@article {pmid35965269, year = {2022}, author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35965269}, issn = {1432-184X}, abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.}, }
@article {pmid35960256, year = {2022}, author = {Johnston, EC and Cunning, R and Burgess, SC}, title = {Cophylogeny and specificity between cryptic coral species (Pocillopora spp.) at Mo'orea and their symbionts (Symbiodiniaceae).}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16654}, pmid = {35960256}, issn = {1365-294X}, abstract = {The congruence between phylogenies of tightly associated groups of organisms (cophylogeny) reflects evolutionary links between ecologically important interactions. However, despite being a classic example of an obligate symbiosis, tests of cophylogeny between scleractinian corals and their photosynthetic algal symbionts have been hampered in the past because both corals and algae contain genetically unresolved and morphologically cryptic species. Here, we studied co-occurring, cryptic Pocillopora species from Mo'orea, French Polynesia, that differ in their relative abundance across depth. We constructed new phylogenies of the host Pocillopora (using complete mitochondrial genomes, genomic loci, and thousands of single nucleotide polymorphisms) and their Symbiodiniaceae symbionts (using ITS2 and psbAncr markers) and tested for cophylogeny. The analysis supported the presence of five Pocillopora species on the fore-reef at Mo'orea that mostly hosted either Cladocopium latusorum or C. pacificum. Only Pocillopora species hosting C. latusorum also hosted taxa from Symbiodinium and Durusdinium. In general, the Cladocopium phylogeny mirrored the Pocillopora phylogeny. Within Cladocopium species, lineages also differed in their associations with Pocillopora haplotypes, except those showing evidence of nuclear introgression, and with depth in the two most common Pocillopora species. We also found evidence for a new Pocillopora species (haplotype 10), that has so far only been sampled from French Polynesia, that warrants formal identification. The linked phylogenies of these Pocillopora and Cladocopium species and lineages suggest that symbiont speciation is driven by niche diversification in the host, but there is still evidence for symbiont flexibility in some cases.}, }
@article {pmid35958152, year = {2022}, author = {Somera, TS and Mazzola, M}, title = {Toward a holistic view of orchard ecosystem dynamics: A comprehensive review of the multiple factors governing development or suppression of apple replant disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {949404}, doi = {10.3389/fmicb.2022.949404}, pmid = {35958152}, issn = {1664-302X}, abstract = {Replant diseases are a common occurrence in perennial cropping systems. In apple, progress toward the development of a universally effective disease management strategy, beyond the use of broad-spectrum soil fumigants, is impeded by inconsistencies in defining replant disease etiology. A preponderance of evidence attributes apple replant disease to plant-induced changes in the soil microbiome including the proliferation of soilborne plant pathogens. Findings from alternative studies suggest that the contribution of abiotic factors, such as the accumulation of phenolic detritus from previous orchard plantings, may play a part as well. Engineering of the resident soil microbiome using resource-based strategies is demonstrating potential to limit activity of replant pathogens and improve productivity in newly established orchards. An understanding of factors promoting the assembly of a disease-suppressive soil microbiome along with consideration of host factors that confer disease tolerance or resistance is imperative to the developing a more holistic view of orchard ecosystem dynamics. Here, we review the literature concerning the transition of orchard soil from a healthy state to a replant disease-conducive state. Included in the scope of this review are studies on the influence of soil type and geography on the apple replant pathogen complex. Furthermore, several tolerance and innate resistance mechanisms that have been described in apple to date, including the role of root chemistry/exudates are discussed. Finally, the interplay between apple rootstock genotype and key resource-based strategies which have been shown to "reshape" the plant holobiont in favor of a more prophylactic or disease-suppressive state is highlighted.}, }
@article {pmid35537462, year = {2022}, author = {Cowen, LJ and Putnam, HM}, title = {Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.}, journal = {Annual review of biomedical data science}, volume = {5}, number = {}, pages = {205-231}, doi = {10.1146/annurev-biodatasci-122120-030732}, pmid = {35537462}