthase (CS) enzyme activity, but not host mitochondrial copy number, were reliable predictors of holobiont respiration. There was a positive association between symbiont density and host CS specific activity (mg protein(-1)), and a negative correlation between host- and symbiont CS specific activities. Notably, partitioning of total CS activity between host and symbiont in this natural E. pallida population was significantly different to the host/symbiont biomass ratio. In re-infected anemones, we found significant between-holobiont differences in the CS specific activity of the algal symbionts. Furthermore, the relationship between the partitioning of total CS activity and the host/symbiont biomass ratio differed between holobionts. These data have broad implications for our understanding of cnidarian-algal symbiosis. Specifically, the long-held assumption of equivalency between symbiont/host biomass and respiration ratios can result in significant overestimation of symbiont respiration and potentially erroneous conclusions regarding the percentage of carbon translocated to the host. The interspecific variability in symbiont aerobic capacity provides further evidence for distinct physiological differences that should be accounted for when studying diverse host-symbiont combinations.}, }
@article {pmid27103626, year = {2016}, author = {Webster, NS and Thomas, T}, title = {The Sponge Hologenome.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00135-16}, pmid = {27103626}, issn = {2150-7511}, mesh = {Animals ; Bacteria/classification/*genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; *Genome, Bacterial ; Microbial Consortia ; Porifera/*microbiology/physiology ; Symbiosis ; }, abstract = {A paradigm shift has recently transformed the field of biological science; molecular advances have revealed how fundamentally important microorganisms are to many aspects of a host's phenotype and evolution. In the process, an era of &quot;holobiont&quot; research has emerged to investigate the intricate network of interactions between a host and its symbiotic microbial consortia. Marine sponges are early-diverging metazoa known for hosting dense, specific, and often highly diverse microbial communities. Here we synthesize current thoughts about the environmental and evolutionary forces that influence the diversity, specificity, and distribution of microbial symbionts within the sponge holobiont, explore the physiological pathways that contribute to holobiont function, and describe the molecular mechanisms that underpin the establishment and maintenance of these symbiotic partnerships. The collective genomes of the sponge holobiont form the sponge hologenome, and we highlight how the forces that define a sponge's phenotype in fact act on the genomic interplay between the different components of the holobiont.}, }
@article {pmid27092120, year = {2016}, author = {Lawler, SN and Kellogg, CA and France, SC and Clostio, RW and Brooke, SD and Ross, SW}, title = {Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {458}, pmid = {27092120}, issn = {1664-302X}, abstract = {Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been analyzed to explore the diversity and abundance of their microbial associates. For this study, 23 samples of the family Anthothelidae were collected from Norfolk (n = 12) and Baltimore Canyons (n = 11) from the western Atlantic in August 2012 and May 2013. Genetic testing found that these samples comprised two Anthothela species (Anthothela grandiflora and Anthothela sp.) and Alcyonium grandiflorum. DNA was extracted and sequenced with primers targeting the V4-V5 variable region of the 16S rRNA gene using 454 pyrosequencing with GS FLX Titanium chemistry. Results demonstrated that the coral host was the primary driver of bacterial community composition. Al. grandiflorum, dominated by Alteromonadales and Pirellulales had much higher species richness, and a distinct bacterial community compared to Anthothela samples. Anthothela species (A. grandiflora and Anthothela sp.) had very similar bacterial communities, dominated by Oceanospirillales and Spirochaetes. Additional analysis of core-conserved bacteria at 90% sample coverage revealed genus level conservation across Anthothela samples. This core included unclassified Oceanospirillales, Kiloniellales, Campylobacterales, and genus Spirochaeta. Members of this core were previously recognized for their functional capabilities in nitrogen cycling and suggest the possibility of a nearly complete nitrogen cycle within Anthothela species. Overall, many of the bacterial associates identified in this study have the potential to contribute to the acquisition and cycling of nutrients within the coral holobiont.}, }
@article {pmid27084955, year = {2016}, author = {Collier, RJ and Casadevall, A}, title = {The Holobiont/Hologenome Concept Series.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00605-16}, doi = {10.1128/mBio.00605-16}, pmid = {27084955}, issn = {2150-7511}, mesh = {Editorial Policies ; *Genome ; Humans ; *Symbiosis ; }, }
@article {pmid27047481, year = {2016}, author = {Lee, ST and Davy, SK and Tang, SL and Kench, PS}, title = {Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {371}, pmid = {27047481}, issn = {1664-302X}, abstract = {It has been proposed that the chemical composition of a coral's mucus can influence the associated bacterial community. However, information on this topic is rare, and non-existent for corals that are under thermal stress. This study therefore compared the carbohydrate composition of mucus in the coral Acropora muricata when subjected to increasing thermal stress from 26 to 31°C, and determined whether this composition correlated with any changes in the bacterial community. Results showed that, at lower temperatures, the main components of mucus were N-acetyl glucosamine and C6 sugars, but these constituted a significantly lower proportion of the mucus in thermally stressed corals. The change in the mucus composition coincided with a shift from a γ-Proteobacteria- to a Verrucomicrobiae- and α-Proteobacteria-dominated community in the coral mucus. Bacteria in the class Cyanobacteria also started to become prominent in the mucus when the coral was thermally stressed. The increase in the relative abundance of the Verrucomicrobiae at higher temperature was strongly associated with a change in the proportion of fucose, glucose, and mannose in the mucus. Increase in the relative abundance of α-Proteobacteria were associated with GalNAc and glucose, while the drop in relative abundance of γ-Proteobacteria at high temperature coincided with changes in fucose and mannose. Cyanobacteria were highly associated with arabinose and xylose. Changes in mucus composition and the bacterial community in the mucus layer occurred at 29°C, which were prior to visual signs of coral bleaching at 31°C. A compositional change in the coral mucus, induced by thermal stress could therefore be a key factor leading to a shift in the associated bacterial community. This, in turn, has the potential to impact the physiological function of the coral holobiont.}, }
@article {pmid27039196, year = {2016}, author = {Shapira, M}, title = {Gut Microbiotas and Host Evolution: Scaling Up Symbiosis.}, journal = {Trends in ecology &amp; evolution}, volume = {31}, number = {7}, pages = {539-549}, doi = {10.1016/j.tree.2016.03.006}, pmid = {27039196}, issn = {1872-8383}, mesh = {Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Microbiota ; *Symbiosis ; }, abstract = {Our understanding of species evolution is undergoing restructuring. It is well accepted that host-symbiont coevolution is responsible for fundamental aspects of biology. However, the emerging importance of plant- and animal-associated microbiotas to their hosts suggests a scale of coevolutionary interactions many-fold greater than previously considered. This review builds on current understanding of symbionts and their contributions to host evolution to evaluate recent data demonstrating similar contributions of gut microbiotas. It further considers a multilayered model for microbiota to account for emerging themes in host-microbiota interactions. Drawing on the structure of bacterial genomes, this model distinguishes between a host-adapted core microbiota, and a flexible, environmentally modulated microbial pool, differing in constraints on their maintenance and in their contributions to host adaptation.}, }
@article {pmid27036743, year = {2015}, author = {Berlanga, M}, title = {Functional symbiosis and communication in microbial ecosystems. The case of wood-eating termites and cockroaches.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {18}, number = {3}, pages = {159-169}, doi = {10.2436/20.1501.01.246.}, pmid = {27036743}, issn = {1139-6709}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Biodiversity ; Cockroaches/metabolism/*microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Isoptera/metabolism/*microbiology ; Phylogeny ; Symbiosis ; Wood/metabolism/microbiology ; }, abstract = {Animal hosts typically have strong specificity for microbial symbionts and their functions. The symbiotic relationships have enhanced the limited metabolic networks of most eukaryotes by contributing several prokaryotic metabolic capabilities, such as methanogenesis, chemolithoautotrophy, nitrogen assimilation, etc. This review will examine the characteristics that determine bacterial &quot;fidelity&quot; to certain groups of animals (e.g., xylophagous insects, such as termites and cockroaches) over generations and throughout evolution. The hindgut bacteria of wood-feeding termites and cockroaches belong to several phyla, including Proteobacteria, especially Deltaproteobacteria, Bacteroidetes, Firmicutes, Actinomycetes, Spirochetes, Verrucomicrobia, and Actinobacteria, as detected by 16S rRNA. Termites effectively feed on many types of lignocelluloses assisted by their gut microbial symbionts. Although the community structures differ between the hosts (termites and cockroaches), with changes in the relative abundances of particular bacterial taxa, the composition of the bacterial community could reflect at least in part the host evolution in that the microbiota may derive from the microbiota of a common ancestor. Therefore, factors other than host phylogeny, such as diet could have had strong influence in shaping the bacterial community structure.}, }
@article {pmid27034285, year = {2016}, author = {Douglas, AE and Werren, JH}, title = {Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e02099}, pmid = {27034285}, issn = {2150-7511}, mesh = {Animals ; Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; *Symbiosis ; }, abstract = {The advent of relatively inexpensive tools for characterizing microbial communities has led to an explosion of research exploring the diversity, ecology, and evolution of microbe-host systems. Some now question whether existing conceptual frameworks are adequate to explain microbe-host systems. One popular paradigm is the &quot;holobiont-hologenome,&quot; which argues that a host and its microbiome evolve as a single cooperative unit of selection (i.e., a superorganism). We argue that the hologenome is based on overly restrictive assumptions which render it an approach of little research utility. A host plus its microbiome is more effectively viewed as an ecological community of organisms that encompasses a broad range of interactions (parasitic to mutualistic), patterns of transmission (horizontal to vertical), and levels of fidelity among partners. The hologenome requires high partner fidelity if it is to evolve as a unit. However, even when this is achieved by particular host-microbe pairs, it is unlikely to hold for the entire host microbiome, and therefore the community is unlikely to evolve as a hologenome. Both mutualistic and antagonistic (fitness conflict) evolution can occur among constituent members of the community, not just adaptations at the &quot;hologenome&quot; level, and there is abundant empirical evidence for such divergence of selective interests among members of host-microbiome communities. We believe that the concepts and methods of ecology, genetics, and evolutionary biology will continue to provide a well-grounded intellectual framework for researching host-microbiome communities, without recourse to the limiting assumption that selection acts predominantly at the holobiont level.}, }
@article {pmid27034284, year = {2016}, author = {Shropshire, JD and Bordenstein, SR}, title = {Speciation by Symbiosis: the Microbiome and Behavior.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e01785}, pmid = {27034284}, issn = {2150-7511}, mesh = {Animals ; Behavior ; Behavior, Animal ; *Genetic Speciation ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {Species are fundamental units of comparison in biology. The newly discovered importance and ubiquity of host-associated microorganisms are now stimulating work on the roles that microbes can play in animal speciation. We previously synthesized the literature and advanced concepts of speciation by symbiosis with notable attention to hybrid sterility and lethality. Here, we review recent studies and relevant data on microbes as players in host behavior and behavioral isolation, emphasizing the patterns seen in these analyses and highlighting areas worthy of additional exploration. We conclude that the role of microbial symbionts in behavior and speciation is gaining exciting traction and that the holobiont and hologenome concepts afford an evolving intellectual framework to promote research and intellectual exchange between disciplines such as behavior, microbiology, genetics, symbiosis, and speciation. Given the increasing centrality of microbiology in macroscopic life, microbial symbiosis is arguably the most neglected aspect of animal and plant speciation, and studying it should yield a better understanding of the origin of species.}, }
@article {pmid27034283, year = {2016}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Microbes Drive Evolution of Animals and Plants: the Hologenome Concept.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e01395}, pmid = {27034283}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; Recombination, Genetic ; Selection, Genetic ; *Symbiosis ; }, abstract = {The hologenome concept of evolution postulates that the holobiont (host plus symbionts) with its hologenome (host genome plus microbiome) is a level of selection in evolution. Multicellular organisms can no longer be considered individuals by the classical definitions of the term. Every natural animal and plant is a holobiont consisting of the host and diverse symbiotic microbes and viruses. Microbial symbionts can be transmitted from parent to offspring by a variety of methods, including via cytoplasmic inheritance, coprophagy, direct contact during and after birth, and the environment. A large number of studies have demonstrated that these symbionts contribute to the anatomy, physiology, development, innate and adaptive immunity, and behavior and finally also to genetic variation and to the origin and evolution of species. Acquisition of microbes and microbial genes is a powerful mechanism for driving the evolution of complexity. Evolution proceeds both via cooperation and competition, working in parallel.}, }
@article {pmid27034282, year = {2016}, author = {McFall-Ngai, M}, title = {Introduction to the Hologenome Special Series.}, journal = {mBio}, volume = {7}, number = {2}, pages = {e00371}, doi = {10.1128/mBio.00371-16}, pmid = {27034282}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animals ; *Biological Evolution ; *Biota ; Humans ; *Microbiota ; Plants ; Selection, Genetic ; *Symbiosis ; }, }
@article {pmid27019410, year = {2016}, author = {Haichar, FEZ and Heulin, T and Guyonnet, JP and Achouak, W}, title = {Stable isotope probing of carbon flow in the plant holobiont.}, journal = {Current opinion in biotechnology}, volume = {41}, number = {}, pages = {9-13}, doi = {10.1016/j.copbio.2016.02.023}, pmid = {27019410}, issn = {1879-0429}, mesh = {Carbon Isotopes/*analysis ; Isotope Labeling/*methods ; Plant Roots/*metabolism/microbiology ; Plants/*metabolism/microbiology ; *Soil Microbiology ; }, abstract = {Microbial communities associated with a plant host, constituting a holobiont, affect the physiology and growth of the plant via metabolites that are mainly derived from their photosynthates. The structure and function of active microbial communities that assimilate root exudates can be tracked by using stable isotope probing (SIP) approaches. This article reviews results from ongoing SIP research in plant-microbe interactions, with a specific focus on investigating the fate of fresh and recalcitrant carbon in the rhizosphere with 13C enriched-root exudates, in addition to identifying key players in carbon cycling. Finally, we discuss new SIP applications that have the potential to identify novel enzymes implicated in rhizoremediation or plant genes dedicated to root exudation by combining SIP approaches and genome wide associations studies.}, }
@article {pmid27014194, year = {2016}, author = {Ding, JY and Shiu, JH and Chen, WM and Chiang, YR and Tang, SL}, title = {Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {251}, pmid = {27014194}, issn = {1664-302X}, abstract = {The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.}, }
@article {pmid26979110, year = {2016}, author = {Greer, R and Dong, X and Morgun, A and Shulzhenko, N}, title = {Investigating a holobiont: Microbiota perturbations and transkingdom networks.}, journal = {Gut microbes}, volume = {7}, number = {2}, pages = {126-135}, pmid = {26979110}, issn = {1949-0984}, support = {R01 DK103761/DK/NIDDK NIH HHS/United States ; U01 AI109695/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics/metabolism ; Bacterial Infections/*microbiology ; Computational Biology ; Host-Pathogen Interactions/*drug effects ; Humans ; Microbiota/*drug effects ; }, abstract = {The scientific community has recently come to appreciate that, rather than existing as independent organisms, multicellular hosts and their microbiota comprise a complex evolving superorganism or metaorganism, termed a holobiont. This point of view leads to a re-evaluation of our understanding of different physiological processes and diseases. In this paper we focus on experimental and computational approaches which, when combined in one study, allowed us to dissect mechanisms (traditionally named host-microbiota interactions) regulating holobiont physiology. Specifically, we discuss several approaches for microbiota perturbation, such as use of antibiotics and germ-free animals, including advantages and potential caveats of their usage. We briefly review computational approaches to characterize the microbiota and, more importantly, methods to infer specific components of microbiota (such as microbes or their genes) affecting host functions. One such approach called transkingdom network analysis has been recently developed and applied in our study. (1) Finally, we also discuss common methods used to validate the computational predictions of host-microbiota interactions using in vitro and in vivo experimental systems.}, }
@article {pmid26953605, year = {2016}, author = {Glasl, B and Herndl, GJ and Frade, PR}, title = {The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance.}, journal = {The ISME journal}, volume = {10}, number = {9}, pages = {2280-2292}, pmid = {26953605}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; *Biodiversity ; Coral Reefs ; DNA, Ribosomal/chemistry/genetics ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.}, }
@article {pmid26926518, year = {2016}, author = {Ryu, T and Seridi, L and Moitinho-Silva, L and Oates, M and Liew, YJ and Mavromatis, C and Wang, X and Haywood, A and Lafi, FF and Kupresanin, M and Sougrat, R and Alzahrani, MA and Giles, E and Ghosheh, Y and Schunter, C and Baumgarten, S and Berumen, ML and Gao, X and Aranda, M and Foret, S and Gough, J and Voolstra, CR and Hentschel, U and Ravasi, T}, title = {Hologenome analysis of two marine sponges with different microbiomes.}, journal = {BMC genomics}, volume = {17}, number = {}, pages = {158}, pmid = {26926518}, issn = {1471-2164}, support = {BB/G022771/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Genome ; High-Throughput Nucleotide Sequencing ; Microbiota/*genetics ; Models, Genetic ; Molecular Sequence Annotation ; Porifera/*genetics/*microbiology ; Receptors, Scavenger/genetics ; Sequence Analysis, DNA ; Symbiosis ; Transcriptome ; }, abstract = {BACKGROUND: Sponges (Porifera) harbor distinct microbial consortia within their mesohyl interior. We herein analysed the hologenomes of Stylissa carteri and Xestospongia testudinaria, which notably differ in their microbiome content.<br><br>RESULTS: Our analysis revealed that S. carteri has an expanded repertoire of immunological domains, specifically Scavenger Receptor Cysteine-Rich (SRCR)-like domains, compared to X. testudinaria. On the microbial side, metatranscriptome analyses revealed an overrepresentation of potential symbiosis-related domains in X. testudinaria.<br><br>CONCLUSIONS: Our findings provide genomic insights into the molecular mechanisms underlying host-symbiont coevolution and may serve as a roadmap for future hologenome analyses.}, }
@article {pmid26925036, year = {2016}, author = {Zozaya-Valdés, E and Roth-Schulze, AJ and Thomas, T}, title = {Effects of Temperature Stress and Aquarium Conditions on the Red Macroalga Delisea pulchra and its Associated Microbial Community.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {161}, pmid = {26925036}, issn = {1664-302X}, abstract = {In recent years, there has been an increase in the rate and severity of diseases affecting habitat-forming marine organisms, such as corals, sponges, and macroalgae. Delisea pulchra is a temperate red macroalga that suffers from a bleaching disease that is more frequent during summer, when seawater temperatures are elevated and the alga's chemical defense is weakened. A bacterial cause for the disease is implied by previous studies showing that some isolated strains can cause bleaching in vitro and that host-associated microbial communities are distinct between diseased and healthy individuals. However, nothing is known about the successional events in the microbial community that occur during the development of the disease. To study this aspect in the future, we aimed here to develop an experimental setup to study the bleaching disease in a controllable aquarium environment. Application of a temperature stress (up to 27°C) did not cause a clear and consistent pattern of bleaching, suggesting that temperature alone might not be the only or main factor to cause the disease. The results also showed that the aquarium conditions alone are sufficient to produce bleaching symptoms. Microbial community analysis based on 16S rRNA gene fingerprinting and sequencing showed significant changes after 15 days in the aquarium, indicating that the native microbial associates of D. pulchra are not stably maintained. Microbial taxa that were enriched in the aquarium-held D. pulchra thalli, however, did not match on a taxonomic level those that have been found to be enriched in natural bleaching events. Together our observations indicate that environmental factors, other than the ones investigated here, might drive the bleaching disease in D. pulchra and that the aquarium conditions have substantial impact on the alga-associated microbiome.}, }
@article {pmid26904096, year = {2016}, author = {Negri, I and Jablonka, E}, title = {Editorial: Epigenetics as a Deep Intimate Dialogue between Host and Symbionts.}, journal = {Frontiers in genetics}, volume = {7}, number = {}, pages = {7}, pmid = {26904096}, issn = {1664-8021}, }
@article {pmid26904020, year = {2016}, author = {Fonseca-García, C and Coleman-Derr, D and Garrido, E and Visel, A and Tringe, SG and Partida-Martínez, LP}, title = {The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity.}, journal = {Frontiers in microbiology}, volume = {7}, number = {}, pages = {150}, pmid = {26904020}, issn = {1664-302X}, abstract = {Cactaceae represents one of the most species-rich families of succulent plants native to arid and semi-arid ecosystems, yet the associations Cacti establish with microorganisms and the rules governing microbial community assembly remain poorly understood. We analyzed the composition, diversity, and factors influencing above- and below-ground bacterial, archaeal, and fungal communities associated with two native and sympatric Cacti species: Myrtillocactus geometrizans and Opuntia robusta. Phylogenetic profiling showed that the composition and assembly of microbial communities associated with Cacti were primarily influenced by the plant compartment; plant species, site, and season played only a minor role. Remarkably, bacterial, and archaeal diversity was higher in the phyllosphere than in the rhizosphere of Cacti, while the opposite was true for fungi. Semi-arid soils exhibited the highest levels of microbial diversity whereas the stem endosphere the lowest. Despite their taxonomic distance, M. geometrizans and O. robusta shared most microbial taxa in all analyzed compartments. Influence of the plant host did only play a larger role in the fungal communities of the stem endosphere. These results suggest that fungi establish specific interactions with their host plant inside the stem, whereas microbial communities in the other plant compartments may play similar functional roles in these two species. Biochemical and molecular characterization of seed-borne bacteria of Cacti supports the idea that these microbial symbionts may be vertically inherited and could promote plant growth and drought tolerance for the fitness of the Cacti holobiont. We envision this knowledge will help improve and sustain agriculture in arid and semi-arid regions of the world.}, }
@article {pmid26865302, year = {2016}, author = {Gardner, SG and Nielsen, DA and Laczka, O and Shimmon, R and Beltran, VH and Ralph, PJ and Petrou, K}, title = {Dimethylsulfoniopropionate, superoxide dismutase and glutathione as stress response indicators in three corals under short-term hyposalinity stress.}, journal = {Proceedings. Biological sciences}, volume = {283}, number = {1824}, pages = {}, pmid = {26865302}, issn = {1471-2954}, mesh = {Animals ; Anthozoa/*physiology ; Dinoflagellida/physiology ; Glutathione/*metabolism ; *Salinity ; Species Specificity ; Stress, Physiological ; Sulfonium Compounds/*metabolism ; Superoxide Dismutase/*metabolism ; Symbiosis ; }, abstract = {Corals are among the most active producers of dimethylsulfoniopropionate (DMSP), a key molecule in marine sulfur cycling, yet the specific physiological role of DMSP in corals remains elusive. Here, we examine the oxidative stress response of three coral species (Acropora millepora, Stylophora pistillata and Pocillopora damicornis) and explore the antioxidant role of DMSP and its breakdown products under short-term hyposalinity stress. Symbiont photosynthetic activity declined with hyposalinity exposure in all three reef-building corals. This corresponded with the upregulation of superoxide dismutase and glutathione in the animal host of all three species. For the symbiont component, there were differences in antioxidant regulation, demonstrating differential responses to oxidative stress between the Symbiodinium subclades. Of the three coral species investigated, only A. millepora provided any evidence of the role of DMSP in the oxidative stress response. Our study reveals variability in antioxidant regulation in corals and highlights the influence life-history traits, and the subcladal differences can have on coral physiology. Our data expand on the emerging understanding of the role of DMSP in coral stress regulation and emphasizes the importance of exploring both the host and symbiont responses for defining the threshold of the coral holobiont to hyposalinity stress.}, }
@article {pmid26843939, year = {2016}, author = {Rouzé, H and Lecellier, G and Saulnier, D and Berteaux-Lecellier, V}, title = {Symbiodinium clades A and D differentially predispose Acropora cytherea to disease and Vibrio spp. colonization.}, journal = {Ecology and evolution}, volume = {6}, number = {2}, pages = {560-572}, pmid = {26843939}, issn = {2045-7758}, abstract = {Coral disease outbreaks have increased over the last three decades, but their causal agents remain mostly unclear (e.g., bacteria, viruses, fungi, protists). This study details a 14-month-long survey of coral colonies in which observations of the development of disease was observed in nearly half of the sampled colonies. A bimonthly qPCR method was used to quantitatively and qualitatively evaluate Symbiodinium assemblages of tagged colonies, and to detect the presence of Vibrio spp. Firstly, our data showed that predisposition to disease development in general, and, more specifically, infection by Vibrio spp. in Acropora cytherea depended on which clades of Symbiodinium were harbored. In both cases, harboring clade D rather than A was beneficial to the coral host. Secondly, the detection of Vibrio spp. in only colonies that developed disease strongly suggests opportunistic traits of the bacteria. Finally, even if sporadic cases of switching and probably shuffling were observed, this long-term survey does not suggest specific-clade recruitment in response to stressors. Altogether, our results demonstrate that the fitness of the coral holobiont depends on its initial consortium of Symbiodinium, which is distinct among colonies, rather than a temporary adaptation achieved through acquiring different Symbiodinium clades.}, }
@article {pmid26840035, year = {2016}, author = {Röthig, T and Ochsenkühn, MA and Roik, A and van der Merwe, R and Voolstra, CR}, title = {Long-term salinity tolerance is accompanied by major restructuring of the coral bacterial microbiome.}, journal = {Molecular ecology}, volume = {25}, number = {6}, pages = {1308-1323}, pmid = {26840035}, issn = {1365-294X}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/*microbiology/*physiology ; Bacteria/classification ; DNA, Bacterial/genetics ; *Microbiota ; Photosynthesis ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Salt Tolerance ; Symbiosis ; }, abstract = {Scleractinian corals are assumed to be stenohaline osmoconformers, although they are frequently subjected to variations in seawater salinity due to precipitation, freshwater run-off and other processes. Observed responses to altered salinity levels include differences in photosynthetic performance, respiration and increased bleaching and mortality of the coral host and its algal symbiont, but a study looking at bacterial community changes is lacking. Here, we exposed the coral Fungia granulosa to strongly increased salinity levels in short- and long-term experiments to disentangle temporal and compartment effects of the coral holobiont (i.e. coral host, symbiotic algae and associated bacteria). Our results show a significant reduction in calcification and photosynthesis, but a stable microbiome after short-term exposure to high-salinity levels. By comparison, long-term exposure yielded unchanged photosynthesis levels and visually healthy coral colonies indicating long-term acclimation to high-salinity levels that were accompanied by a major coral microbiome restructuring. Importantly, a bacterium in the family Rhodobacteraceae was succeeded by Pseudomonas veronii as the numerically most abundant taxon. Further, taxonomy-based functional profiling indicates a shift in the bacterial community towards increased osmolyte production, sulphur oxidation and nitrogen fixation. Our study highlights that bacterial community composition in corals can change within days to weeks under altered environmental conditions, where shifts in the microbiome may enable adjustment of the coral to a more advantageous holobiont composition.}, }
@article {pmid26818718, year = {2016}, author = {Dessaux, Y and Grandclément, C and Faure, D}, title = {Engineering the Rhizosphere.}, journal = {Trends in plant science}, volume = {21}, number = {3}, pages = {266-278}, doi = {10.1016/j.tplants.2016.01.002}, pmid = {26818718}, issn = {1878-4372}, mesh = {Botany/*methods ; Microbiota ; Plants/microbiology ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {All components of the rhizosphere can be engineered to promote plant health and growth, two features that strongly depend upon the interactions of living organisms with their environment. This review describes the progress in plant and microbial molecular genetics and ecology that has led to a wealth of potential applications. Recent efforts especially deal with the plant defense machinery that is instrumental in engineering plant resistance to biotic stresses. Another approach involves microbial population engineering rather than single strain engineering. More generally, the plants (and the associated microbes) are no longer seen as 'individual' but rather as a holobiont, in other words a unit of selection in evolution, a concept that holds great promise for future plant breeding programs.}, }
@article {pmid26788878, year = {2016}, author = {Agler, MT and Ruhe, J and Kroll, S and Morhenn, C and Kim, ST and Weigel, D and Kemen, EM}, title = {Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation.}, journal = {PLoS biology}, volume = {14}, number = {1}, pages = {e1002352}, pmid = {26788878}, issn = {1545-7885}, mesh = {Arabidopsis/genetics/*microbiology ; Bacteria ; Basidiomycota/physiology ; Endophytes/physiology ; *Microbiota ; Oomycetes/physiology ; }, abstract = {Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe-microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe-microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial &quot;hubs,&quot; are strongly interconnected and have a severe effect on communities. By documenting these microbe-microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on &quot;hub&quot; microbes, which, via microbe-microbe interactions, transmit the effects to the microbial community. We analyzed two &quot;hub&quot; microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial &quot;hubs&quot; and their importance in phyllosphere microbiome structuring has crucial implications for plant-pathogen and microbe-microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via &quot;hub&quot; microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome &quot;keystone&quot; pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes.}, }
@article {pmid26779145, year = {2015}, author = {Lachnit, T and Thomas, T and Steinberg, P}, title = {Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1489}, pmid = {26779145}, issn = {1664-302X}, abstract = {Marine seaweeds are holobionts comprised of the macroalgal hosts and their associated microbiota. While the composition of the bacterial component of seaweed microbiomes is increasingly studied, almost nothing is known about the presence, diversity and composition of viruses in macroalgae in situ. In this study, we characterize for the first time the viruses associated with a red macroalga, Delisea pulchra. Using transmission electron microscopy we identified diverse morphotypes of virus-like particles in D. pulchra ranging from icosahedral to bacilliform to coiled pleomorphic as well as bacteriophages. Virome sequencing revealed the presence of a diverse group of dsRNA viruses affiliated to the genus Totivirus, known to infect plant pathogenic fungi. We further identified a ssRNA virus belonging to the order Picornavirales with a close phylogenetic relationship to a pathogenic virus infecting marine diatoms. The results of this study shed light on a so far neglected part of the seaweed holobiont, and suggest that some of the identified viruses may be possible pathogens for a host that is already known to be significantly impacted by bacterial infections.}, }
@article {pmid26763678, year = {2016}, author = {Hacquard, S}, title = {Disentangling the factors shaping microbiota composition across the plant holobiont.}, journal = {The New phytologist}, volume = {209}, number = {2}, pages = {454-457}, doi = {10.1111/nph.13760}, pmid = {26763678}, issn = {1469-8137}, mesh = {Bacteria/genetics ; *Microbiota ; *Plants ; RNA, Ribosomal, 16S ; Rhizosphere ; Soil Microbiology ; }, }
@article {pmid26759710, year = {2016}, author = {Lu, HL and Price, DR and Wikramanayake, A and Chang, CC and Wilson, AC}, title = {Ontogenetic differences in localization of glutamine transporter ApGLNT1 in the pea aphid demonstrate that mechanisms of host/symbiont integration are not similar in the maternal versus embryonic bacteriome.}, journal = {EvoDevo}, volume = {7}, number = {}, pages = {1}, pmid = {26759710}, issn = {2041-9139}, abstract = {BACKGROUND: Obligate intracellular symbionts of insects are metabolically and developmentally integrated with their hosts. Typically, reproduction fails in many insect nutritional endosymbioses when host insects are cured of their bacterial symbionts, and yet remarkably little is known about the processes that developmentally integrate host and symbiont. Here in the best studied insect obligate intracellular symbiosis, that of the pea aphid, Acyrthosiphon pisum, with the gammaproteobacterium Buchnera aphidicola, we tracked the expression and localization of amino acid transporter ApGLNT1 gene products during asexual embryogenesis. Recently being characterized as a glutamine transporter, ApGLNT1 has been proposed to be a key regulator of amino acid biosynthesis in A. pisum bacteriocytes. To determine when this important mediator of the symbiosis becomes expressed in aphid embryonic bacteriocytes, we applied whole-mount in situ hybridization and fluorescent immunostaining with a specific anti-ApGLNT1 antibody to detect the temporal and spatial expression of ApGLNT1 gene products during asexual embryogenesis.<br><br>RESULTS: During embryogenesis, ApGLNT1 mRNA and protein localize to the follicular epithelium that surrounds parthenogenetic viviparous embryos, where we speculate that it functions to supply developing embryos with glutamine from maternal hemolymph. Unexpectedly, in the embryonic bacteriome ApGLNT1 protein does not localize to the membrane of bacteriocytes, a pattern that leads us to conclude that the regulation of amino acid metabolism in the embryonic bacteriome mechanistically differs from that in the maternal bacteriome. Paralleling our earlier report of punctate cytoplasmic localization of ApGLNT1 in maternal bacteriocytes, we find ApGLNT1 protein localizing as cytoplasmic puncta throughout development in association with Buchnera.<br><br>CONCLUSIONS: Our work that documents ontogenetic shifts in the localization of ApGLNT1 protein in the host bacteriome demonstrates that maternal and embryonic bacteriomes are not equivalent. Significantly, the persistent punctate cytoplasmic localization of ApGLNT1 in association with Buchnera in embryos prior to bacteriocyte formation and later in both embryonic and maternal bacteriomes suggests that ApGLNT1 plays multiple roles in this symbiosis, roles that include amino acid transport and possibly nutrient sensing.}, }
@article {pmid26749251, year = {2016}, author = {Moore, A}, title = {Getting fat from an inflamed relationship? The revenge of the holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {2}, pages = {119}, doi = {10.1002/bies.201600001}, pmid = {26749251}, issn = {1521-1878}, mesh = {Anti-Bacterial Agents/adverse effects ; Food Additives/adverse effects ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/*etiology/*microbiology ; Intestines/microbiology ; Obesity/*etiology/*microbiology ; }, }
@article {pmid26739062, year = {2016}, author = {Poutahidis, T and Erdman, SE}, title = {Commensal bacteria modulate the tumor microenvironment.}, journal = {Cancer letters}, volume = {380}, number = {1}, pages = {356-358}, pmid = {26739062}, issn = {1872-7980}, support = {R01 CA108854/CA/NCI NIH HHS/United States ; U01 CA164337/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/immunology/metabolism/*pathogenicity ; *Cell Transformation, Neoplastic/immunology/metabolism/pathology ; *Gastrointestinal Microbiome ; Host-Pathogen Interactions ; Humans ; Neoplasms/immunology/metabolism/*microbiology/pathology ; Risk Factors ; Signal Transduction ; Symbiosis ; *Tumor Microenvironment ; }, abstract = {It has been recently shown that gut microbes modulate whole host immune and hormonal factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. This raises the possibility that the tumor microenvironment interacts with broader systemic microbial-immune networks. These accumulated findings suggest novel therapeutic opportunities for holobiont engineering in emerging tumor microenvironments.}, }
@article {pmid26734000, year = {2015}, author = {Martin, M and Barbeyron, T and Martin, R and Portetelle, D and Michel, G and Vandenbol, M}, title = {The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1487}, pmid = {26734000}, issn = {1664-302X}, abstract = {Bacteria degrading algal polysaccharides are key players in the global carbon cycle and in algal biomass recycling. Yet the water column, which has been studied largely by metagenomic approaches, is poor in such bacteria and their algal-polysaccharide-degrading enzymes. Even more surprisingly, the few published studies on seaweed-associated microbiomes have revealed low abundances of such bacteria and their specific enzymes. However, as macroalgal cell-wall polysaccharides do not accumulate in nature, these bacteria and their unique polysaccharidases must not be that uncommon. We, therefore, looked at the polysaccharide-degrading activity of the cultivable bacterial subpopulation associated with Ascophyllum nodosum. From A. nodosum triplicates, 324 bacteria were isolated and taxonomically identified. Out of these isolates, 78 (~25%) were found to act on at least one tested algal polysaccharide (agar, ι- or κ-carrageenan, or alginate). The isolates &quot;active&quot; on algal-polysaccharides belong to 11 genera: Cellulophaga, Maribacter, Algibacter, and Zobellia in the class Flavobacteriia (41) and Pseudoalteromonas, Vibrio, Cobetia, Shewanella, Colwellia, Marinomonas, and Paraglaceciola in the class Gammaproteobacteria (37). A major part represents likely novel species. Different proportions of bacterial phyla and classes were observed between the isolated cultivable subpopulation and the total microbial community previously identified on other brown algae. Here, Bacteroidetes and Gammaproteobacteria were found to be the most abundant and some phyla (as Planctomycetes and Cyanobacteria) frequently encountered on brown algae weren't identified. At a lower taxonomic level, twelve genera, well-known to be associated with algae (with the exception for Colwellia), were consistently found on all three A. nosodum samples. Even more interesting, 9 of the 11 above mentioned genera containing polysaccharolytic isolates were predominant in this common core. The cultivable fraction of the bacterial community associated with A. nodosum is, thus, significantly enriched in macroalgal-polysaccharide-degrading bacteria and these bacteria seem important for the seaweed holobiont even though they are under-represented in alga-associated microbiome studies.}, }
@article {pmid26696324, year = {2016}, author = {Lema, KA and Clode, PL and Kilburn, MR and Thornton, R and Willis, BL and Bourne, DG}, title = {Imaging the uptake of nitrogen-fixing bacteria into larvae of the coral Acropora millepora.}, journal = {The ISME journal}, volume = {10}, number = {7}, pages = {1804-1808}, pmid = {26696324}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; In Situ Hybridization, Fluorescence ; Larva ; Nitrogen/*metabolism ; Nitrogen Fixation ; Nitrogen-Fixing Bacteria/*metabolism ; }, abstract = {Diazotrophic bacteria are instrumental in generating biologically usable forms of nitrogen by converting abundant dinitrogen gas (N2) into available forms, such as ammonium. Although nitrogen is crucial for coral growth, direct observation of associations between diazotrophs and corals has previously been elusive. We applied fluorescence in situ hybridization (FISH) and nanoscale secondary ion mass spectrometry to observe the uptake of (15)N-enriched diazotrophic Vibrio sp. isolated from Acropora millepora into conspecific coral larvae. Incorporation of Vibrio sp. cells was observed in coral larvae after 4-h incubation with enriched bacteria. Uptake was restricted to the aboral epidermis of larvae, where Vibrio cells clustered in elongated aggregations. Other bacterial associates were also observed in epidermal areas in FISH analyses. Although the fate and role of these bacteria requires additional investigation, this study describes a powerful approach to further explore cell associations and nutritional pathways in the early life stages of the coral holobiont.}, }
@article {pmid26659364, year = {2015}, author = {Kemp, DW and Rivers, AR and Kemp, KM and Lipp, EK and Porter, JW and Wares, JP}, title = {Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.}, journal = {PloS one}, volume = {10}, number = {12}, pages = {e0143790}, pmid = {26659364}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/genetics/growth &amp; development/*isolation &amp; purification ; Biodiversity ; Coral Reefs ; Florida ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sequence Analysis, RNA ; }, abstract = {Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance), underside (low irradiance), and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations.}, }
@article {pmid26658023, year = {2015}, author = {Fragoso Ados Santos, H and Duarte, GA and Rachid, CT and Chaloub, RM and Calderon, EN and Marangoni, LF and Bianchini, A and Nudi, AH and do Carmo, FL and van Elsas, JD and Rosado, AS and Castro, CB and Peixoto, RS}, title = {Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {18268}, pmid = {26658023}, issn = {2045-2322}, mesh = {Bacteria/classification/genetics/metabolism ; *Biodegradation, Environmental ; *Biotransformation ; *Coral Reefs ; Hydrocarbons/metabolism ; *Microbiota ; *Petroleum Pollution ; Photochemical Processes ; *Probiotics ; Water Pollutants, Chemical ; }, abstract = {Several anthropogenic factors, including contamination by oil spills, constitute a threat to coral reef health. Current methodologies to remediate polluted marine environments are based on the use of chemical dispersants; however, these can be toxic to the coral holobiont. In this study, a probiotic bacterial consortium was produced from the coral Mussismilia harttii and was trained to degrade water-soluble oil fractions (WSFs). Additionally, we assessed the effect of WSFs on the health of M. harttii in tanks and evaluated the bacterial consortium as a bioremediation agent. The consortium was responsible for the highly efficient degradation of petroleum hydrocarbons, and it minimised the effects of WSFs on coral health, as indicated by raised photosynthetic efficiencies. Moreover, the impact of WSFs on the coral microbiome was diminished by the introduced bacterial consortium. Following introduction, the bacterial consortium thus had a dual function, i.e promoting oil WSF degradation and improving coral health with its probiotic features.}, }
@article {pmid26640464, year = {2015}, author = {Wong, AC and Holmes, A and Ponton, F and Lihoreau, M and Wilson, K and Raubenheimer, D and Simpson, SJ}, title = {Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1359}, pmid = {26640464}, issn = {1664-302X}, abstract = {The role of microbes as a part of animal systems has historically been an under-appreciated aspect of animal life histories. Recently, evidence has emerged that microbes have wide-ranging influences on animal behavior. Elucidating the complex relationships between host-microbe interactions and behavior requires an expanded ecological perspective, involving the host, the microbiome and the environment; which, in combination, is termed the holobiont. We begin by seeking insights from the literature on host-parasite interactions, then expand to consider networks of interactions between members of the microbial community. A central aspect of the environment is host nutrition. We describe how interactions between the nutrient environment, the metabolic and behavioral responses of the host and the microbiome can be studied using an integrative framework called nutritional geometry, which integrates and maps multiple aspects of the host and microbial response in multidimensional nutrient intake spaces.}, }
@article {pmid26636661, year = {2015}, author = {Moran, NA and Sloan, DB}, title = {The Hologenome Concept: Helpful or Hollow?.}, journal = {PLoS biology}, volume = {13}, number = {12}, pages = {e1002311}, pmid = {26636661}, issn = {1545-7885}, support = {GM108477/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Genome ; *Genome, Microbial ; Genomics/*methods/trends ; Humans ; *Microbiota ; *Models, Genetic ; Symbiosis ; Terminology as Topic ; }, abstract = {With the increasing appreciation for the crucial roles that microbial symbionts play in the development and fitness of plant and animal hosts, there has been a recent push to interpret evolution through the lens of the &quot;hologenome&quot;--the collective genomic content of a host and its microbiome. But how symbionts evolve and, particularly, whether they undergo natural selection to benefit hosts are complex issues that are associated with several misconceptions about evolutionary processes in host-associated microbial communities. Microorganisms can have intimate, ancient, and/or mutualistic associations with hosts without having undergone natural selection to benefit hosts. Likewise, observing host-specific microbial community composition or greater community similarity among more closely related hosts does not imply that symbionts have coevolved with hosts, let alone that they have evolved for the benefit of the host. Although selection at the level of the symbiotic community, or hologenome, occurs in some cases, it should not be accepted as the null hypothesis for explaining features of host-symbiont associations.}, }
@article {pmid26598731, year = {2016}, author = {Eisthen, HL and Theis, KR}, title = {Animal-microbe interactions and the evolution of nervous systems.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {371}, number = {1685}, pages = {20150052}, pmid = {26598731}, issn = {1471-2970}, mesh = {Animals ; *Bacteria ; Behavior, Animal ; *Biological Evolution ; Central Nervous System/*anatomy &amp; histology/*physiology ; Invertebrates/anatomy &amp; histology/*microbiology/physiology ; Vertebrates/anatomy &amp; histology/*microbiology/physiology ; }, abstract = {Animals ubiquitously interact with environmental and symbiotic microbes, and the effects of these interactions on animal physiology are currently the subject of intense interest. Nevertheless, the influence of microbes on nervous system evolution has been largely ignored. We illustrate here how taking microbes into account might enrich our ideas about the evolution of nervous systems. For example, microbes are involved in animals' communicative, defensive, predatory and dispersal behaviours, and have likely influenced the evolution of chemo- and photosensory systems. In addition, we speculate that the need to regulate interactions with microbes at the epithelial surface may have contributed to the evolutionary internalization of the nervous system.}, }
@article {pmid26568407, year = {2016}, author = {Mushegian, AA and Ebert, D}, title = {Rethinking &quot;mutualism&quot; in diverse host-symbiont communities.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {38}, number = {1}, pages = {100-108}, doi = {10.1002/bies.201500074}, pmid = {26568407}, issn = {1521-1878}, mesh = {Bacterial Physiological Phenomena/*genetics ; *Biological Evolution ; Ecosystem ; Eukaryota/genetics ; Microbiota/*genetics ; Symbiosis/*genetics ; }, abstract = {While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called &quot;mutualistic&quot; even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate. We suggest reserving the terms &quot;mutualism&quot; and &quot;parasitism&quot; for pairwise interactions where the relationship is largely independent of other species and can be verified by measuring the fitness effect experienced by both partners. In hosts with diverse microbial communities, we propose re-formulating some of the essential questions of symbiosis research - e.g. concerning specificity, transmission mode, and common evolutionary fates - as questions of community ecology and ecosystem function, allowing important biological interactions to be investigated without making assumptions about reciprocity. Understanding the fitness of host-associated bacteria is a crucial component of investigations into the role of microbes in eukaryote evolution.}, }
@article {pmid26556047, year = {2015}, author = {Shelburne, SA and Ajami, NJ and Chibucos, MC and Beird, HC and Tarrand, J and Galloway-Peña, J and Albert, N and Chemaly, RF and Ghantoji, SS and Marsh, L and Pemmaraju, N and Andreeff, M and Shpall, EJ and Wargo, JA and Rezvani, K and Alousi, A and Bruno, VM and Futreal, PA and Petrosino, JF and Kontoyiannis, DP}, title = {Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.}, journal = {PloS one}, volume = {10}, number = {11}, pages = {e0139851}, pmid = {26556047}, issn = {1932-6203}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; R01AI089891/AI/NIAID NIH HHS/United States ; R01 CA061508/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; U19AI110820/AI/NIAID NIH HHS/United States ; HHSN272200900009C//PHS HHS/United States ; HHSN272200900009C/AI/NIAID NIH HHS/United States ; R01 AI089891/AI/NIAID NIH HHS/United States ; }, mesh = {Antifungal Agents/therapeutic use ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Chemotherapy-Induced Febrile Neutropenia ; Fungal Proteins/genetics ; Fungemia/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genome, Fungal ; Host-Pathogen Interactions ; Humans ; Leukemia, Myeloid, Acute/*complications ; Male ; Middle Aged ; Mucor/*genetics/isolation &amp; purification ; Mucormycosis/drug therapy/*microbiology ; Neoplasm Proteins/genetics ; Onychomycosis/complications ; Opportunistic Infections/drug therapy/*microbiology ; }, abstract = {Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.}, }
@article {pmid26555246, year = {2016}, author = {Hester, ER and Barott, KL and Nulton, J and Vermeij, MJ and Rohwer, FL}, title = {Stable and sporadic symbiotic communities of coral and algal holobionts.}, journal = {The ISME journal}, volume = {10}, number = {5}, pages = {1157-1169}, pmid = {26555246}, issn = {1751-7370}, mesh = {Algorithms ; Animals ; Anthozoa/*microbiology ; Archaea/*classification ; Bacteria/classification ; DNA Barcoding, Taxonomic ; DNA, Ribosomal/analysis ; Environment ; Evolution, Molecular ; Fungi/classification ; *Microbiota ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Viruses/classification ; }, abstract = {Coral and algal holobionts are assemblages of macroorganisms and microorganisms, including viruses, Bacteria, Archaea, protists and fungi. Despite a decade of research, it remains unclear whether these associations are spatial-temporally stable or species-specific. We hypothesized that conflicting interpretations of the data arise from high noise associated with sporadic microbial symbionts overwhelming signatures of stable holobiont members. To test this hypothesis, the bacterial communities associated with three coral species (Acropora rosaria, Acropora hyacinthus and Porites lutea) and two algal guilds (crustose coralline algae and turf algae) from 131 samples were analyzed using a novel statistical approach termed the Abundance-Ubiquity (AU) test. The AU test determines whether a given bacterial species would be present given additional sampling effort (that is, stable) versus those species that are sporadically associated with a sample. Using the AU test, we show that coral and algal holobionts have a high-diversity group of stable symbionts. Stable symbionts are not exclusive to one species of coral or algae. No single bacterial species was ubiquitously associated with one host, showing that there is not strict heredity of the microbiome. In addition to the stable symbionts, there was a low-diversity community of sporadic symbionts whose abundance varied widely across individual holobionts of the same species. Identification of these two symbiont communities supports the holobiont model and calls into question the hologenome theory of evolution.}, }
@article {pmid26547794, year = {2016}, author = {Berg, G and Rybakova, D and Grube, M and Köberl, M}, title = {The plant microbiome explored: implications for experimental botany.}, journal = {Journal of experimental botany}, volume = {67}, number = {4}, pages = {995-1002}, pmid = {26547794}, issn = {1460-2431}, support = {J 3638//Austrian Science Fund FWF/Austria ; }, mesh = {Botany/*trends ; *Microbiota ; Plants/*microbiology ; }, abstract = {The importance of microbial root inhabitants for plant growth and health was recognized as early as 100 years ago. Recent insights reveal a close symbiotic relationship between plants and their associated microorganisms, and high structural and functional diversity within plant microbiomes. Plants provide microbial communities with specific habitats, which can be broadly categorized as the rhizosphere, phyllosphere, and endosphere. Plant-associated microbes interact with their host in essential functional contexts. They can stimulate germination and growth, help plants fend off disease, promote stress resistance, and influence plant fitness. Therefore, plants have to be considered as metaorganisms within which the associated microbes usually outnumber the cells belonging to the plant host. The structure of the plant microbiome is determined by biotic and abiotic factors but follows ecological rules. Metaorganisms are co-evolved species assemblages. The metabolism and morphology of plants and their microbiota are intensively connected with each other, and the interplay of both maintains the functioning and fitness of the holobiont. Our study of the current literature shows that analysis of plant microbiome data has brought about a paradigm shift in our understanding of the diverse structure and functioning of the plant microbiome with respect to the following: (i) the high interplay of bacteria, archaea, fungi, and protists; (ii) the high specificity even at cultivar level; (iii) the vertical transmission of core microbiomes; (iv) the extraordinary function of endophytes; and (v) several unexpected functions and metabolic interactions. The plant microbiome should be recognized as an additional factor in experimental botany and breeding strategies.}, }
@article {pmid26539166, year = {2015}, author = {Kuang, W and Li, J and Zhang, S and Long, L}, title = {Diversity and distribution of Actinobacteria associated with reef coral Porites lutea.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1094}, pmid = {26539166}, issn = {1664-302X}, abstract = {Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater.}, }
@article {pmid26536917, year = {2015}, author = {Zhang, Y and Ling, J and Yang, Q and Wen, C and Yan, Q and Sun, H and Van Nostrand, JD and Shi, Z and Zhou, J and Dong, J}, title = {The functional gene composition and metabolic potential of coral-associated microbial communities.}, journal = {Scientific reports}, volume = {5}, number = {}, pages = {16191}, pmid = {26536917}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*genetics/*metabolism ; Carbon/metabolism ; Ecosystem ; Genetic Variation/genetics ; Homeostasis/genetics ; Nitrogen/metabolism ; Phosphorus/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; }, abstract = {The phylogenetic diversity of coral-associated microbes has been extensively examined, but some contention remains regarding whether coral-associated microbial communities are species-specific or site-specific. It is suggested that corals may associate with microbes in terms of function, although little is known about the differences in coral-associated microbial functional gene composition and metabolic potential among coral species. Here, 16S rRNA Illumina sequencing and functional gene array (GeoChip 5.0) were used to assess coral-associated microbial communities. Our results indicate that both host species and environmental variables significantly correlate with shifts in the microbial community structure and functional potential. Functional genes related to key biogeochemical cycles including carbon, nitrogen, sulfur and phosphorus cycling, metal homeostasis, organic remediation, antibiotic resistance and secondary metabolism were shown to significantly vary between and among the four study corals (Galaxea astreata, Porites lutea, Porites andrewsi and Pavona decussata). Genes specific for anammox were also detected for the first time in the coral holobiont and positively correlated with ammonium. This study reveals that variability in the functional potential of coral-associated microbial communities is largely driven by changes in environmental factors and further demonstrates the importance of linking environmental parameters with genomic data in complex environmental systems.}, }
@article {pmid26510159, year = {2015}, author = {Kaniewska, P and Chan, CK and Kline, D and Ling, EY and Rosic, N and Edwards, D and Hoegh-Guldberg, O and Dove, S}, title = {Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.}, journal = {PloS one}, volume = {10}, number = {10}, pages = {e0139223}, pmid = {26510159}, issn = {1932-6203}, mesh = {Analysis of Variance ; Animals ; Anthozoa/*genetics/*physiology ; Carbon Dioxide/analysis ; *Climate Change ; Gene Expression Profiling ; Gene Ontology ; *Oceans and Seas ; Protein Binding ; Protein Interaction Maps ; Seawater ; Temperature ; Transcriptome/*genetics ; }, abstract = {Tropical reef-building coral stress levels will intensify with the predicted rising atmospheric CO2 resulting in ocean temperature and acidification increase. Most studies to date have focused on the destabilization of coral-dinoflagellate symbioses due to warming oceans, or declining calcification due to ocean acidification. In our study, pH and temperature conditions consistent with the end-of-century scenarios of the Intergovernmental Panel on Climate Change (IPCC) caused major changes in photosynthesis and respiration, in addition to decreased calcification rates in the coral Acropora millepora. Population density of symbiotic dinoflagellates (Symbiodinium) under high levels of ocean acidification and temperature (Representative Concentration Pathway, RCP8.5) decreased to half of that found under present day conditions, with photosynthetic and respiratory rates also being reduced by 40%. These physiological changes were accompanied by evidence for gene regulation of calcium and bicarbonate transporters along with components of the organic matrix. Metatranscriptomic RNA-Seq data analyses showed an overall down regulation of metabolic transcripts, and an increased abundance of transcripts involved in circadian clock control, controlling the damage of oxidative stress, calcium signaling/homeostasis, cytoskeletal interactions, transcription regulation, DNA repair, Wnt signaling and apoptosis/immunity/ toxins. We suggest that increased maintenance costs under ocean acidification and warming, and diversion of cellular ATP to pH homeostasis, oxidative stress response, UPR and DNA repair, along with metabolic suppression, may underpin why Acroporid species tend not to thrive under future environmental stress. Our study highlights the potential increased energy demand when the coral holobiont is exposed to high levels of ocean warming and acidification.}, }
@article {pmid26483769, year = {2015}, author = {Moreira, AP and Meirelles, PM and Santos, Ede O and Amado-Filho, GM and Francini-Filho, RB and Thompson, CC and Thompson, FL}, title = {Turbulence-driven shifts in holobionts and planktonic microbial assemblages in St. Peter and St. Paul Archipelago, Mid-Atlantic Ridge, Brazil.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {1038}, pmid = {26483769}, issn = {1664-302X}, abstract = {The aim of this study was to investigate the planktonic and the holobiont Madracis decactis (Scleractinia) microbial diversity along a turbulence-driven upwelling event, in the world's most isolated tropical island, St Peter and St Paul Archipelago (SPSPA, Brazil). Twenty one metagenomes were obtained for seawater (N = 12), healthy and bleached holobionts (N = 9) before, during and after the episode of high seawater turbulence and upwelling. Microbial assemblages differed between low turbulence-low nutrient (LLR) and high-turbulence-high nutrient (HHR) regimes in seawater. During LLR there was a balance between autotrophy and heterotrophy in the bacterioplankton and the ratio cyanobacteria:heterotrophs ~1 (C:H). Prochlorales, unclassified Alphaproteobacteria and Euryarchaeota were the dominant bacteria and archaea, respectively. Basic metabolisms and cyanobacterial phages characterized the LLR. During HHR C:H < < 0.05 and Gammaproteobacteria approximated 50% of the most abundant organisms in seawater. Alteromonadales, Oceanospirillales, and Thaumarchaeota were the dominant bacteria and archaea. Prevailing metabolisms were related to membrane transport, virulence, disease, and defense. Phages targeting heterotrophs and virulence factor genes characterized HHR. Shifts were also observed in coral microbiomes, according to both annotation-indepent and -dependent methods. HHR bleached corals metagenomes were the most dissimilar and could be distinguished by their di- and tetranucleotides frequencies, Iron Acquision metabolism and virulence genes, such as V. cholerae-related virulence factors. The healthy coral holobiont was shown to be less sensitive to transient seawater-related perturbations than the diseased animals. A conceptual model for the turbulence-induced shifts is put forward.}, }
@article {pmid26478771, year = {2015}, author = {Hunt, T}, title = {The Microcosm within: An interview with William B. Miller, Jr., on the Extended Hologenome theory of evolution.}, journal = {Communicative &amp; integrative biology}, volume = {8}, number = {3}, pages = {e1000711}, pmid = {26478771}, issn = {1942-0889}, abstract = {There is a singular unifying reality underlying every biologic interaction on our planet. In immunology, that which does not kill you makes you different. -William B. Miller, Jr. We are experiencing a revolution in our understanding of inner space on a par with our exponentially increasing understanding of outer space. In biology, we are learning that the genetic and epigenetic complexity within organisms is far deeper than suspected. This is a key theme in William B. Miller Jr.'s book, The Microcosm Within: Evolution and Extinction in the Hologenome. We are learning also that a focus on the human genome alone is misleading when it comes to who we really are as biological entities, and in terms of how we and other creatures have evolved. Rather than being defined by the human genome alone, we are instead defined by the &quot;hologenome,&quot; the sum of the human genome and the far larger genetic endowment of the microbiome and symbiotic communities that reside within and around us. Miller is a medical doctor previously in private practice in Pennsylvania and Phoenix, Arizona. This book is his first foray into evolutionary theory. His book could have been titled &quot;The Origin of Variation&quot; because this is his primary focus. He accepts that natural selection plays a role in evolution, but he demotes this mechanism to a less important role than the Modern Synthesis suggests. His main gripe, however, concerns random variation. He argues that random variation is unable to explain the origin and evolution of biological forms that we see in the world around us and in the historical record. Miller suggests that, rather than random variation as the engine of novelty, there is a creative impulse at the heart of cellular life, and even at the level of the genetic aggregate, that generates novelty on a regular basis. I probe this assertion in the interview below. He also highlights the strong role of &quot;exogenous genetic assault&quot; in variation and in his immunological model of evolution.}, }
@article {pmid26451236, year = {2015}, author = {Meyer, JL and Dillard, BA and Rodgers, JM and Ritchie, KB and Paul, VJ and Teplitski, M}, title = {Draft genome sequence of Halomonas meridiana R1t3 isolated from the surface microbiota of the Caribbean Elkhorn coral Acropora palmata.}, journal = {Standards in genomic sciences}, volume = {10}, number = {}, pages = {75}, pmid = {26451236}, issn = {1944-3277}, abstract = {Members of the gammaproteobacterial genus Halomonas are common in marine environments. Halomonas and other members of the Oceanospirillales have recently been identified as prominent members of the surface microbiota of reef-building corals. Halomonas meridiana strain R1t3 was isolated from the surface mucus layer of the scleractinian coral Acropora palmata in 2005 from the Florida Keys. This strain was chosen for genome sequencing to provide insight into the role of commensal heterotrophic bacteria in the coral holobiont. The draft genome consists of 290 scaffolds, totaling 3.5 Mbp in length and contains 3397 protein-coding genes.}, }
@article {pmid26442023, year = {2015}, author = {Smith, DL and Subramanian, S and Lamont, JR and Bywater-Ekegärd, M}, title = {Signaling in the phytomicrobiome: breadth and potential.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {709}, pmid = {26442023}, issn = {1664-462X}, abstract = {Higher plants have evolved intimate, complex, subtle, and relatively constant relationships with a suite of microbes, the phytomicrobiome. Over the last few decades we have learned that plants and microbes can use molecular signals to communicate. This is well-established for the legume-rhizobia nitrogen-fixing symbiosis, and reasonably elucidated for mycorrhizal associations. Bacteria within the phytomircobiome communicate among themselves through quorum sensing and other mechanisms. Plants also detect materials produced by potential pathogens and activate pathogen-response systems. This intercommunication dictates aspects of plant development, architecture, and productivity. Understanding this signaling via biochemical, genomics, proteomics, and metabolomic studies has added valuable knowledge regarding development of effective, low-cost, eco-friendly crop inputs that reduce fossil fuel intense inputs. This knowledge underpins phytomicrobiome engineering: manipulating the beneficial consortia that manufacture signals/products that improve the ability of the plant-phytomicrobiome community to deal with various soil and climatic conditions, leading to enhanced overall crop plant productivity.}, }
@article {pmid26441903, year = {2015}, author = {Minard, G and Tran, FH and Van, VT and Goubert, C and Bellet, C and Lambert, G and Kim, KL and Thuy, TH and Mavingui, P and Valiente Moro, C}, title = {French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {970}, pmid = {26441903}, issn = {1664-302X}, abstract = {The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.}, }
@article {pmid26414414, year = {2015}, author = {Blackall, LL and Wilson, B and van Oppen, MJ}, title = {Coral-the world's most diverse symbiotic ecosystem.}, journal = {Molecular ecology}, volume = {24}, number = {21}, pages = {5330-5347}, doi = {10.1111/mec.13400}, pmid = {26414414}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/genetics/*microbiology ; Archaea/classification ; Bacteria/*classification ; Biodiversity ; *Coral Reefs ; DNA, Bacterial/genetics ; DNA, Ribosomal Spacer/genetics ; Dinoflagellida/*classification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Zooxanthellate corals (i.e. those harbouring Symbiodinium) are the main builders of the world's shallow-water marine coral reefs. They represent intimate diverse symbioses between coral animals, single-celled photosynthetic dinoflagellates (Symbiodinium spp.), other microscopic eukaryotes, prokaryotes and viruses. Crabs and other crustaceans, worms, sponges, bivalves and hydrozoans, fishes, sea urchins, octopuses and sea stars are itinerant members of these 'rainforests of the sea'. This review focuses on the biodiversity of scleractinian coral animals and their best studied microscopic epi- and endosymbionts. In relation to coral-associated species diversity, Symbiodinium internal transcribed spacer region sequence types tally 10(2) -10(3) or up to ~15 different operational taxonomic units (OTUs, or putative species at the 97% sequence identity level; this cut-off was chosen based on intragenomic sequence diversity observed in monoclonal cultures) and prokaryotes (mostly bacterial) total 10(2) -10(4) OTUs. We analysed all publically accessible 16S rRNA gene sequence data and found Gammaproteobacteria were extremely abundant, followed by Alphaproteobacteria. Notably, Archaea were poorly represented and 'unassigned OTUs' were abundant in data generated by high-throughput DNA sequencing studies of corals. We outline and compare model systems that could be used in future studies of the coral holobiont. In our future directions, we recommend a global coral sampling effort including substantial attention being paid to method of coral tissue acquisition, which compartments (mucus, tissue, skeleton) to explore, broadening the holobiont members considered and linking biodiversity with functional investigations.}, }
@article {pmid26388838, year = {2015}, author = {Har, JY and Helbig, T and Lim, JH and Fernando, SC and Reitzel, AM and Penn, K and Thompson, JR}, title = {Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {818}, pmid = {26388838}, issn = {1664-302X}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; }, abstract = {We have characterized the molecular and genomic diversity of the microbiota of the starlet sea anemone Nematostella vectensis, a cnidarian model for comparative developmental and functional biology and a year-round inhabitant of temperate salt marshes. Molecular phylogenetic analysis of 16S rRNA gene clone libraries revealed four ribotypes associated with N. vectensis at multiple locations and times. These associates include two novel ribotypes within the ε-Proteobacterial order Campylobacterales and the Spirochetes, respectively, each sharing <85% identity with cultivated strains, and two γ-Proteobacterial ribotypes sharing >99% 16S rRNA identity with Endozoicomonas elysicola and Pseudomonas oleovorans, respectively. Species-specific PCR revealed that these populations persisted in N. vectensis asexually propagated under laboratory conditions. cDNA indicated expression of the Campylobacterales and Endozoicomonas 16S rRNA in anemones from Sippewissett Marsh, MA. A collection of bacteria from laboratory raised N. vectensis was dominated by isolates from P. oleovorans and Rhizobium radiobacter. Isolates from field-collected anemones revealed an association with Limnobacter and Stappia isolates. Genomic DNA sequencing was carried out on 10 cultured bacterial isolates representing field- and laboratory-associates, i.e., Limnobacter spp., Stappia spp., P. oleovorans and R. radiobacter. Genomes contained multiple genes identified as virulence (host-association) factors while S. stellulata and L. thiooxidans genomes revealed pathways for mixotrophic sulfur oxidation. A pilot metatranscriptome of laboratory-raised N. vectensis was compared to the isolate genomes and indicated expression of ORFs from L. thiooxidans with predicted functions of motility, nutrient scavenging (Fe and P), polyhydroxyalkanoate synthesis for carbon storage, and selective permeability (porins). We hypothesize that such activities may mediate acclimation and persistence of bacteria in a N. vectensis holobiont defined by both internal and external gradients of chemicals and nutrients in a dynamic coastal habitat.}, }
@article {pmid26311127, year = {2016}, author = {Meisterhans, G and Raymond, N and Girault, E and Lambert, C and Bourrasseau, L and de Montaudouin, X and Garabetian, F and Jude-Lemeilleur, F}, title = {Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals.}, journal = {Microbial ecology}, volume = {71}, number = {1}, pages = {194-206}, pmid = {26311127}, issn = {1432-184X}, mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bivalvia/*microbiology ; *Microbiota ; Shellfish/*microbiology ; }, abstract = {Marine invertebrate microbiota has a key function in host physiology and health. To date, knowledge about bivalve microbiota is poorly documented except public health concerns. This study used a molecular approach to characterize the microbiota associated with the bivalve Manila clam (Ruditapes philippinarum) by determining (1) the difference among organs either or not under the influence of host habitat, (2) small-scale variability of microbiota, and (3) the experimental response of the Manila clam microbiota submitted to different lateral transmissions. These questions were investigated by sampling two groups of individuals living in contrasting habitats and carrying out a transplant experiment. Manila clam microbiota (i.e., bacterial community structure) was determined at organ-scale (gills, gut, and a pool of remaining tissues) by capillary electrophoresis DNA fingerprinting (CE fingerprinting). The Manila clam microbiota structure differed among organs indicating a selection of Manila clam microbiota at organ scale. Habitat strongly influenced gill and gut microbiota. In contrast, microbiota associated with remaining tissues was similar between group individuals suggesting that these communities are mostly autochthonous, i.e., Manila clam specific. Transplant experiment showed that improving living condition did not induce any change in microbiota associated with remaining tissues. In contrast, the reduction in individual habitat quality led to individuals in declining health as strongly suggested by the increase in phagocytosis activity and decrease in condition index together with the change in internal organ microbiota. This study provides a first description of the Manila clam holobiont which can withstand disturbance and respond opportunistically to improved environmental conditions.}, }
@article {pmid26300848, year = {2015}, author = {Voss, JD and Leon, JC and Dhurandhar, NV and Robb, FT}, title = {Pawnobiome: manipulation of the hologenome within one host generation and beyond.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {697}, pmid = {26300848}, issn = {1664-302X}, }
@article {pmid26293603, year = {2016}, author = {Nogales, A and Nobre, T and Valadas, V and Ragonezi, C and Döring, M and Polidoros, A and Arnholdt-Schmitt, B}, title = {Can functional hologenomics aid tackling current challenges in plant breeding?.}, journal = {Briefings in functional genomics}, volume = {15}, number = {4}, pages = {288-297}, doi = {10.1093/bfgp/elv030}, pmid = {26293603}, issn = {2041-2657}, mesh = {Genomics/*methods ; Phenotype ; *Plant Breeding ; Plants/*genetics ; *Quantitative Trait Loci ; }, abstract = {Molecular plant breeding usually overlooks the genetic variability that arises from the association of plants with endophytic microorganisms, when looking at agronomic interesting target traits. This source of variability can have crucial effects on the functionality of the organism considered as a whole (the holobiont), and therefore can be selectable in breeding programs. However, seeing the holobiont as a unit for selection and improvement in breeding programs requires novel approaches for genotyping and phenotyping. These should not focus just at the plant level, but also include the associated endophytes and their functional effects on the plant, to make effective desirable trait screenings. The present review intends to draw attention to a new research field on functional hologenomics that if associated with adequate phenotyping tools could greatly increase the efficiency of breeding programs.}, }
@article {pmid26291447, year = {2015}, author = {Krediet, CJ and DeNofrio, JC and Caruso, C and Burriesci, MS and Cella, K and Pringle, JR}, title = {Rapid, Precise, and Accurate Counts of Symbiodinium Cells Using the Guava Flow Cytometer, and a Comparison to Other Methods.}, journal = {PloS one}, volume = {10}, number = {8}, pages = {e0135725}, pmid = {26291447}, issn = {1932-6203}, mesh = {Animals ; Cnidaria/cytology ; Dinoflagellida/cytology ; Flow Cytometry/*methods ; Symbiosis/physiology ; }, abstract = {In studies of both the establishment and breakdown of cnidarian-dinoflagellate symbiosis, it is often necessary to determine the number of Symbiodinium cells relative to the quantity of host tissue. Ideally, the methods used should be rapid, precise, and accurate. In this study, we systematically evaluated methods for sample preparation and storage and the counting of algal cells using the hemocytometer, a custom image-analysis program for automated counting of the fluorescent algal cells, the Coulter Counter, or the Millipore Guava flow-cytometer. We found that although other methods may have value in particular applications, for most purposes, the Guava flow cytometer provided by far the best combination of precision, accuracy, and efficient use of investigator time (due to the instrument's automated sample handling), while also allowing counts of algal numbers over a wide range and in small volumes of tissue homogenate. We also found that either of two assays of total homogenate protein provided a precise and seemingly accurate basis for normalization of algal counts to the total amount of holobiont tissue.}, }
@article {pmid26284777, year = {2015}, author = {Bordenstein, SR and Theis, KR}, title = {Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes.}, journal = {PLoS biology}, volume = {13}, number = {8}, pages = {e1002226}, pmid = {26284777}, issn = {1545-7885}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Humans ; *Metagenome ; Microbiota/*genetics ; Mutation ; Plants/genetics ; Selection, Genetic ; Symbiosis/*genetics ; }, abstract = {Groundbreaking research on the universality and diversity of microorganisms is now challenging the life sciences to upgrade fundamental theories that once seemed untouchable. To fully appreciate the change that the field is now undergoing, one has to place the epochs and foundational principles of Darwin, Mendel, and the modern synthesis in light of the current advances that are enabling a new vision for the central importance of microbiology. Animals and plants are no longer heralded as autonomous entities but rather as biomolecular networks composed of the host plus its associated microbes, i.e., &quot;holobionts.&quot; As such, their collective genomes forge a &quot;hologenome,&quot; and models of animal and plant biology that do not account for these intergenomic associations are incomplete. Here, we integrate these concepts into historical and contemporary visions of biology and summarize a predictive and refutable framework for their evaluation. Specifically, we present ten principles that clarify and append what these concepts are and are not, explain how they both support and extend existing theory in the life sciences, and discuss their potential ramifications for the multifaceted approaches of zoology and botany. We anticipate that the conceptual and evidence-based foundation provided in this essay will serve as a roadmap for hypothesis-driven, experimentally validated research on holobionts and their hologenomes, thereby catalyzing the continued fusion of biology's subdisciplines. At a time when symbiotic microbes are recognized as fundamental to all aspects of animal and plant biology, the holobiont and hologenome concepts afford a holistic view of biological complexity that is consistent with the generally reductionist approaches of biology.}, }
@article {pmid29587997, year = {2015}, author = {Schwarz, RS and Huang, Q and Evans, JD}, title = {Hologenome theory and the honey bee pathosphere.}, journal = {Current opinion in insect science}, volume = {10}, number = {}, pages = {1-7}, doi = {10.1016/j.cois.2015.04.006}, pmid = {29587997}, issn = {2214-5753}, abstract = {Recent research has provided improved genome-level views of diversity across global honey bee populations, the gut microbiota residing within them, and the expanding pathosphere challenging honey bees. Different combinations of bee/microbiota/pathosphere genome complexes may explain regional variation in apiculture productivity and mortality. To understand this, we must consider management and research approaches in light of a hologenome paradigm: that honey bee fitness is determined by the composite bee and microbiota genomes. Only by considering the hologenome can we truly interpret and address impacts from the pathosphere, pesticides, toxins, nutrition, climate and other stressors affecting bee health.}, }
@article {pmid26177948, year = {2015}, author = {Kramer, P and Bressan, P}, title = {Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior.}, journal = {Perspectives on psychological science : a journal of the Association for Psychological Science}, volume = {10}, number = {4}, pages = {464-481}, doi = {10.1177/1745691615583131}, pmid = {26177948}, issn = {1745-6924}, mesh = {Animals ; Behavior/*physiology ; Brain/*microbiology/parasitology/*virology ; *Genomic Imprinting ; Humans ; *Microbiota ; *Viruses ; }, abstract = {Psychologists and psychiatrists tend to be little aware that (a) microbes in our brains and guts are capable of altering our behavior; (b) viral DNA that was incorporated into our DNA millions of years ago is implicated in mental disorders; (c) many of us carry the cells of another human in our brains; and (d) under the regulation of viruslike elements, the paternally inherited and maternally inherited copies of some genes compete for domination in the offspring, on whom they have opposite physical and behavioral effects. This article provides a broad overview, aimed at a wide readership, of the consequences of our coexistence with these selfish entities. The overarching message is that we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are.}, }
@article {pmid26099965, year = {2015}, author = {Aires, T and Moalic, Y and Serrao, EA and Arnaud-Haond, S}, title = {Hologenome theory supported by cooccurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa).}, journal = {FEMS microbiology ecology}, volume = {91}, number = {7}, pages = {}, doi = {10.1093/femsec/fiv067}, pmid = {26099965}, issn = {1574-6941}, mesh = {Animals ; Anthozoa ; Bacteria/*genetics ; Biodiversity ; Caulerpa/genetics/*microbiology ; Endophytes/*genetics ; Mediterranean Sea ; Microbial Consortia/*genetics ; Plants ; Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Species Specificity ; }, abstract = {The siphonous algae of the Caulerpa genus harbor internal microbial communities hypothesized to play important roles in development, defense and metabolic activities of the host. Here, we characterize the endophytic bacterial community of four Caulerpa taxa in the Mediterranean Sea, through 16S rRNA amplicon sequencing. Results reveal a striking alpha diversity of the bacterial communities, similar to levels found in sponges and coral holobionts. These comprise (1) a very small core community shared across all hosts (< 1% of the total community), (2) a variable portion (ca. 25%) shared by some Caulerpa taxa but not by all, which might represent environmentally acquired bacteria and (3) a large (>70%) species-specific fraction of the community, forming very specific clusters revealed by modularity in networks of cooccurrence, even in areas where distinct Caulerpa taxa occurred in sympatry. Indirect inferences based on sequence homology suggest that these communities may play an important role in the metabolism of their host, in particular on their ability to grow on anoxic sediment. These findings support the hologenome theory and the need for a holistic framework in ecological and evolutionary studies of these holobionts that frequently become invasive.}, }
@article {pmid26097896, year = {2015}, author = {Zhao, Y and Lukiw, WJ}, title = {Microbiome-generated amyloid and potential impact on amyloidogenesis in Alzheimer's disease (AD).}, journal = {Journal of nature and science}, volume = {1}, number = {7}, pages = {}, pmid = {26097896}, issn = {2377-2700}, support = {R01 AG018031/AG/NIA NIH HHS/United States ; R01 AG038834/AG/NIA NIH HHS/United States ; R01 EY006311/EY/NEI NIH HHS/United States ; }, abstract = {According to the 'amyloid cascade hypothesis of Alzheimer's disease' first proposed about 16 years ago, the accumulation of Aβ peptides in the human central nervous system (CNS) is the primary influence driving Alzheimer's disease (AD) pathogenesis, and Aβ peptide accretion is the result of an imbalance between Aβ peptide production and clearance. In the last 18 months multiple laboratories have reported two particularly important observations: (i) that because the microbes of the human microbiome naturally secrete large amounts of amyloid, lipopolysaccharides (LPS) and other related pro-inflammatory pathogenic signals, these may contribute to both the systemic and CNS amyloid burden in aging humans; and (ii) that the clearance of Aβ peptides appears to be intrinsically impaired by deficits in the microglial plasma-membrane enriched triggering receptor expressed in microglial/myeloid-2 cells (TREM2). This brief general commentary-perspective paper: (i) will highlight some of these very recent findings on microbiome-secreted amyloids and LPS and the potential contribution of these microbial-derived pro-inflammatory and neurotoxic exudates to age-related inflammatory and AD-type neurodegeneration in the host; and (ii) will discuss the contribution of a defective microglial-based TREM2 transmembrane sensor-receptor system to amyloidogenesis in AD that is in contrast to the normal, homeostatic clearance of Aβ peptides from the human CNS.}, }
@article {pmid26064625, year = {2015}, author = {Pinzón, JH and Kamel, B and Burge, CA and Harvell, CD and Medina, M and Weil, E and Mydlarz, LD}, title = {Whole transcriptome analysis reveals changes in expression of immune-related genes during and after bleaching in a reef-building coral.}, journal = {Royal Society open science}, volume = {2}, number = {4}, pages = {140214}, pmid = {26064625}, issn = {2054-5703}, abstract = {Climate change is negatively affecting the stability of natural ecosystems, especially coral reefs. The dissociation of the symbiosis between reef-building corals and their algal symbiont, or coral bleaching, has been linked to increased sea surface temperatures. Coral bleaching has significant impacts on corals, including an increase in disease outbreaks that can permanently change the entire reef ecosystem. Yet, little is known about the impacts of coral bleaching on the coral immune system. In this study, whole transcriptome analysis of the coral holobiont and each of the associate components (i.e. coral host, algal symbiont and other associated microorganisms) was used to determine changes in gene expression in corals affected by a natural bleaching event as well as during the recovery phase. The main findings include evidence that the coral holobiont and the coral host have different responses to bleaching, and the host immune system appears suppressed even a year after a bleaching event. These results support the hypothesis that coral bleaching changes the expression of innate immune genes of corals, and these effects can last even after recovery of symbiont populations. Research on the role of immunity on coral's resistance to stressors can help make informed predictions on the future of corals and coral reefs.}, }
@article {pmid26047662, year = {2016}, author = {Stilling, RM and Dinan, TG and Cryan, JF}, title = {The brain's Geppetto-microbes as puppeteers of neural function and behaviour?.}, journal = {Journal of neurovirology}, volume = {22}, number = {1}, pages = {14-21}, pmid = {26047662}, issn = {1538-2443}, mesh = {Animals ; *Behavior ; Behavior, Animal ; Biological Evolution ; Brain/*microbiology/parasitology/physiopathology/virology ; Diet ; Feeding Behavior ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/*microbiology/parasitology/physiopathology/virology ; *Host-Pathogen Interactions ; Humans ; Symbiosis/physiology ; }, abstract = {Research on the microbiome and its interaction with various host organs, including the brain, is increasingly gaining momentum. With more evidence establishing a comprehensive microbiota-gut-brain axis, questions have been raised as to the extent to which microbes influence brain physiology and behaviour. In parallel, there is a growing literature showing active behavioural manipulation in favour of the microbe for certain parasites. However, it seems unclear where the hidden majority of microbes are localised on the parasitism-mutualism spectrum. A long evolutionary history intimately connects host and microbiota, which complicates this classification. In this conceptual minireview, we discuss current hypotheses on host-microbe interaction and argue that novel experimental approaches and theoretical concepts, such as the hologenome theory, are necessary to incorporate transgenerational epigenetic inheritance of the microbiome into evolutionary theories.}, }
@article {pmid26039986, year = {2015}, author = {Wilson, AC and Duncan, RP}, title = {Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {112}, number = {33}, pages = {10255-10261}, pmid = {26039986}, issn = {1091-6490}, mesh = {Amino Acids/chemistry ; Amino Acids, Branched-Chain/chemistry ; Animals ; Bacteria/genetics ; Buchnera/genetics ; Cell Lineage ; Cytoplasm/metabolism ; *Evolution, Molecular ; Gene Expression Profiling ; Gene Transfer, Horizontal ; Genome ; Genome, Bacterial ; Hemiptera/*genetics/*microbiology ; Pantothenic Acid/chemistry ; *Symbiosis ; }, abstract = {The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research.}, }
@article {pmid26028424, year = {2015}, author = {Price, DR and Wilson, AC and Luetje, CW}, title = {Proton-dependent glutamine uptake by aphid bacteriocyte amino acid transporter ApGLNT1.}, journal = {Biochimica et biophysica acta}, volume = {1848}, number = {10 Pt A}, pages = {2085-2091}, doi = {10.1016/j.bbamem.2015.05.019}, pmid = {26028424}, issn = {0006-3002}, support = {DC011091/DC/NIDCD NIH HHS/United States ; }, mesh = {Animals ; Aphids/*microbiology ; Buchnera/*metabolism ; Cells, Cultured ; Glutamine/*pharmacokinetics ; Ion Channel Gating/*physiology ; Membrane Potentials/*physiology ; Oocytes/*physiology ; Protons ; Xenopus laevis ; }, abstract = {Aphids house large populations of the gammaproteobacterial symbiont Buchnera aphidicola in specialized bacteriocyte cells. The combined biosynthetic capability of the holobiont (Acyrthosiphon pisum and Buchnera) is sufficient for biosynthesis of all twenty protein coding amino acids, including amino acids that animals alone cannot synthesize; and that are present at low concentrations in A. pisum's plant phloem sap diet. Collaborative holobiont amino acid biosynthesis depends on glutamine import into bacteriocytes, which serves as a nitrogen-rich amino donor for biosynthesis of other amino acids. Recently, we characterized A. pisum glutamine transporter 1 (ApGLNT1), a member of the amino acid/auxin permease family, as the dominant bacteriocyte plasma membrane glutamine transporter. Here we show ApGLNT1 to be structurally and functionally related to mammalian proton-dependent amino acid transporters (PATs 1-4). Using functional expression in Xenopus laevis oocytes, combined with two-electrode voltage clamp electrophysiology we demonstrate that ApGLNT1 is electrogenic and that glutamine induces large inward currents. ApGLNT1 glutamine induced currents are dependent on external glutamine concentration, proton (H+) gradient across the membrane, and membrane potential. Based on these transport properties, ApGLNT1-mediated glutamine uptake into A. pisum bacteriocytes can be regulated by changes in either proton gradients across the plasma membrane or membrane potential.}, }
@article {pmid26026593, year = {2015}, author = {Dheilly, NM and Poulin, R and Thomas, F}, title = {Biological warfare: Microorganisms as drivers of host-parasite interactions.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {34}, number = {}, pages = {251-259}, doi = {10.1016/j.meegid.2015.05.027}, pmid = {26026593}, issn = {1567-7257}, mesh = {Animals ; *Biological Warfare ; *Host-Parasite Interactions ; Humans ; Microbiota ; Parasitic Diseases/*microbiology/parasitology ; Symbiosis ; }, abstract = {Understanding parasite strategies for evasion, manipulation or exploitation of hosts is crucial for many fields, from ecology to medical sciences. Generally, research has focused on either the host response to parasitic infection, or the parasite virulence mechanisms. More recently, integrated studies of host-parasite interactions have allowed significant advances in theoretical and applied biology. However, these studies still provide a simplistic view of these as mere two-player interactions. Host and parasite are associated with a myriad of microorganisms that could benefit from the improved fitness of their partner. Illustrations of such complex multi-player interactions have emerged recently from studies performed in various taxa. In this conceptual article, we propose how these associated microorganisms may participate in the phenotypic alterations induced by parasites and hence in host-parasite interactions, from an ecological and evolutionary perspective. Host- and parasite-associated microorganisms may participate in the host-parasite interaction by interacting directly or indirectly with the other partner. As a result, parasites may develop (i) the disruptive strategy in which the parasite alters the host microbiota to its advantage, and (ii) the biological weapon strategy where the parasite-associated microorganism contributes to or modulates the parasite's virulence. Some phenotypic alterations induced by parasite may also arise from conflicts of interests between the host or parasite and its associated microorganism. For each situation, we review the literature and propose new directions for future research. Specifically, investigating the role of host- and parasite-associated microorganisms in host-parasite interactions at the individual, local and regional level will lead to a holistic understanding of how the co-evolution of the different partners influences how the other ones respond, both ecologically and evolutionary. The conceptual framework we propose here is important and relevant to understand the proximate basis of parasite strategies, to predict their evolutionary dynamics and potentially to prevent therapeutic failures.}, }
@article {pmid26020776, year = {2015}, author = {Gudenkauf, BM and Hewson, I}, title = {Metatranscriptomic Analysis of Pycnopodia helianthoides (Asteroidea) Affected by Sea Star Wasting Disease.}, journal = {PloS one}, volume = {10}, number = {5}, pages = {e0128150}, pmid = {26020776}, issn = {1932-6203}, mesh = {Animals ; *Energy Metabolism ; *Gene Expression Regulation ; Starfish/genetics/*metabolism ; *Transcriptome ; Wasting Syndrome/genetics/*metabolism/pathology/*veterinary ; }, abstract = {Sea star wasting disease (SSWD) describes a suite of symptoms reported in asteroids of the North American Pacific Coast. We performed a metatranscriptomic survey of asymptomatic and symptomatic sunflower star (Pycnopodia helianthoides) body wall tissues to understand holobiont gene expression in tissues affected by SSWD. Metatranscriptomes were highly variable between replicate libraries, and most differentially expressed genes represented either transcripts of associated microorganisms (particularly Pseudomonas and Vibrio relatives) or low-level echinoderm transcripts of unknown function. However, the pattern of annotated host functional genes reflects enhanced apoptotic and tissue degradation processes and decreased energy metabolism, while signalling of death-related proteins was greater in asymptomatic and symptomatic tissues. Our results suggest that the body wall tissues of SSWD-affected asteroids may undergo structural changes during disease progression, and that they are stimulated to undergo autocatalytic cell death processes.}, }
@article {pmid26018191, year = {2015}, author = {Roder, C and Bayer, T and Aranda, M and Kruse, M and Voolstra, CR}, title = {Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences.}, journal = {Molecular ecology}, volume = {24}, number = {13}, pages = {3501-3511}, pmid = {26018191}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; Biodiversity ; Coral Reefs ; *Environment ; Indian Ocean ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; Sequence Analysis, DNA ; Spatio-Temporal Analysis ; }, abstract = {The significance of bacteria for eukaryotic functioning is increasingly recognized. Coral reef ecosystems critically rely on the relationship between coral hosts and their intracellular photosynthetic dinoflagellates, but the role of the associated bacteria remains largely theoretical. Here, we set out to relate coral-associated bacterial communities of the fungid host species Ctenactis echinata to environmental settings (geographic location, substrate cover, summer/winter, nutrient and suspended matter concentrations) and coral host abundance. We show that bacterial diversity of C. echinata aligns with ecological differences between sites and that coral colonies sampled at the species' preferred habitats are primarily structured by one bacterial taxon (genus Endozoicomonas) representing more than 60% of all bacteria. In contrast, host microbiomes from lower populated coral habitats are less structured and more diverse. Our study demonstrates that the content and structure of the coral microbiome aligns with environmental differences and denotes habitat adequacy. Availability of a range of coral host habitats might be important for the conservation of distinct microbiome structures and diversity.}, }
@article {pmid25989369, year = {2015}, author = {Baker, DM and Freeman, CJ and Knowlton, N and Thacker, RW and Kim, K and Fogel, ML}, title = {Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses.}, journal = {The ISME journal}, volume = {9}, number = {12}, pages = {2620-2629}, pmid = {25989369}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*physiology ; Biological Evolution ; Carbon Cycle ; Caribbean Region ; Dinoflagellida/classification/genetics/isolation &amp; purification/*physiology ; Photosynthesis ; Phylogeny ; *Symbiosis ; }, abstract = {Many cnidarians host endosymbiotic dinoflagellates from the genus Symbiodinium. It is generally assumed that the symbiosis is mutualistic, where the host benefits from symbiont photosynthesis while providing protection and photosynthetic substrates. Diverse assemblages of symbiotic gorgonian octocorals can be found in hard bottom communities throughout the Caribbean. While current research has focused on the phylo- and population genetics of gorgonian symbiont types and their photo-physiology, relatively less work has focused on biogeochemical benefits conferred to the host and how these benefits vary across host species. Here we examine this symbiosis among 11 gorgonian species collected in Bocas del Toro, Panama. By coupling light and dark bottle incubations (P/R) with (13)C-bicarbonate tracers, we quantified the link between holobiont oxygen metabolism with carbon assimilation and translocation from symbiont to host. Our data show that P/R varied among species, and was correlated with colony morphology and polyp size. Sea fans and sea plumes were net autotrophs (P/R>1.5), while nine species of sea rods were net heterotrophs with most below compensation (P/R<1.0). (13)C assimilation corroborated the P/R results, and maximum δ(13)Chost values were strongly correlated with polyp size, indicating higher productivity by colonies with high polyp SA:V. A survey of gorgonian-Symbiodinium associations revealed that productive species maintain specialized, obligate symbioses and are more resistant to coral bleaching, whereas generalist and facultative associations are common among sea rods that have higher bleaching sensitivities. Overall, productivity and polyp size had strong phylogenetic signals with carbon fixation and polyp size showing evidence of trait covariance.}, }
@article {pmid25977840, year = {2015}, author = {Zhao, Y and Dua, P and Lukiw, WJ}, title = {Microbial Sources of Amyloid and Relevance to Amyloidogenesis and Alzheimer's Disease (AD).}, journal = {Journal of Alzheimer's disease &amp; Parkinsonism}, volume = {5}, number = {1}, pages = {177}, pmid = {25977840}, issn = {2161-0460}, support = {R01 EY006311/EY/NEI NIH HHS/United States ; R01 AG018031/AG/NIA NIH HHS/United States ; P50 AG016573/AG/NIA NIH HHS/United States ; R01 AG038834/AG/NIA NIH HHS/United States ; P30 GM103340/GM/NIGMS NIH HHS/United States ; }, abstract = {Since the inception of the human microbiome project (HMP) by the US National Institutes of Health (NIH) in 2007 there has been a keen resurgence in our recognition of the human microbiome and its contribution to development, immunity, neurophysiology, metabolic and nutritive support to central nervous system (CNS) health and disease. What is not generally appreciated is that (i) the ~1014 microbial cells that comprise the human microbiome outnumber human host cells by approximately one hundred-to-one; (ii) together the microbial genes of the microbiome outnumber human host genes by about one hundred-and-fifty to one; (iii) collectively these microbes constitute the largest 'diffuse organ system' in the human body, more metabolically active than the liver; strongly influencing host nutritive-, innate-immune, neuroinflammatory-, neuromodulatory- and neurotransmission-functions; and (iv) that these microbes actively secrete highly complex, immunogenic mixtures of lipopolysaccharide (LPS) and amyloid from their outer membranes into their immediate environment. While secreted LPS and amyloids are generally quite soluble as monomers over time they form into highly insoluble fibrous protein aggregates that are implicated in the progressive degenerative neuropathology of several common, age-related disorders of the human CNS including Alzheimer's disease (AD). This general commentary-perspective paper will highlight some recent findings on microbial-derived secreted LPS and amyloids and the potential contribution of these neurotoxic and proinflammatory microbial exudates to age-related inflammatory amyloidogenesis and neurodegeneration, with specific reference to AD wherever possible.}, }
@article {pmid25972851, year = {2015}, author = {Fiore, CL and Labrie, M and Jarett, JK and Lesser, MP}, title = {Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {364}, pmid = {25972851}, issn = {1664-302X}, abstract = {Compared to our understanding of the taxonomic composition of the symbiotic microbes in marine sponges, the functional diversity of these symbionts is largely unknown. Furthermore, the application of genomic, transcriptomic, and proteomic techniques to functional questions on sponge host-symbiont interactions is in its infancy. In this study, we generated a transcriptome for the host and a metatranscriptome of its microbial symbionts for the giant barrel sponge, Xestospongia muta, from the Caribbean. In combination with a gene-specific approach, our goals were to (1) characterize genetic evidence for nitrogen cycling in X. muta, an important limiting nutrient on coral reefs (2) identify which prokaryotic symbiont lineages are metabolically active and, (3) characterize the metabolic potential of the prokaryotic community. Xestospongia muta expresses genes from multiple nitrogen transformation pathways that when combined with the abundance of this sponge, and previous data on dissolved inorganic nitrogen fluxes, shows that this sponge is an important contributor to nitrogen cycling biogeochemistry on coral reefs. Additionally, we observed significant differences in gene expression of the archaeal amoA gene, which is involved in ammonia oxidation, between coral reef locations consistent with differences in the fluxes of dissolved inorganic nitrogen previously reported. In regards to symbiont metabolic potential, the genes in the biosynthetic pathways of several amino acids were present in the prokaryotic metatranscriptome dataset but in the host-derived transcripts only the catabolic reactions for these amino acids were present. A similar pattern was observed for the B vitamins (riboflavin, biotin, thiamin, cobalamin). These results expand our understanding of biogeochemical cycling in sponges, and the metabolic interchange highlighted here advances the field of symbiont physiology by elucidating specific metabolic pathways where there is high potential for host-prokaryote interactions.}, }
@article {pmid28357290, year = {2015}, author = {Zarraonaindia, I and Gilbert, JA}, title = {Understanding grapevine-microbiome interactions: implications for viticulture industry.}, journal = {Microbial cell (Graz, Austria)}, volume = {2}, number = {5}, pages = {171-173}, doi = {10.15698/mic2015.05.204}, pmid = {28357290}, issn = {2311-2638}, abstract = {Until recently, the analysis of complex communities such as that of the grapevine-microbe holobiont has been limited by the fact that most microbes are not culturable under laboratory conditions (less than 1%). However, metagenomics, the study of the genetic material recovered directly from environmental samples without the need for enrichment or of culturing, has led to open an unprecedented era in the field of microbiology. Importantly, this technological advance has now become so pervasive that it is being regularly applied to explore soils and plants of agricultural interest. Interestingly, many large companies are taking notice, with significant financial investment being used to exploring ways to manipulate the productivity, disease resistance and stress tolerance for crops by influencing the microbiome. To understand which microbes one needs to manipulate to influence this valuable characteristics, we need to sequence the microbiome and capture the genetic and hence functional metabolic information contained therein. For viticulture and other agricultural fields where the crop is also associated to particular flavor properties that may also be manipulated, understanding how the bacteria, fungi and viruses influence the development and hence chemical makeup of the crop is essential.}, }
@article {pmid25903335, year = {2015}, author = {Roossinck, MJ}, title = {Move over, bacteria! Viruses make their mark as mutualistic microbial symbionts.}, journal = {Journal of virology}, volume = {89}, number = {13}, pages = {6532-6535}, pmid = {25903335}, issn = {1098-5514}, mesh = {Animals ; Bacteria/*virology ; Insecta/*virology ; Mammals/*virology ; Plants/*virology ; *Symbiosis ; *Virus Physiological Phenomena ; Viruses/*growth &amp; development ; }, abstract = {Viruses are being redefined as more than just pathogens. They are also critical symbiotic partners in the health of their hosts. In some cases, viruses have fused with their hosts in symbiogenetic relationships. Mutualistic interactions are found in plant, insect, and mammalian viruses, as well as with eukaryotic and prokaryotic microbes, and some interactions involve multiple players of the holobiont. With increased virus discovery, more mutualistic interactions are being described and more will undoubtedly be discovered.}, }
@article {pmid25894127, year = {2015}, author = {Land, WG}, title = {How evolution tells us to induce allotolerance.}, journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation}, volume = {13 Suppl 1}, number = {}, pages = {46-54}, pmid = {25894127}, issn = {2146-8427}, mesh = {Animals ; Bacteria/immunology ; *Evolution, Molecular ; Female ; Graft Rejection/*immunology/metabolism/prevention &amp; control ; *Graft Survival ; Host-Pathogen Interactions ; Humans ; Immunity, Innate ; Immunity, Mucosal ; Intestines/immunology/microbiology ; Models, Immunological ; Organ Transplantation/*adverse effects ; Placenta/immunology ; Pregnancy ; Signal Transduction ; *Transplantation Tolerance ; Treatment Outcome ; }, abstract = {Modern immunology, in many ways, is based on 3 major paradigms: the clonal selection theory (Medawar, Burnet; 1953/1959), the pattern recognition theory (Janeway; 1989), and the danger/injury theory (Matzinger, Land; 1994). The last theory holds that any cell stress and tissue injury including allograft injury, via induction of damage-associated molecular patterns, induces immunity including alloimmunity leading to allograft rejection. On the other hand, the concept precludes that &quot;non-self &quot; per se induces immunity as proposed by the two former theories. Today, the danger/injury model has been largely accepted by immunologists, as documented by a steadily increasing number of publications. In particular, overwhelming evidence in support of the correctness of the model has come from recent studies on the gut microbiota representing a huge assemblage of &quot;non-self. &quot; Here, harmless noninjurious commensal microbes are protected by innate immunity-based immune tolerance whereas intestinal injury-causing pathogenic microbes are immunology attacked. The ability of the immune system to discriminate between harmless beneficial &quot;non-self &quot; to induce tolerance and harmful life-threatening &quot;non-self &quot; to induce immunity has apparently emerged during evolution: Protection of innate immunity-controlled beneficial &quot;non-self &quot; (eg, as reflected by microbiotas but also by the fetus of placental mammals) as well as immune defense responses to injuring/injured &quot;non-self &quot; (eg, as reflected by plant resistance to biotic and abiotic stress and allograft rejection in mammals) evolved under pressure across the tree of life, that is, in plants, lower and higher invertebrates as well as lower and higher vertebrates. And evolution tells us why the overall existence of protected microbiotas really makes sense: It is the formation of the &quot;holobiont, &quot; - a metaorganism - that is, the host plus all of its associated microorganisms that - in terms of a strong unit of selection in evolution - provides that kind of fitness to all species on earth to successfully live, survive and reproduce. In other words: &quot;We all evolve, develop, grow, and reproduce as multigenomic ecosystems! Regarding reproduction, another impressive example of active immunologic protection of &quot;nonself &quot; refers to pregnancy in placental mammals that emerged about 400 millions of years ago. Similar to &quot;non-self &quot; microbiotas, pregnancy in placental mammals reflects an evolution-driven phenomenon on the basis of innate immunity-controlled tolerance induction to semiallogeneic non-injuring/non-injured &quot;non-self &quot; aiming to ensure reproduction! Altogether, the lesson learned from evolution of how to avoid allograft rejection is clear: prevent allograft injury to induce allotolerance, in other words: create a &quot;transplant holobiont. &quot;.}, }
@article {pmid25868684, year = {2015}, author = {Rädecker, N and Pogoreutz, C and Voolstra, CR and Wiedenmann, J and Wild, C}, title = {Nitrogen cycling in corals: the key to understanding holobiont functioning?.}, journal = {Trends in microbiology}, volume = {23}, number = {8}, pages = {490-497}, doi = {10.1016/j.tim.2015.03.008}, pmid = {25868684}, issn = {1878-4380}, mesh = {Animals ; Anthozoa/*metabolism/*microbiology ; Archaea/growth &amp; development/metabolism ; Bacteria/growth &amp; development/metabolism ; Dinoflagellida/*metabolism/physiology ; Fungi/growth &amp; development/metabolism ; Nitrogen/*metabolism ; *Nitrogen Cycle ; *Symbiosis ; }, abstract = {Corals are animals that form close mutualistic associations with endosymbiotic photosynthetic algae of the genus Symbiodinium. Together they provide the calcium carbonate framework of coral reef ecosystems. The importance of the microbiome (i.e., bacteria, archaea, fungi, and viruses) to holobiont functioning has only recently been recognized. Given that growth and density of Symbiodinium within the coral host is highly dependent on nitrogen availability, nitrogen-cycling microbes may be of fundamental importance to the stability of the coral-algae symbiosis and holobiont functioning, in particular under nutrient-enriched and -depleted scenarios. We summarize what is known about nitrogen cycling in corals and conclude that disturbance of microbial nitrogen cycling may be tightly linked to coral bleaching and disease.}, }
@article {pmid25852650, year = {2015}, author = {Balzano, S and Corre, E and Decelle, J and Sierra, R and Wincker, P and Da Silva, C and Poulain, J and Pawlowski, J and Not, F}, title = {Transcriptome analyses to investigate symbiotic relationships between marine protists.}, journal = {Frontiers in microbiology}, volume = {6}, number = {}, pages = {98}, pmid = {25852650}, issn = {1664-302X}, abstract = {Rhizaria are an important component of oceanic plankton communities worldwide. A number of species harbor eukaryotic microalgal symbionts, which are horizontally acquired in the environment at each generation. Although these photosymbioses are determinant for Rhizaria ability to thrive in oceanic ecosystems, the mechanisms for symbiotic interactions are unclear. Using high-throughput sequencing technology (i.e., 454), we generated large Expressed Sequence Tag (EST) datasets from four uncultured Rhizaria, an acantharian (Amphilonche elongata), two polycystines (Collozoum sp. and Spongosphaera streptacantha), and one phaeodarian (Aulacantha scolymantha). We assessed the main genetic features of the host/symbionts consortium (i.e., the holobiont) transcriptomes and found rRNA sequences affiliated to a wide range of bacteria and protists in all samples, suggesting that diverse microbial communities are associated with the holobionts. A particular focus was then carried out to search for genes potentially involved in symbiotic processes such as the presence of c-type lectins-coding genes, which are proteins that play a role in cell recognition among eukaryotes. Unigenes coding putative c-type lectin domains (CTLD) were found in the species bearing photosynthetic symbionts (A. elongata, Collozoum sp., and S. streptacantha) but not in the non-symbiotic one (A. scolymantha). More particularly, phylogenetic analyses group CTLDs from A. elongata and Collozoum sp. on a distinct branch from S. streptacantha CTLDs, which contained carbohydrate-binding motifs typically observed in other marine photosymbiosis. Our data suggest that similarly to other well-known marine photosymbiosis involving metazoans, the interactions of glycans with c-type lectins is likely involved in modulation of the host/symbiont specific recognition in Radiolaria.}, }
@article {pmid25786308, year = {2014}, author = {Provorov, NA and Tikhonovich, IA}, title = {[Super-species genetic systems].}, journal = {Zhurnal obshchei biologii}, volume = {75}, number = {4}, pages = {247-260}, pmid = {25786308}, issn = {0044-4596}, mesh = {Gene Transfer, Horizontal/*physiology ; Metagenome/*physiology ; Microbial Consortia/*physiology ; *Models, Biological ; Quorum Sensing/physiology ; Symbiosis/physiology ; }, abstract = {Genetic integration of diverse organisms results in generation of three types of the super-species systems of heredity: metagenome (set of genetic factors of the microbial community which occupies a certain ecological niche), symbiogenome (functionally integrated system of the partners' symbiotic genes) and hologenome (entire hereditary system of a symbiotically originated organism). The integrity of metagenome is based on the cross-regulation and horizontal transfer of genes in co-evolving organisms which in the soil microbial communities are accompanied by maintenance of the stable extracellular DNA pool. Formation of symbiogenome is related to the highly specific partners' signaling interactions which are responsible for development of the joint metabolic pathways based on the specialized cellular and tissue structures. Transitions of symbiogenome into hologenome are due to the endosymbiotic gene transfer from microsymbionts to their hosts. In symbiotic bacteria, these transitions are coupled with establishments of multi-component, reduced and rudimentary genomes revealed for the ecologically obligatory symbionts, genetically obligatory symbionts, and cellular organelles, respectively. Their evolution is related to the stringency of transmission of microsymbionts by hosts increased from pseudo-vertical (via environment) to the trans-embryonic (via embryos and the surrounding tissues) and trans-ovarian transmission (via germ cells) which are culminated in the cytoplasmic inheritance of cellular organelles. We suggest the hypothesis about generation of endophytic plant symbiogenome on the basis of soil metagenome subjected to the control of host by its involvement into the quorum sensing auto-regulation of microbial community.}, }
@article {pmid25773891, year = {2015}, author = {Metian, M and Hédouin, L and Ferrier-Pagès, C and Teyssié, JL and Oberhansli, F and Buschiazzo, E and Warnau, M}, title = {Metal bioconcentration in the scleractinian coral Stylophora pistillata: investigating the role of different components of the holobiont using radiotracers.}, journal = {Environmental monitoring and assessment}, volume = {187}, number = {4}, pages = {178}, pmid = {25773891}, issn = {1573-2959}, mesh = {Animals ; Anthozoa/*chemistry/physiology ; Environment ; Environmental Monitoring/*methods ; Metals/*analysis ; Water Pollutants, Chemical/*analysis ; }, abstract = {Bioconcentration kinetics of five metals (Ag, Cd, Co, Mn, and Zn) were determined in the scleractinian coral Stylophora pistillata (entire symbiotic association vs. cultured symbionts), using radiotracer techniques. Among contrasting element behaviors observed in S. pistillata, the highest efficiency of concentration and retention was observed for Ag in the symbiotic association (CFss reaching 5000 and T b½>1 year). Predominant proportion of this metal was found associated with the skeleton whereas the other metals were mainly present in the coral tissues (including host tissues and symbionts). A 96-h exposure of cultured symbionts (isolated zooxantellae from S. pistillata) indicated that they displayed a very high potential for metal bioconcentration (higher by 1 to 3 orders of magnitude compared to the skeleton). In addition, among the five elements investigated, Ag had the highest concentration factor in the cultured symbionts. Contrasting kinetic characteristics of skeleton vs. tissues offer interesting implications for biomonitoring purposes. Indeed, the skeleton was shown to display stable metal concentrations after an exposure (long retention time) and thereby allows recording contamination event on the long term, whereas the concentrations within coral tissues rapidly increased during the exposure and dropped when non-contaminating conditions were restored, allowing information on the current (short term) contamination status. The present study confirms that the coral can be seen as a two-compartment box model for metal bioconcentration: the tissues sensus latto as a first box governing metal entrance (with a crucial role played by the symbionts) and the skeleton as a second box where metal detoxification (storage) is taking place; the first box also depurates toward the environment when non-contaminating conditions are restored.}, }
@article {pmid25756121, year = {2014}, author = {Nguyen-Kim, H and Bouvier, T and Bouvier, C and Doan-Nhu, H and Nguyen-Ngoc, L and Rochelle-Newall, E and Baudoux, AC and Desnues, C and Reynaud, S and Ferrier-Pages, C and Bettarel, Y}, title = {High occurrence of viruses in the mucus layer of scleractinian corals.}, journal = {Environmental microbiology reports}, volume = {6}, number = {6}, pages = {675-682}, doi = {10.1111/1758-2229.12185}, pmid = {25756121}, issn = {1758-2229}, mesh = {Animals ; Anthozoa/*virology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Molecular Sequence Data ; Phylogeny ; Viruses/classification/genetics/*isolation &amp; purification ; }, abstract = {Viruses attract increasing interest from environmental microbiologists seeking to understand their function and role in coral health. However, little is known about their main ecological traits within the coral holobiont. In this study, a quantitative and qualitative characterization of viral and bacterial communities was conducted on the mucus of seven different coral species of the Van Phong Bay (Vietnam). On average, the concentrations of viruses and bacteria were, respectively, 17- and twofold higher in the mucus than in the surrounding water. The examination of bacterial community composition also showed remarkable differences between mucus and water samples. The percentage of active respiring cells was nearly threefold higher in mucus (m = 24.8%) than in water (m = 8.6%). Interestingly, a positive and highly significant correlation was observed between the proportion of active cells and viral abundance in the mucus, suggesting that the metabolism of the bacterial associates is probably a strong determinant of the distribution of viruses within the coral holobiont. Overall, coral mucus, given its unique physicochemical characteristics and sticking properties, can be regarded as a highly selective biotope for abundant, diversified and specialized symbiotic microbial and viral organisms.}, }
@article {pmid25745427, year = {2015}, author = {Wichard, T and Charrier, B and Mineur, F and Bothwell, JH and Clerck, OD and Coates, JC}, title = {The green seaweed Ulva: a model system to study morphogenesis.}, journal = {Frontiers in plant science}, volume = {6}, number = {}, pages = {72}, pmid = {25745427}, issn = {1664-462X}, abstract = {Green macroalgae, mostly represented by the Ulvophyceae, the main multicellular branch of the Chlorophyceae, constitute important primary producers of marine and brackish coastal ecosystems. Ulva or sea lettuce species are some of the most abundant representatives, being ubiquitous in coastal benthic communities around the world. Nonetheless the genus also remains largely understudied. This review highlights Ulva as an exciting novel model organism for studies of algal growth, development and morphogenesis as well as mutualistic interactions. The key reasons that Ulva is potentially such a good model system are: (i) patterns of Ulva development can drive ecologically important events, such as the increasing number of green tides observed worldwide as a result of eutrophication of coastal waters, (ii) Ulva growth is symbiotic, with proper development requiring close association with bacterial epiphytes, (iii) Ulva is extremely developmentally plastic, which can shed light on the transition from simple to complex multicellularity and (iv) Ulva will provide additional information about the evolution of the green lineage.}, }
@article {pmid25737238, year = {2015}, author = {Wang, J and Kalyan, S and Steck, N and Turner, LM and Harr, B and Künzel, S and Vallier, M and Häsler, R and Franke, A and Oberg, HH and Ibrahim, SM and Grassl, GA and Kabelitz, D and Baines, JF}, title = {Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome.}, journal = {Nature communications}, volume = {6}, number = {}, pages = {6440}, pmid = {25737238}, issn = {2041-1723}, mesh = {Animals ; Base Sequence ; *Biological Evolution ; Crosses, Genetic ; DNA Primers/genetics ; Flow Cytometry ; Gastrointestinal Microbiome/*genetics ; Genetics, Population ; Genome/*genetics ; Germany ; Hybridization, Genetic/*genetics ; Mice/*genetics/microbiology ; *Models, Genetic ; Molecular Sequence Data ; Quantitative Trait Loci ; Selection, Genetic ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Recent evidence suggests that natural selection operating on hosts to maintain their microbiome contributes to the emergence of new species, that is, the 'hologenomic basis of speciation'. Here we analyse the gut microbiota of two house mice subspecies, Mus musculus musculus and M. m. domesticus, across their Central European hybrid zone, in addition to hybrids generated in the lab. Hybrid mice display widespread transgressive phenotypes (that is, exceed or fall short of parental values) in a variety of measures of bacterial community structure, which reveals the importance of stabilizing selection operating on the intestinal microbiome within species. Further genetic and immunological analyses reveal genetic incompatibilities, aberrant immune gene expression and increased intestinal pathology associated with altered community structure among hybrids. These results provide unique insight into the consequences of evolutionary divergence in a vertebrate 'hologenome', which may be an unrecognized contributing factor to reproductive isolation in this taxonomic group.}, }
@article {pmid25732740, year = {2015}, author = {Bosch, TC and Grasis, JA and Lachnit, T}, title = {Microbial ecology in Hydra: why viruses matter.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {53}, number = {3}, pages = {193-200}, pmid = {25732740}, issn = {1976-3794}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; 5F32AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteriophages/*physiology ; Biological Evolution ; Cnidaria/*virology ; Hydra/*virology ; Hydrobiology ; Microbiota/physiology ; Species Specificity ; *Symbiosis ; *Virus Physiological Phenomena ; }, abstract = {While largely studied because of their harmful effects on human health, there is growing appreciation that viruses are also important members of the animal holobiont. This review highlights recent findings on viruses associated with Hydra and related Cnidaria. These early evolutionary diverging animals not only select their bacterial communities but also select for viral communities in a species-specific manner. The majority of the viruses associating with these animals are bacteriophages. We demonstrate that the animal host and its virome have evolved into a homeostatic, symbiotic relationship and propose that viruses are an important part of the Hydra holobiont by controlling the species-specific microbiome. We conclude that beneficial virus-bacterial-host interactions should be considered as an integral part of animal development and evolution.}, }
@article {pmid25724277, year = {2015}, author = {Peterson, BF and Stewart, HL and Scharf, ME}, title = {Quantification of symbiotic contributions to lower termite lignocellulose digestion using antimicrobial treatments.}, journal = {Insect biochemistry and molecular biology}, volume = {59}, number = {}, pages = {80-88}, doi = {10.1016/j.ibmb.2015.02.009}, pmid = {25724277}, issn = {1879-0240}, mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/metabolism ; Gastrointestinal Tract/metabolism/microbiology ; Isoptera/*drug effects/metabolism/microbiology ; Lignin/*metabolism ; Symbiosis ; }, abstract = {Animal-microbe co-evolution and symbiosis are broadly distributed across the animal kingdom. Insects form a myriad of associations with microbes ranging from vectoring of pathogens to intracellular, mutualistic relationships. Lower termites are key models for insect-microbe symbiosis because of the diversity, complexity and functionality of their unique tripartite symbiosis. This collaboration allows termites to live on a diet of nitrogen-poor lignocellulose. Recent functional investigations of lignocellulose digestion in lower termites have primarily focused on the contributions of the eukaryotic members of the termite holobiont (termite and protist). Here, using multiple antimicrobial treatments, we induced differing degrees of dysbiosis in the termite gut, leading to variably altered symbiont abundance and diversity, and lignocellulolytic capacity. Although protists are clearly affected by antimicrobial treatments, our findings provide novel evidence that the removal of distinct groups of bacteria partially reduces, but does not abolish, the saccharolytic potential of the termite gut holobiont. This is specifically manifested by reductions of 23-47% and 30-52% in glucose and xylose yields respectively from complex lignocellulose. Thus, all members of the lower termite holobiont (termite, protist and prokaryotes) are involved in the process of efficient, sustained lignocellulase activity. This unprecedented quantification of the relative importance of prokaryotes in this system emphasizes the collaborative nature of the termite holobiont, and the relevance of lower termites as models for inter-domain symbioses.}, }
@article {pmid25673681, year = {2015}, author = {Dheilly, NM and Maure, F and Ravallec, M and Galinier, R and Doyon, J and Duval, D and Leger, L and Volkoff, AN and Missé, D and Nidelet, S and Demolombe, V and Brodeur, J and Gourbal, B and Thomas, F and Mitta, G}, title = {Who is the puppet master? Replication of a parasitic wasp-associated virus correlates with host behaviour manipulation.}, journal = {Proceedings. Biological sciences}, volume = {282}, number = {1803}, pages = {20142773}, pmid = {25673681}, issn = {1471-2954}, mesh = {Animals ; Coleoptera/*parasitology/physiology/*virology ; Female ; Host-Parasite Interactions ; Larva/parasitology/virology ; Molecular Sequence Data ; Oviducts/virology ; RNA Viruses/*physiology ; Wasps/physiology/*virology ; }, abstract = {Many parasites modify their host behaviour to improve their own transmission and survival, but the proximate mechanisms remain poorly understood. An original model consists of the parasitoid Dinocampus coccinellae and its coccinellid host, Coleomegilla maculata; during the behaviour manipulation, the parasitoid is not in contact with its host anymore. We report herein the discovery and characterization of a new RNA virus of the parasitoid (D. coccinellae paralysis virus, DcPV). Using a combination of RT-qPCR and transmission electron microscopy, we demonstrate that DcPV is stored in the oviduct of parasitoid females, replicates in parasitoid larvae and is transmitted to the host during larval development. Next, DcPV replication in the host's nervous tissue induces a severe neuropathy and antiviral immune response that correlate with the paralytic symptoms characterizing the behaviour manipulation. Remarkably, virus clearance correlates with recovery of normal coccinellid behaviour. These results provide evidence that changes in ladybeetle behaviour most likely result from DcPV replication in the cerebral ganglia rather than by manipulation by the parasitoid. This offers stimulating prospects for research on parasitic manipulation by suggesting for the first time that behaviour manipulation could be symbiont-mediated.}, }
@article {pmid25668159, year = {2015}, author = {Pantos, O and Bongaerts, P and Dennis, PG and Tyson, GW and Hoegh-Guldberg, O}, title = {Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix.}, journal = {The ISME journal}, volume = {9}, number = {9}, pages = {1916-1927}, pmid = {25668159}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/genetics ; Australia ; *Coral Reefs ; Gammaproteobacteria/genetics ; Genotype ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rhodobacteraceae/genetics ; }, abstract = {Reef-building corals form complex relationships with a range of microorganisms including bacteria, archaea, fungi and the unicellular microalgae of the genus Symbiodinium, which together form the coral holobiont. These symbionts are known to have both beneficial and deleterious effects on their coral host, but little is known about what the governing factors of these relationships are, or the interactions that exist between the different members of the holobiont and their environment. Here we used 16S ribosomal RNA gene amplicon sequencing to investigate how archaeal and bacterial communities associated with the widespread scleractinian coral Seriatopora hystrix are influenced by extrinsic (reef habitat and geographic location) and intrinsic (host genotype and Symbiodinium subclade) factors. Bacteria dominate the microbiome of S. hystrix, with members of the Alphaproteobacteria, Gammaproteobacteria and Bacteriodetes being the most predominant in all samples. The richness and evenness of these communities varied between reef habitats, but there was no significant difference between distinct coral host lineages or corals hosting distinct Symbiodinium subclades. The coral microbiomes correlated to reef habitat (depth) and geographic location, with a negative correlation between Alpha- and Gammaproteobacteria, driven by the key members of both groups (Rhodobacteraceae and Hahellaceae, respectively), which showed significant differences between location and depth. This study suggests that the control of microbial communities associated with the scleractinian coral S. hystrix is driven primarily by external environmental conditions rather than by those directly associated with the coral holobiont.}, }
@article {pmid25655016, year = {2015}, author = {Vandenkoornhuyse, P and Quaiser, A and Duhamel, M and Le Van, A and Dufresne, A}, title = {The importance of the microbiome of the plant holobiont.}, journal = {The New phytologist}, volume = {206}, number = {4}, pages = {1196-1206}, doi = {10.1111/nph.13312}, pmid = {25655016}, issn = {1469-8137}, mesh = {Biological Evolution ; *Microbiota ; Plants/*microbiology ; }, abstract = {Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.}, }
@article {pmid25621279, year = {2014}, author = {Thompson, JR and Rivera, HE and Closek, CJ and Medina, M}, title = {Microbes in the coral holobiont: partners through evolution, development, and ecological interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {176}, pmid = {25621279}, issn = {2235-2988}, mesh = {Animals ; Anthozoa/genetics/*microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Biological Evolution ; *Ecosystem ; Symbiosis ; }, abstract = {In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health-not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions.}, }
@article {pmid25615440, year = {2015}, author = {Tout, J and Jeffries, TC and Petrou, K and Tyson, GW and Webster, NS and Garren, M and Stocker, R and Ralph, PJ and Seymour, JR}, title = {Chemotaxis by natural populations of coral reef bacteria.}, journal = {The ISME journal}, volume = {9}, number = {8}, pages = {1764-1777}, pmid = {25615440}, issn = {1751-7370}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*drug effects/genetics ; Chemotactic Factors/pharmacology ; Chemotaxis/*drug effects ; *Coral Reefs ; DNA, Bacterial/analysis ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/microbiology ; Sulfonium Compounds/pharmacology ; Vibrio/genetics ; }, abstract = {Corals experience intimate associations with distinct populations of marine microorganisms, but the microbial behaviours underpinning these relationships are poorly understood. There is evidence that chemotaxis is pivotal to the infection process of corals by pathogenic bacteria, but this evidence is limited to experiments using cultured isolates under laboratory conditions. We measured the chemotactic capabilities of natural populations of coral-associated bacteria towards chemicals released by corals and their symbionts, including amino acids, carbohydrates, ammonium and dimethylsulfoniopropionate (DMSP). Laboratory experiments, using a modified capillary assay, and in situ measurements, using a novel microfabricated in situ chemotaxis assay, were employed to quantify the chemotactic responses of natural microbial assemblages on the Great Barrier Reef. Both approaches showed that bacteria associated with the surface of the coral species Pocillopora damicornis and Acropora aspera exhibited significant levels of chemotaxis, particularly towards DMSP and amino acids, and that these levels of chemotaxis were significantly higher than that of bacteria inhabiting nearby, non-coral-associated waters. This pattern was supported by a significantly higher abundance of chemotaxis and motility genes in metagenomes within coral-associated water types. The phylogenetic composition of the coral-associated chemotactic microorganisms, determined using 16S rRNA amplicon pyrosequencing, differed from the community in the seawater surrounding the coral and comprised known coral associates, including potentially pathogenic Vibrio species. These findings indicate that motility and chemotaxis are prevalent phenotypes among coral-associated bacteria, and we propose that chemotaxis has an important role in the establishment and maintenance of specific coral-microbe associations, which may ultimately influence the health and stability of the coral holobiont.}, }
@article {pmid25548731, year = {2014}, author = {Freeman, CJ and Easson, CG and Baker, DM}, title = {Metabolic diversity and niche structure in sponges from the Miskito Cays, Honduras.}, journal = {PeerJ}, volume = {2}, number = {}, pages = {e695}, pmid = {25548731}, issn = {2167-8359}, abstract = {Hosting symbionts provides many eukaryotes with access to the products of microbial metabolism that are crucial for host performance. On tropical coral reefs, many (High Microbial Abundance [HMA]) but not all (Low Microbial Abundance [LMA]) marine sponges host abundant symbiont communities. Although recent research has revealed substantial variation in these sponge-microbe associations (termed holobionts), little is known about the ecological implications of this diversity. We investigated the expansion of diverse sponge species across isotopic niche space by calculating niche size (as standard ellipse area [SEA c ]) and assessing the relative placement of common sponge species in bivariate (δ (13)C and δ (15)N) plots. Sponges for this study were collected from the relatively isolated reefs within the Miskito Cays of Honduras. These reefs support diverse communities of HMA and LMA species that together span a gradient of photosymbiont abundance, as revealed by chlorophyll a analysis. HMA sponges occupied unique niche space compared to LMA species, but the placement of some HMA sponges was driven by photosymbiont abundance. In addition, photosymbiont abundance explained a significant portion of the variation in isotope values, suggesting that access to autotrophic metabolism provided by photosymbionts is an important predictor in the location of species within isotopic space. Host identity accounted for over 70% of the variation in isotope values within the Miskito Cays and there was substantial variation in the placement of individual species within isotopic niche space, suggesting that holobiont metabolic diversity may allow taxonomically diverse sponge species to utilize unique sources of nutrients within a reef system. This study provides initial evidence that microbial symbionts allow sponges to expand into novel physiochemical niche space. This expansion may reduce competitive interactions within coral reefs and promote diversification of these communities.}, }
@article {pmid25477868, year = {2014}, author = {Hardoim, CC and Cardinale, M and Cúcio, AC and Esteves, AI and Berg, G and Xavier, JR and Cox, CJ and Costa, R}, title = {Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine sponges.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {611}, pmid = {25477868}, issn = {1664-302X}, abstract = {Complex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and Ircinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.}, }
@article {pmid25467196, year = {2014}, author = {Rosic, N and Kaniewska, P and Chan, CK and Ling, EY and Edwards, D and Dove, S and Hoegh-Guldberg, O}, title = {Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {1052}, pmid = {25467196}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/*genetics/metabolism ; Computational Biology ; Coral Reefs ; Energy Metabolism ; Gene Expression Profiling ; *Gene Expression Regulation ; Molecular Sequence Annotation ; Oxidation-Reduction ; Photosynthesis ; Stress, Physiological/*genetics ; Temperature ; *Transcription, Genetic ; }, abstract = {BACKGROUND: Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include coral bleaching (reduced concentrations of algal symbionts), decreased coral growth and calcification, and increased incidence of diseases and mortality. Understanding how elevated temperatures and nutrient concentration affect early transcriptional changes in corals and their algal endosymbionts is critically important for evaluating the responses of coral reefs to global changes happening in the environment. Here, we investigated the expression of genes in colonies of the reef-building coral Acropora aspera exposed to short-term sub-lethal levels of thermal (+6°C) and nutrient stress (ammonium-enrichment: 20 μM).<br><br>RESULTS: The RNA-Seq data provided hundreds of differentially expressed genes (DEGs) corresponding to various stress regimes, with 115 up- and 78 down-regulated genes common to all stress regimes. A list of DEGs included up-regulated coral genes like cytochrome c oxidase and NADH-ubiquinone oxidoreductase and up-regulated photosynthetic genes of algal origin, whereas coral GFP-like fluorescent chromoprotein and sodium/potassium-transporting ATPase showed reduced transcript levels. Taxonomic analyses of the coral holobiont disclosed the dominant presence of transcripts from coral (~70%) and Symbiodinium (~10-12%), as well as ~15-20% of unknown sequences which lacked sequence identity to known genes. Gene ontology analyses revealed enriched pathways, which led to changes in the dynamics of protein networks affecting growth, cellular processes, and energy requirement.<br><br>CONCLUSIONS: In corals with preserved symbiont physiological performance (based on Fv/Fm, photo-pigment and symbiont density), transcriptomic changes and DEGs provided important insight into early stages of the stress response in the coral holobiont. Although there were no signs of coral bleaching after exposure to short-term thermal and nutrient stress conditions, we managed to detect oxidative stress and apoptotic changes on a molecular level and provide a list of prospective stress biomarkers for both partners in symbiosis. Consequently, our findings are important for understanding and anticipating impacts of anthropogenic global climate change on coral reefs.}, }
@article {pmid25467066, year = {2015}, author = {Iluz, D and Dubinsky, Z}, title = {Coral photobiology: new light on old views.}, journal = {Zoology (Jena, Germany)}, volume = {118}, number = {2}, pages = {71-78}, doi = {10.1016/j.zool.2014.08.003}, pmid = {25467066}, issn = {1873-2720}, mesh = {Acclimatization/physiology ; Animals ; Anthozoa/*physiology ; Calcification, Physiologic/physiology ; Chlorophyta/physiology ; Energy Metabolism ; *Light ; Photobiology ; Photosynthesis/physiology ; *Symbiosis ; }, abstract = {The relationship between reef-building corals and light-harvesting pigments of zooxanthellae (Symbiodinium sp.) has been acknowledged for decades. The photosynthetic activity of the algal endocellular symbionts may provide up to 90% of the energy needed for the coral holobiont. This relationship limits the bathymetric distribution of coral reefs to the upper 100 m of tropical shorelines. However, even corals growing under high light intensities have to supplement the photosynthates translocated from the algae by predation on nutrient-rich zooplankton. New information has revealed how the fate of carbon acquired through photosynthesis differs from that secured by predation, whose rates are controlled by light-induced tentacular extension. The Goreau paradigm of &quot;light-enhanced calcification&quot; is being reevaluated, based on evidence that blue light stimulates coral calcification independently from photosynthesis rates. Furthermore, under dim light, calcification rates were stoichiometrically uncoupled from photosynthesis. The rates of photosynthesis of the zooxanthellae exhibit a clear endogenous rhythmicity maintained by light patterns. This daily pattern is concomitant with a periodicity of all the antioxidant protective mechanisms that wax and wane to meet the concomitant fluctuation in oxygen evolution. The phases of the moon are involved in the triggering of coral reproduction and control the spectacular annual mass-spawning events taking place in several reefs. The intensity and directionality of the underwater light field affect the architecture of coral colonies, leading to an optimization of the exposure of the zooxanthellae to light. We present a summary of major gaps in our understanding of the relationship between light and corals as a roadmap for future research.}, }
@article {pmid25431341, year = {2015}, author = {Hoppers, A and Stoudenmire, J and Wu, S and Lopanik, NB}, title = {Antibiotic activity and microbial community of the temperate sponge, Haliclona sp.}, journal = {Journal of applied microbiology}, volume = {118}, number = {2}, pages = {419-430}, doi = {10.1111/jam.12709}, pmid = {25431341}, issn = {1365-2672}, mesh = {Animals ; Anti-Bacterial Agents/isolation &amp; purification/*pharmacology ; Bacteria/genetics/isolation &amp; purification ; Haliclona/chemistry/genetics/*microbiology ; Seawater/microbiology ; }, abstract = {AIMS: Sessile marine invertebrates engage in a diverse array of beneficial interactions with bacterial symbionts. One feature of some of these relationships is the presence of bioactive natural products that can defend the holobiont from predation, competition or disease. In this study, we investigated the antimicrobial activity and microbial community of a common temperate sponge from coastal North Carolina.<br><br>METHODS AND RESULTS: The sponge was identified as a member of the genus Haliclona, a prolific source of bioactive natural products, based on its 18S rRNA gene sequence. The crude chemical extract and methanol partition had broad activity against the assayed Gram-negative and Gram-positive pathogenic bacteria. Further fractionation resulted in two groups of compounds with differing antimicrobial activity, primarily against Gram-positive test organisms. There was, however, notable activity against the Gram-negative marine pathogen, Vibrio parahaemolyticus. Microbial community analysis of the sponge and surrounding sea water via denaturing gradient gel electrophoresis (DGGE) indicates that it harbours a distinct group of bacterial associates.<br><br>CONCLUSIONS: The common temperate sponge, Haliclona sp., is a source of multiple antimicrobial compounds and has some consistent microbial community members that may play a role in secondary metabolite production.<br><br>These data suggest that common temperate sponges can be a source of bioactive chemical and microbial diversity. Further studies may reveal the importance of the microbial associates to the sponge and natural product biosynthesis.}, }
@article {pmid25430522, year = {2016}, author = {Salvucci, E}, title = {Microbiome, holobiont and the net of life.}, journal = {Critical reviews in microbiology}, volume = {42}, number = {3}, pages = {485-494}, doi = {10.3109/1040841X.2014.962478}, pmid = {25430522}, issn = {1549-7828}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Biological Evolution ; Humans ; *Microbiota ; *Symbiosis ; }, abstract = {Holistic emerging approaches allow us to understand that every organism is the result of integration mechanisms observed at every level of nature: integration of DNA from virus and bacteria in metazoans, endosymbiotic relationships and holobionts. Horizontal gene transfer events in Bacteria, Archaea and Eukaryotes have resulted in the chimeric nature of genomes. As a continuity of this genomic landscape, the human body contains more bacterial than human cells. Human microbiome has co-evolved with the human being as a unity called holobiont. The loss of part of our microbiome along evolution can explain the continuous increasing incidence of immune and inflammatory-related diseases. Life is a continuous process in which the organism experiences its environment and this interaction impacts in the epigenetic system and the genomic structure. The emerging perspectives restitute the great importance of Lamarck's theoretical contributions (the milieu) and Darwin's pangenesis theory.}, }
@article {pmid25401092, year = {2014}, author = {Stilling, RM and Bordenstein, SR and Dinan, TG and Cryan, JF}, title = {Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {147}, pmid = {25401092}, issn = {2235-2988}, support = {R01 GM085163/GM/NIGMS NIH HHS/United States ; R01GM085163/GM/NIGMS NIH HHS/United States ; }, mesh = {Adaptation, Biological ; Animals ; Behavior ; *Biological Evolution ; Brain/*physiology ; Epigenesis, Genetic ; Gene-Environment Interaction ; Host-Pathogen Interactions/*physiology ; Humans ; Microbiota ; Symbiosis ; }, abstract = {The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a &quot;social triangle&quot; that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective.}, }
@article {pmid25387109, year = {2015}, author = {Denman, SE and McSweeney, CS}, title = {The early impact of genomics and metagenomics on ruminal microbiology.}, journal = {Annual review of animal biosciences}, volume = {3}, number = {}, pages = {447-465}, doi = {10.1146/annurev-animal-022114-110705}, pmid = {25387109}, issn = {2165-8110}, mesh = {Animals ; Dietary Fiber/metabolism ; Genomics ; Methane/biosynthesis ; Microbiota/*genetics ; Phylogeny ; Rumen/*microbiology ; Ruminants/*microbiology ; }, abstract = {Knowledge gained from early and recent studies that define the functions of microbial populations within the rumen microbiome is essential to allow for directed rumen manipulation strategies. A large number of omic studies have focused on carbohydrate active enzymes either for improved fiber digestion within the animal or for use in industries such as biofuels. Studies of the rumen microbiome with respect to methane production and abatement strategies have led to initiatives for defining the microbiome of low- and high-methane-emitting animals while ensuring optimal feed conversion. With advances in omic technologies, the ability to link host genetics and the rumen microbiome by studying all the biological components (holobiont) through the use of hologenomics has begun. However, a program to culture and isolate microbial species for the purpose of standard microbial characterization to aid in assigning function to genomic data remains critical, especially for genes of unknown function.}, }
@article {pmid25360746, year = {2014}, author = {Schrameyer, V and Wangpraseurt, D and Hill, R and Kühl, M and Larkum, AW and Ralph, PJ}, title = {Light respiratory processes and gross photosynthesis in two scleractinian corals.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e110814}, pmid = {25360746}, issn = {1932-6203}, mesh = {Animals ; Anthozoa/*metabolism/physiology/*radiation effects ; Biological Transport/radiation effects ; Carbon Dioxide/metabolism ; *Light ; Oxygen/metabolism ; Photosynthesis/*radiation effects ; Respiration/*radiation effects ; Symbiosis/radiation effects ; }, abstract = {The light dependency of respiratory activity of two scleractinian corals was examined using O2 microsensors and CO2 exchange measurements. Light respiration increased strongly but asymptotically with elevated irradiance in both species. Light respiration in Pocillopora damicornis was higher than in Pavona decussata under low irradiance, indicating species-specific differences in light-dependent metabolic processes. Overall, the coral P. decussata exhibited higher CO2 uptake rates than P. damicornis over the experimental irradiance range. P. decussata also harboured twice as many algal symbionts and higher total protein biomass compared to P. damicornis, possibly resulting in self-shading of the symbionts and/or changes in host tissue specific light distribution. Differences in light respiration and CO2 availability could be due to host-specific characteristics that modulate the symbiont microenvironment, its photosynthesis, and hence the overall performance of the coral holobiont.}, }
@article {pmid25343582, year = {2014}, author = {Grasis, JA and Lachnit, T and Anton-Erxleben, F and Lim, YW and Schmieder, R and Fraune, S and Franzenburg, S and Insua, S and Machado, G and Haynes, M and Little, M and Kimble, R and Rosenstiel, P and Rohwer, FL and Bosch, TC}, title = {Species-specific viromes in the ancestral holobiont Hydra.}, journal = {PloS one}, volume = {9}, number = {10}, pages = {e109952}, pmid = {25343582}, issn = {1932-6203}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; 1F32AI098518/AI/NIAID NIH HHS/United States ; 1R21AI094534/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/isolation &amp; purification/virology ; Bacteriophages/genetics/isolation &amp; purification/metabolism ; Hydra/metabolism/microbiology/ultrastructure/*virology ; Reproducibility of Results ; Sequence Analysis, DNA ; Species Specificity ; *Symbiosis ; Viruses/genetics/isolation &amp; purification/*metabolism ; }, abstract = {Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.}, }
@article {pmid25309882, year = {2014}, author = {Apidianakis, Y and Ferrandon, D}, title = {Modeling hologenome imbalances in inflammation and cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {4}, number = {}, pages = {134}, pmid = {25309882}, issn = {2235-2988}, mesh = {Animals ; Humans ; Inflammation/*complications/*etiology ; Neoplasms/*complications/*etiology ; }, }
@article {pmid25278474, year = {2014}, author = {Grover, R and Ferrier-Pagès, C and Maguer, JF and Ezzat, L and Fine, M}, title = {Nitrogen fixation in the mucus of Red Sea corals.}, journal = {The Journal of experimental biology}, volume = {217}, number = {Pt 22}, pages = {3962-3963}, doi = {10.1242/jeb.111591}, pmid = {25278474}, issn = {1477-9145}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida/*metabolism ; Indian Ocean ; Mucus ; Nitrogen/*analysis ; *Nitrogen Fixation ; Nitrogen Isotopes ; Seawater/*chemistry ; Symbiosis ; }, abstract = {Scleractinian corals are essential constituents of tropical reef ecological diversity. They live in close association with diazotrophs [dinitrogen (N2)-fixing microbes], which can fix high rates of N2. Whether corals benefit from this extrinsic nitrogen source is still under debate. Until now, N2 fixation rates have been indirectly estimated using the acetylene reduction assay, which does not permit assessment of the amount of nitrogen incorporated into the different compartments of the coral holobiont. In the present study, the (15)N2 technique was applied for the first time on three Red Sea coral species. Significant (15)N enrichment was measured in particles released by corals to the surrounding seawater. N2 fixation rates were species specific and as high as 1.6-2 ng N day(-1) l(-1). However, no significant enrichment was measured in the symbiotic dinoflagellates or the coral host tissues, suggesting that corals do not benefit from diazotrophic N2 fixation.}, }
@article {pmid25272328, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.}, journal = {Marine drugs}, volume = {12}, number = {10}, pages = {5089-5122}, pmid = {25272328}, issn = {1660-3397}, mesh = {Animals ; Archaea/physiology ; Bacteria/metabolism ; Fungi/physiology ; Humans ; Porifera/*microbiology ; Quorum Sensing/*physiology ; Symbiosis/*physiology ; }, abstract = {Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.}, }
@article {pmid25213651, year = {2015}, author = {Fernando, SC and Wang, J and Sparling, K and Garcia, GD and Francini-Filho, RB and de Moura, RL and Paranhos, R and Thompson, FL and Thompson, JR}, title = {Microbiota of the major South Atlantic reef building coral Mussismilia.}, journal = {Microbial ecology}, volume = {69}, number = {2}, pages = {267-280}, pmid = {25213651}, issn = {1432-184X}, support = {P30-ES002109/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Brazil ; Cloning, Molecular ; Coral Reefs ; DNA, Bacterial/genetics ; Gammaproteobacteria/classification/genetics/isolation &amp; purification ; Gene Library ; *Microbiota ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation.}, }
@article {pmid25205353, year = {2014}, author = {Bosch, TC and Adamska, M and Augustin, R and Domazet-Loso, T and Foret, S and Fraune, S and Funayama, N and Grasis, J and Hamada, M and Hatta, M and Hobmayer, B and Kawai, K and Klimovich, A and Manuel, M and Shinzato, C and Technau, U and Yum, S and Miller, DJ}, title = {How do environmental factors influence life cycles and development? An experimental framework for early-diverging metazoans.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {36}, number = {12}, pages = {1185-1194}, pmid = {25205353}, issn = {1521-1878}, support = {F32 AI098418/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Biological Evolution ; Cnidaria/classification/genetics/*growth &amp; development ; Ecosystem ; Extinction, Biological ; Gene Expression Regulation, Developmental ; *Gene-Environment Interaction ; Life Cycle Stages/*genetics ; Metamorphosis, Biological/genetics ; Phylogeny ; Porifera/classification/genetics/*growth &amp; development ; Signal Transduction ; }, abstract = {Ecological developmental biology (eco-devo) explores the mechanistic relationships between the processes of individual development and environmental factors. Recent studies imply that some of these relationships have deep evolutionary origins, and may even pre-date the divergences of the simplest extant animals, including cnidarians and sponges. Development of these early diverging metazoans is often sensitive to environmental factors, and these interactions occur in the context of conserved signaling pathways and mechanisms of tissue homeostasis whose detailed molecular logic remain elusive. Efficient methods for transgenesis in cnidarians together with the ease of experimental manipulation in cnidarians and sponges make them ideal models for understanding causal relationships between environmental factors and developmental mechanisms. Here, we identify major questions at the interface between animal evolution and development and outline a road map for research aimed at identifying the mechanisms that link environmental factors to developmental mechanisms in early diverging metazoans. Also watch the Video Abstract.}, }
@article {pmid25202306, year = {2014}, author = {Parkinson, JE and Baums, IB}, title = {The extended phenotypes of marine symbioses: ecological and evolutionary consequences of intraspecific genetic diversity in coral-algal associations.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {445}, pmid = {25202306}, issn = {1664-302X}, abstract = {Reef-building corals owe much of their success to a symbiosis with dinoflagellate microalgae in the genus Symbiodinium. In this association, the performance of each organism is tied to that of its partner, and together the partners form a holobiont that can be subject to selection. Climate change affects coral reefs, which are declining globally as a result. Yet the extent to which coral holobionts will be able to acclimate or evolve to handle climate change and other stressors remains unclear. Selection acts on individuals and evidence from terrestrial systems demonstrates that intraspecific genetic diversity plays a significant role in symbiosis ecology and evolution. However, we have a limited understanding of the effects of such diversity in corals. As molecular methods have advanced, so too has our recognition of the taxonomic and functional diversity of holobiont partners. Resolving the major components of the holobiont to the level of the individual will help us assess the importance of intraspecific diversity and partner interactions in coral-algal symbioses. Here, we hypothesize that unique combinations of coral and algal individuals yield functional diversity that affects not only the ecology and evolution of the coral holobiont, but associated communities as well. Our synthesis is derived from reviewing existing evidence and presenting novel data. By incorporating the effects of holobiont extended phenotypes into predictive models, we may refine our understanding of the evolutionary trajectory of corals and reef communities responding to climate change.}, }
@article {pmid25202301, year = {2014}, author = {Roth, MS}, title = {The engine of the reef: photobiology of the coral-algal symbiosis.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {422}, pmid = {25202301}, issn = {1664-302X}, abstract = {Coral reef ecosystems thrive in tropical oligotrophic oceans because of the relationship between corals and endosymbiotic dinoflagellate algae called Symbiodinium. Symbiodinium convert sunlight and carbon dioxide into organic carbon and oxygen to fuel coral growth and calcification, creating habitat for these diverse and productive ecosystems. Light is thus a key regulating factor shaping the productivity, physiology, and ecology of the coral holobiont. Similar to all oxygenic photoautotrophs, Symbiodinium must safely harvest sunlight for photosynthesis and dissipate excess energy to prevent oxidative stress. Oxidative stress is caused by environmental stressors such as those associated with global climate change, and ultimately leads to breakdown of the coral-algal symbiosis known as coral bleaching. Recently, large-scale coral bleaching events have become pervasive and frequent threatening and endangering coral reefs. Because the coral-algal symbiosis is the biological engine producing the reef, the future of coral reef ecosystems depends on the ecophysiology of the symbiosis. This review examines the photobiology of the coral-algal symbiosis with particular focus on the photophysiological responses and timescales of corals and Symbiodinium. Additionally, this review summarizes the light environment and its dynamics, the vulnerability of the symbiosis to oxidative stress, the abiotic and biotic factors influencing photosynthesis, the diversity of the coral-algal symbiosis, and recent advances in the field. Studies integrating physiology with the developing &quot;omics&quot; fields will provide new insights into the coral-algal symbiosis. Greater physiological and ecological understanding of the coral-algal symbiosis is needed for protection and conservation of coral reefs.}, }
@article {pmid25199498, year = {2014}, author = {Pillai, P and Gouhier, TC and Vollmer, SV}, title = {The cryptic role of biodiversity in the emergence of host-microbial mutualisms.}, journal = {Ecology letters}, volume = {17}, number = {11}, pages = {1437-1446}, doi = {10.1111/ele.12349}, pmid = {25199498}, issn = {1461-0248}, mesh = {*Biodiversity ; Ecosystem ; Genetic Fitness ; Microbiota ; *Models, Biological ; *Symbiosis ; }, abstract = {The persistence of mutualisms in host-microbial - or holobiont - systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist 'cheater' species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host-microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales.}, }
@article {pmid25191338, year = {2014}, author = {Gilbert, SF}, title = {A holobiont birth narrative: the epigenetic transmission of the human microbiome.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {282}, pmid = {25191338}, issn = {1664-8021}, abstract = {This essay plans to explore, expand, and re-tell the human birth narrative. Usually, human birth narratives focus on the origins of a new individual, focusing on the mother and fetus. This essay discusses birth as the origin of a new community. For not only is the eukaryotic body being reproduced, but so also are the bodies of its symbiotic microbes and so is the set of relationships between these organic components. Several parts of the new narrative are surprising: (1) bacterial symbionts might cause some of the characteristics of pregnancy and prepare a symbiotic community for transfer; (2) the first bacterial colonizers of the mammalian organism my enter the fetus prior to the lysing of the amniotic membrane and birth; (3) the same signals that often cause immunological attack against a microbe may serve under these conditions to signal homeostatic stability between symbiont and host; and (4) the mother may actively provide substances that promote the growth and settlement of helpful bacteria. The birth of the holobiont exemplifies principles of co-evolution, co-development, niche construction, and scaffolding. Birth is nothing less than the passage from one set of symbiotic relationships to another.}, }
@article {pmid25178787, year = {2014}, author = {Watson, J and Degnan, B and Degnan, S and Krömer, JO}, title = {Determining the biomass composition of a sponge holobiont for flux analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1191}, number = {}, pages = {107-125}, doi = {10.1007/978-1-4939-1170-7_7}, pmid = {25178787}, issn = {1940-6029}, mesh = {Animals ; Biomass ; Bisbenzimidazole ; DNA/*analysis ; Fluorometry/methods ; Metabolic Flux Analysis/*methods ; *Models, Biological ; Porifera/anatomy &amp; histology/growth &amp; development/*metabolism/*microbiology ; Proteins/analysis ; Species Specificity ; *Symbiosis ; }, abstract = {The first step on the path of flux analysis of a new organism with little available literature is the determination of the biomass composition. Once the content of the macromolecular components (protein, RNA, DNA, carbohydrates, lipids) and their composition is known, this composition can be converted into a biomass equation. The biomass equation is an important part of metabolic flux analysis. This equation provides the information about the precursor and energy needs for growth. In many experiments the determination of the growth rate is the simplest flux to be determined, yet this rate determines the net fluxes of a whole range of anabolic pathways in the system and often is used as the objective function in FBA analysis. The challenge for the scientist is to create a biomass equation that represents the organisms of choice under the conditions studied. This chapter outlines basic protocols that can be applied to the quantification of the macromolecular components, using the marine demosponge Amphimedon queenslandica as a case study. As is true for all other sponges and indeed marine animals, A. queenslandica is a holobiont, comprising an animal host plus symbiotic and other associated microbial cells. We show how this complexity can be overcome by developing a fast, yet robust, method for biomass quantification of sponges using the displacement volume. The analytical protocols we describe herein are widely applicable not only to other organisms sampled from complex environments but also to cell cultures. The second part of the chapter highlights the procedures needed to convert a macromolecular composition into a biomass equation.}, }
@article {pmid25171444, year = {2015}, author = {Bettarel, Y and Bouvier, T and Nguyen, HK and Thu, PT}, title = {The versatile nature of coral-associated viruses.}, journal = {Environmental microbiology}, volume = {17}, number = {10}, pages = {3433-3439}, doi = {10.1111/1462-2920.12579}, pmid = {25171444}, issn = {1462-2920}, mesh = {Animals ; Anthozoa/microbiology/*virology ; Bacteria/*virology ; Bacteriophages/growth &amp; development ; Coral Reefs ; Dinoflagellida/*virology ; Phycodnaviridae/*growth &amp; development ; }, abstract = {A recent hypothesis considers that many coral pathologies are the result of a sudden structural alteration of the epibiotic bacterial communities in response to environmental disturbances. However, the ecological mechanisms that lead to shifts in their composition are still unclear. In the ocean, viruses represent a major bactericidal agent but little is known on their occurrence within the coral holobiont. Recent reports have revealed that viruses are abundant and diversified within the coral mucus and therefore could be decisive for coral health. However, their mode of action is still unknown, and there is now an urgent need to shed light on the nature of the relationships they might have with the other prokaryotic and eukaryotic members of the holobiont. In this opinion letter, we are putting forward the hypothesis that coral-associated viruses (mostly bacterial and algal viruses), depending on the environmental conditions might either reinforce coral stability or conversely fasten their decline. We propose that these processes are presumably based on an environmentally driven shift in infection strategies allowing viruses to regulate, circumstantially, both coral symbionts (bacteria or Symbiodinium) and surrounding pathogens.}, }
@article {pmid25156176, year = {2014}, author = {Lema, KA and Bourne, DG and Willis, BL}, title = {Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora.}, journal = {Molecular ecology}, volume = {23}, number = {19}, pages = {4682-4695}, doi = {10.1111/mec.12899}, pmid = {25156176}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; Bacteria/*classification/genetics ; Genes, Bacterial ; Life Cycle Stages ; Molecular Sequence Data ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Symbiosis ; }, abstract = {Early establishment of coral-microbial symbioses is fundamental to the fitness of corals, but comparatively little is known about the onset and succession of bacterial communities in their early life history stages. In this study, bacterial associates of the coral Acropora millepora were characterized throughout the first year of life, from larvae and 1-week-old juveniles reared in laboratory conditions in the absence of the dinoflagellate endosymbiont Symbiodinium to field-outplanted juveniles with established Symbiodinium symbioses, and sampled at 2 weeks and at 3, 6 and 12 months. Using an amplicon pyrosequencing approach, the diversity of both nitrogen-fixing bacteria and of bacterial communities overall was assessed through analysis of nifH and 16S rRNA genes, respectively. The consistent presence of sequences affiliated with diazotrophs of the order Rhizobiales (23-58% of retrieved nifH sequences; 2-12% of 16S rRNA sequences), across all samples from larvae to 12-month-old coral juveniles, highlights the likely functional importance of this nitrogen-fixing order to the coral holobiont. Dominance of Roseobacter-affiliated sequences (>55% of retrieved 16S rRNA sequences) in larvae and 1-week-old juveniles, and the consistent presence of sequences related to Oceanospirillales and Altermonadales throughout all early life history stages, signifies their potential importance as coral associates. Increased diversity of bacterial communities once juveniles were transferred to the field, particularly of Cyanobacteria and Deltaproteobacteria, demonstrates horizontal (environmental) uptake of coral-associated bacterial communities. Although overall bacterial communities were dynamic, bacteria with likely important functional roles remain stable throughout early life stages of Acropora millepora.}, }
@article {pmid25120558, year = {2014}, author = {Dittami, SM and Barbeyron, T and Boyen, C and Cambefort, J and Collet, G and Delage, L and Gobet, A and Groisillier, A and Leblanc, C and Michel, G and Scornet, D and Siegel, A and Tapia, JE and Tonon, T}, title = {Genome and metabolic network of &quot;Candidatus Phaeomarinobacter ectocarpi&quot; Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae.}, journal = {Frontiers in genetics}, volume = {5}, number = {}, pages = {241}, pmid = {25120558}, issn = {1664-8021}, abstract = {Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of &quot;Candidatus Phaeomarinobacter ectocarpi&quot; Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The &quot;Ca. P. ectocarpi&quot; genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, &quot;Ca. P. ectocarpi&quot; has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus &quot;Phaeomarinobacter&quot; may comprise several species, which may colonize different niches.}, }
@article {pmid25117532, year = {2015}, author = {Davis, TS}, title = {The ecology of yeasts in the bark beetle holobiont: a century of research revisited.}, journal = {Microbial ecology}, volume = {69}, number = {4}, pages = {723-732}, pmid = {25117532}, issn = {1432-184X}, mesh = {Animals ; Larva/growth &amp; development/microbiology ; Ovum/growth &amp; development/microbiology ; Pheromones/physiology ; Pupa/growth &amp; development/microbiology ; *Symbiosis ; Weevils/growth &amp; development/*microbiology ; Yeasts/*physiology ; }, abstract = {Yeasts are extremely common associates of scolytine bark beetles, yet the basic ecology of yeasts in the bark beetle holobiont remains poorly understood. Yeasts are present in all beetle life stages and consistently isolated from adult, larval, and pupal integuments and mycangial structures, but yeasts are also found in oviposition galleries, pupal chambers, larval and adult digestive tracts, as well as phloem and xylem tissues. Yeasts in the Saccharomycetaceae family are the most prevalent associates, and most individual beetles are associated with only one or several yeast species. Kuraishia capsulata and Ogataea pini are the most commonly encountered yeast species in surveys of Dendroctonus and Ips beetles; most beetles that have been surveyed are vectors for one or both yeasts. Yeasts have significant but often overlooked functional roles in bark beetle ecology. Infochemicals resulting from volatile production by yeast have wide-ranging bioactivity for arthropods: Yeast emissions attract beetles at low concentrations but repel beetles at high concentrations, and yeast emissions can also serve as cues to predators and parasites of bark beetles. In some cases, yeasts can modify tree chemistry over time or metabolize toxic terpenoids, though potential consequences for beetle performance or the growth of nutritional fungi remain to be demonstrated. Also, the presence of yeast species can restrict or promote the establishment and growth of filamentous fungi, including mutualists, entomopathogens, and opportunistic saprophytes. The role of yeasts as nutritional symbionts has received mixed support, though a nutritional hypothesis has not been extensively tested. Continued research on the functional ecology of bark beetle-yeast associations is needed to better understand the emergent properties of these complex symbiont assemblages.}, }
@article {pmid25071729, year = {2014}, author = {Zchori-Fein, E and Lahav, T and Freilich, S}, title = {Variations in the identity and complexity of endosymbiont combinations in whitefly hosts.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {310}, pmid = {25071729}, issn = {1664-302X}, abstract = {The target of natural selection is suggested to be the holobiont - the organism together with its associated symbiotic microorganisms. The well-defined endosymbiotic communities of insects make them a useful model for exploring the role of symbiotic interactions in shaping the functional repertoire of plants and animals. Here, we studied the variations in the symbiotic communities of the sweet potato whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) by compiling a dataset of over 2000 individuals derived from several independent screenings. The secondary endosymbionts harbored by each individual were clustered into entities termed Facultative Endosymbiont Combinations (FECs), each representing a natural assemblage of co-occurring bacterial genera. The association of FECs with whitefly individuals stratified the otherwise homogeneous population into holobiont units. We both identified bacterial assemblages that are specific to whitefly groups sharing unique genetic backgrounds, and characterized the FEC variations within these groups. The analysis revealed that FEC complexity is positively correlated with both distance from the equator and specificity of the genetic clade of the host insect. These findings highlight the importance of symbiotic combinations in shaping the distribution patterns of B. tabaci and possibly other insect species.}, }
@article {pmid25070863, year = {2014}, author = {Doo, SS and Fujita, K and Byrne, M and Uthicke, S}, title = {Fate of calcifying tropical symbiont-bearing large benthic foraminifera: living sands in a changing ocean.}, journal = {The Biological bulletin}, volume = {226}, number = {3}, pages = {169-186}, doi = {10.1086/BBLv226n3p169}, pmid = {25070863}, issn = {1939-8697}, mesh = {Animals ; Calcification, Physiologic ; Climate Change ; Coral Reefs ; Foraminifera/*physiology ; Geologic Sediments ; Oceans and Seas ; *Symbiosis ; Tropical Climate ; }, abstract = {Concerns regarding the response of calcifiers in future warmer and more acidic oceans have been raised in many studies. Tropical large benthic foraminifera (LBF) are important carbonate producers that reside in coral reefs worldwide. Similar to corals, these organisms live in symbioses with microalgae, which promote high calcification rates. The contribution of LBFs to reef sediments is under threat due to climate change. In this review, we synthesize research conducted on the effects of increased temperature and acidification on these organisms, and assess the potential impacts on reef carbonate production. A meta-analysis of all available experimental data (18 publications, 84 individual experiments) on the effects of ocean warming and acidification on LBF holobiont health was performed using log-transformed response ratios (LnRR) comparing present-day ambient and projected future scenarios. For the latter, we used Representative Concentration Pathway 8.5 from the Intergovernmental Panel on Climate Change, which projects changes of +4 °C and -0.3 pH units by the year 2100. Overall, a general negative trend on holobiont growth was observed across most species of LBFs in response to both stressors. The only exception was the hyaline species (porous CaCO3 test composed of interlocking microcrystals) that have diatom symbionts. Species in this group appear resilient to future ocean acidification scenarios. Differences in the response of LBF species to warming and acidifying oceans may be due to (1) differences in the carbonate species' use in formation of the CaCO3 skeleton (CO2 vs. CO3(2-)), (2) varied responses of the symbiont types (diatom, dinoflagellate, rhodophyte) to stressors, or (3) the degree of nutritional dependence of the host to its symbiont. We also summarize current estimates of carbonate production by LBFs to provide a context of their contribution to reefs. Finally, we outline major gaps in knowledge in addressing the potential for LBF species persistence in a changing ocean.}, }
@article {pmid25058318, year = {2014}, author = {Moree, WJ and McConnell, OJ and Nguyen, DD and Sanchez, LM and Yang, YL and Zhao, X and Liu, WT and Boudreau, PD and Srinivasan, J and Atencio, L and Ballesteros, J and Gavilán, RG and Torres-Mendoza, D and Guzmán, HM and Gerwick, WH and Gutiérrez, M and Dorrestein, PC}, title = {Microbiota of healthy corals are active against fungi in a light-dependent manner.}, journal = {ACS chemical biology}, volume = {9}, number = {10}, pages = {2300-2308}, pmid = {25058318}, issn = {1554-8937}, support = {TW006634/TW/FIC NIH HHS/United States ; S10 RR029121/RR/NCRR NIH HHS/United States ; S10RR029121/RR/NCRR NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 TW006634/TW/FIC NIH HHS/United States ; AI095125/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anthozoa/*microbiology ; Antifungal Agents/isolation &amp; purification/*pharmacology ; Fungi/*drug effects ; *Light ; *Microbiota ; Molecular Sequence Data ; Pseudoalteromonas/growth &amp; development/*isolation &amp; purification ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Symbiosis/*physiology ; }, abstract = {Coral reefs are intricate ecosystems that harbor diverse organisms, including 25% of all marine fish. Healthy corals exhibit a complex symbiosis between coral polyps, endosymbiotic alga, and an array of microorganisms, called the coral holobiont. Secretion of specialized metabolites by coral microbiota is thought to contribute to the defense of this sessile organism against harmful biotic and abiotic factors. While few causative agents of coral diseases have been unequivocally identified, fungi have been implicated in the massive destruction of some soft corals worldwide. Because corals are nocturnal feeders, they may be more vulnerable to fungal infection at night, and we hypothesized that the coral microbiota would have the capability to enhance their defenses against fungi in the dark. A Pseudoalteromonas sp. isolated from a healthy octocoral displayed light-dependent antifungal properties when grown adjacent to Penicillium citrinum (P. citrinum) isolated from a diseased Gorgonian octocoral. Microbial MALDI-imaging mass spectrometry (IMS) coupled with molecular network analyses revealed that Pseudoalteromonas produced higher levels of antifungal polyketide alteramides in the dark than in the light. The alteramides were inactivated by light through a photoinduced intramolecular cyclization. Further NMR studies led to a revision of the stereochemical structure of the alteramides. Alteramide A exhibited antifungal properties and elicited changes in fungal metabolite distributions of mycotoxin citrinin and citrinadins. These data support the hypothesis that coral microbiota use abiotic factors such as light to regulate the production of metabolites with specialized functions to combat opportunistic pathogens at night.}, }
@article {pmid25050199, year = {2014}, author = {Erdman, SE and Poutahidis, T}, title = {The microbiome modulates the tumor macroenvironment.}, journal = {Oncoimmunology}, volume = {3}, number = {}, pages = {e28271}, pmid = {25050199}, issn = {2162-4011}, support = {P30 ES002109/ES/NIEHS NIH HHS/United States ; U01 CA164337/CA/NCI NIH HHS/United States ; }, abstract = {Earlier investigations of the tumor microenvironment unveiled systemic networks presenting novel therapeutic opportunities. It has been recently shown that gut microbes modulate whole host immune and neuroendocrine factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. These findings establish a new paradigm of holobiont therapeutic engineering in emerging tumor macroenvironments.}, }
@article {pmid25044878, year = {2014}, author = {Grottoli, AG and Warner, ME and Levas, SJ and Aschaffenburg, MD and Schoepf, V and McGinley, M and Baumann, J and Matsui, Y}, title = {The cumulative impact of annual coral bleaching can turn some coral species winners into losers.}, journal = {Global change biology}, volume = {20}, number = {12}, pages = {3823-3833}, doi = {10.1111/gcb.12658}, pmid = {25044878}, issn = {1365-2486}, mesh = {Acclimatization/*physiology ; Analysis of Variance ; Animals ; Anthozoa/*microbiology/*physiology ; Caribbean Region ; Dinoflagellida/*physiology ; Photosynthesis/physiology ; Species Specificity ; Stress, Physiological/*physiology ; *Symbiosis ; *Temperature ; }, abstract = {Mass coral bleaching events caused by elevated seawater temperatures result in extensive coral loss throughout the tropics, and are projected to increase in frequency and severity. If bleaching becomes an annual event later in this century, more than 90% of coral reefs worldwide may be at risk of long-term degradation. While corals can recover from single isolated bleaching and can acclimate to recurring bleaching events that are separated by multiple years, it is currently unknown if and how they will survive and possibly acclimatize to annual coral bleaching. Here, we demonstrate for the first time that annual coral bleaching can dramatically alter thermal tolerance in Caribbean corals. We found that high coral energy reserves and changes in the dominant algal endosymbiont type (Symbiodinium spp.) facilitated rapid acclimation in Porites divaricata, whereas low energy reserves and a lack of algal phenotypic plasticity significantly increased susceptibility in Porites astreoides to bleaching the following year. Phenotypic plasticity in the dominant endosymbiont type of Orbicella faveolata did not prevent repeat bleaching, but may have facilitated rapid recovery. Thus, coral holobiont response to an isolated single bleaching event is not an accurate predictor of its response to bleaching the following year. Rather, the cumulative impact of annual coral bleaching can turn some coral species 'winners' into 'losers', and can also facilitate acclimation and turn some coral species 'losers' into 'winners'. Overall, these findings indicate that cumulative impact of annual coral bleaching could result in some species becoming increasingly susceptible to bleaching and face a long-term decline, while phenotypically plastic coral species will acclimatize and persist. Thus, annual coral bleaching and recovery could contribute to the selective loss of coral diversity as well as the overall decline of coral reefs in the Caribbean.}, }
@article {pmid25016412, year = {2014}, author = {Gust, KA and Najar, FZ and Habib, T and Lotufo, GR and Piggot, AM and Fouke, BW and Laird, JG and Wilbanks, MS and Rawat, A and Indest, KJ and Roe, BA and Perkins, EJ}, title = {Coral-zooxanthellae meta-transcriptomics reveals integrated response to pollutant stress.}, journal = {BMC genomics}, volume = {15}, number = {}, pages = {591}, pmid = {25016412}, issn = {1471-2164}, mesh = {Animals ; Anthozoa/drug effects/*genetics/metabolism ; Dinoflagellida/drug effects/*genetics/metabolism ; Molecular Sequence Annotation ; Oligonucleotide Array Sequence Analysis ; Stress, Physiological ; Symbiosis ; Transcriptome/*drug effects ; Triazines/*pharmacology ; Water Pollutants, Chemical/*pharmacology ; }, abstract = {BACKGROUND: Corals represent symbiotic meta-organisms that require harmonization among the coral animal, photosynthetic zooxanthellae and associated microbes to survive environmental stresses. We investigated integrated-responses among coral and zooxanthellae in the scleractinian coral Acropora formosa in response to an emerging marine pollutant, the munitions constituent, 1,3,5-trinitro-1,3,5 triazine (RDX; 5 day exposures to 0 (control), 0.5, 0.9, 1.8, 3.7, and 7.2 mg/L, measured in seawater).<br><br>RESULTS: RDX accumulated readily in coral soft tissues with bioconcentration factors ranging from 1.1 to 1.5. Next-generation sequencing of a normalized meta-transcriptomic library developed for the eukaryotic components of the A. formosa coral holobiont was leveraged to conduct microarray-based global transcript expression analysis of integrated coral/zooxanthellae responses to the RDX exposure. Total differentially expressed transcripts (DET) increased with increasing RDX exposure concentrations as did the proportion of zooxanthellae DET relative to the coral animal. Transcriptional responses in the coral demonstrated higher sensitivity to RDX compared to zooxanthellae where increased expression of gene transcripts coding xenobiotic detoxification mechanisms (i.e. cytochrome P450 and UDP glucuronosyltransferase 2 family) were initiated at the lowest exposure concentration. Increased expression of these detoxification mechanisms was sustained at higher RDX concentrations as well as production of a physical barrier to exposure through a 40% increase in mucocyte density at the maximum RDX exposure. At and above the 1.8 mg/L exposure concentration, DET coding for genes involved in central energy metabolism, including photosynthesis, glycolysis and electron-transport functions, were decreased in zooxanthellae although preliminary data indicated that zooxanthellae densities were not affected. In contrast, significantly increased transcript expression for genes involved in cellular energy production including glycolysis and electron-transport pathways was observed in the coral animal.<br><br>CONCLUSIONS: Transcriptional network analysis for central energy metabolism demonstrated highly correlated responses to RDX among the coral animal and zooxanthellae indicative of potential compensatory responses to lost photosynthetic potential within the holobiont. These observations underscore the potential for complex integrated responses to RDX exposure among species comprising the coral holobiont and highlight the need to understand holobiont-species interactions to accurately assess pollutant impacts.}, }
@article {pmid24995875, year = {2014}, author = {McFall-Ngai, MJ}, title = {The importance of microbes in animal development: lessons from the squid-vibrio symbiosis.}, journal = {Annual review of microbiology}, volume = {68}, number = {}, pages = {177-194}, pmid = {24995875}, issn = {1545-3251}, support = {R01 AI050661/AI/NIAID NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Decapodiformes/*growth &amp; development/*microbiology/physiology ; *Symbiosis ; Vibrio/*physiology ; }, abstract = {Developmental biology is among the many subdisciplines of the life sciences being transformed by our increasing awareness of the role of coevolved microbial symbionts in health and disease. Most symbioses are horizontally acquired, i.e., they begin anew each generation. In such associations, the embryonic period prepares the animal to engage with the coevolved partner(s) with fidelity following birth or hatching. Once interactions are underway, the microbial partners drive maturation of tissues that are either directly associated with or distant from the symbiont populations. Animal alliances often involve complex microbial communities, such as those in the vertebrate gastrointestinal tract. A series of simpler-model systems is providing insight into the basic rules and principles that govern the establishment and maintenance of stable animal-microbe partnerships. This review focuses on what biologists have learned about the developmental trajectory of horizontally acquired symbioses through the study of the binary squid-vibrio model.}, }
@article {pmid24992663, year = {2014}, author = {Dheilly, NM}, title = {Holobiont-Holobiont interactions: redefining host-parasite interactions.}, journal = {PLoS pathogens}, volume = {10}, number = {7}, pages = {e1004093}, pmid = {24992663}, issn = {1553-7374}, mesh = {Animals ; *Host-Pathogen Interactions ; Humans ; Plant Diseases ; Plants ; }, }
@article {pmid24982156, year = {2014}, author = {Kelly, LW and Williams, GJ and Barott, KL and Carlson, CA and Dinsdale, EA and Edwards, RA and Haas, AF and Haynes, M and Lim, YW and McDole, T and Nelson, CE and Sala, E and Sandin, SA and Smith, JE and Vermeij, MJ and Youle, M and Rohwer, F}, title = {Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {28}, pages = {10227-10232}, pmid = {24982156}, issn = {1091-6490}, mesh = {*Adaptation, Physiological ; *Bacteria/genetics/metabolism ; *Coral Reefs ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; Pacific Ocean ; *Water Pollution ; }, abstract = {Holobionts are species-specific associations between macro- and microorganisms. On coral reefs, the benthic coverage of coral and algal holobionts varies due to natural and anthropogenic forcings. Different benthic macroorganisms are predicted to have specific microbiomes. In contrast, local environmental factors are predicted to select for specific metabolic pathways in microbes. To reconcile these two predictions, we hypothesized that adaptation of microbiomes to local conditions is facilitated by the horizontal transfer of genes responsible for specific metabolic capabilities. To test this hypothesis, microbial metagenomes were sequenced from 22 coral reefs at 11 Line Islands in the central Pacific that together span a wide range of biogeochemical and anthropogenic influences. Consistent with our hypothesis, the percent cover of major benthic functional groups significantly correlated with particular microbial taxa. Reefs with higher coral cover had a coral microbiome with higher abundances of Alphaproteobacteria (such as Rhodobacterales and Sphingomonadales), whereas microbiomes of algae-dominated reefs had higher abundances of Gammaproteobacteria (such as Alteromonadales, Pseudomonadales, and Vibrionales), Betaproteobacteria, and Bacteriodetes. In contrast to taxa, geography was the strongest predictor of microbial community metabolism. Microbial communities on reefs with higher nutrient availability (e.g., equatorial upwelling zones) were enriched in genes involved in nutrient-related metabolisms (e.g., nitrate and nitrite ammonification, Ton/Tol transport, etc.). On reefs further from the equator, microbes had more genes encoding chlorophyll biosynthesis and photosystems I/II. These results support the hypothesis that core microbiomes are determined by holobiont macroorganisms, and that those core taxa adapt to local conditions by selecting for advantageous metabolic genes.}, }
@article {pmid24960461, year = {2014}, author = {Watson, JR and Brennan, TC and Degnan, BM and Degnan, SM and Krömer, JO}, title = {Analysis of the biomass composition of the demosponge Amphimedon queenslandica on Heron Island Reef, Australia.}, journal = {Marine drugs}, volume = {12}, number = {6}, pages = {3733-3753}, pmid = {24960461}, issn = {1660-3397}, mesh = {Amino Acids/chemistry/isolation &amp; purification ; Animals ; Australia ; *Biomass ; Fatty Acids/chemistry/isolation &amp; purification ; Genome ; Genomics/*methods ; Models, Genetic ; Porifera/genetics/*metabolism ; }, abstract = {Marine sponges are a potential source of important pharmaceutical drugs, the commercialisation of which is restricted by the difficulties of obtaining a sufficient and regular supply of biomass. One way to optimize commercial cell lines for production is the in-depth characterization and target identification through genome scale metabolic modeling and flux analysis. By applying these tools to a sponge, we hope to gain insights into how biomass is formed. We chose Amphimedon queenslandica as it has an assembled and annotated genome, a prerequisite for genome scale modeling. The first stepping stone on the way to metabolic flux analysis in a sponge holobiont, is the characterization of its biomass composition. In this study we quantified the macromolecular composition and investigated the variation between and within sponges of a single population. We found lipids and protein to be the most abundant macromolecules, while carbohydrates were the most variable. We also analysed the composition and abundance of the fatty acids and amino acids, the important building blocks required to synthesise the abundant macromolecule types, lipids, and protein. These data complement the extensive genomic information available for A. queenslandica and lay the basis for genome scale modelling and flux analysis.}, }
@article {pmid24950107, year = {2014}, author = {Closek, CJ and Sunagawa, S and DeSalvo, MK and Piceno, YM and DeSantis, TZ and Brodie, EL and Weber, MX and Voolstra, CR and Andersen, GL and Medina, M}, title = {Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.}, journal = {The ISME journal}, volume = {8}, number = {12}, pages = {2411-2422}, pmid = {24950107}, issn = {1751-7370}, mesh = {Alveolata/classification/isolation &amp; purification ; Animals ; Anthozoa/*genetics/metabolism/*microbiology ; Bacteria/*classification/isolation &amp; purification ; *Transcriptome ; }, abstract = {Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.}, }
@article {pmid24860563, year = {2014}, author = {Luter, HM and Gibb, K and Webster, NS}, title = {Eutrophication has no short-term effect on the Cymbastela stipitata holobiont.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {216}, pmid = {24860563}, issn = {1664-302X}, abstract = {Levels of nitrogen in coastal areas have been rapidly increasing due to accumulative inputs of sewage and terrigenous sediments carrying fertilizers. Sponges have an immense filtering capacity and may be directly impacted (positively or negatively) by elevated concentrations of nitrogen. Sponges also host a wide diversity of microbes involved in nitrogen metabolism, yet little is known about the effects of nitrogen loading on these symbiotic partnerships. Manipulative experiments were undertaken to examine the potential effects of excess nitrogen (up to 240 μM) on microbial symbiosis in the abundant sponge species Cymbastela stipitata. Microbial composition and activity were examined using 454-pyrotag sequencing of DNA- and RNA-derived samples. Despite the high levels of nitrogen exposure (up to 124-fold above ambient), sponges appeared visibly unaffected at all treatment concentrations. At the phylum level, the microbial community was consistent between all sponge samples regardless of nitrogen treatment, with Cyanobacteria and Thaumarchaeota being the dominant taxa. Higher microbial diversity was observed at the operational taxonomic units (OTU) level (97% sequence similarity), with only 40% of OTUs shared between samples from all treatments. However, a single cyanobacterial OTU dominated the community of all individuals (average 73.5%) and this OTU did not vary with nitrogen treatment. The conserved microbial community in all sponges irrespective of nitrogen treatment highlights the stability of the sponge-microbe relationship and indicates that the holobiont is resistant to short pulses of nitrogen at levels mimicking sewage effluent.}, }
@article {pmid24847321, year = {2014}, author = {Weynberg, KD and Wood-Charlson, EM and Suttle, CA and van Oppen, MJ}, title = {Generating viral metagenomes from the coral holobiont.}, journal = {Frontiers in microbiology}, volume = {5}, number = {}, pages = {206}, pmid = {24847321}, issn = {1664-302X}, abstract = {Reef-building corals comprise multipartite symbioses where the cnidarian animal is host to an array of eukaryotic and prokaryotic organisms, and the viruses that infect them. These viruses are critical elements of the coral holobiont, serving not only as agents of mortality, but also as potential vectors for lateral gene flow, and as elements encoding a variety of auxiliary metabolic functions. Consequently, understanding the functioning and health of the coral holobiont requires detailed knowledge of the associated viral assemblage and its function. Currently, the most tractable way of uncovering viral diversity and function is through metagenomic approaches, which is inherently difficult in corals because of the complex holobiont community, an extracellular mucus layer that all corals secrete, and the variety of sizes and structures of nucleic acids found in viruses. Here we present the first protocol for isolating, purifying and amplifying viral nucleic acids from corals based on mechanical disruption of cells. This method produces at least 50% higher yields of viral nucleic acids, has very low levels of cellular sequence contamination and captures wider viral diversity than previously used chemical-based extraction methods. We demonstrate that our mechanical-based method profiles a greater diversity of DNA and RNA genomes, including virus groups such as Retro-transcribing and ssRNA viruses, which are absent from metagenomes generated via chemical-based methods. In addition, we briefly present (and make publically available) the first paired DNA and RNA viral metagenomes from the coral Acropora tenuis.}, }
@article {pmid24814756, year = {2014}, author = {Hardoim, CC and Costa, R}, title = {Temporal dynamics of prokaryotic communities in the marine sponge Sarcotragus spinosulus.}, journal = {Molecular ecology}, volume = {23}, number = {12}, pages = {3097-3112}, doi = {10.1111/mec.12789}, pmid = {24814756}, issn = {1365-294X}, mesh = {Animals ; Archaea/*classification/genetics ; Bacteria/*classification/genetics ; DNA, Archaeal/genetics ; DNA, Bacterial/genetics ; *Microbiota ; Molecular Sequence Data ; Phylogeny ; Porifera/genetics/*microbiology ; RNA, Ribosomal,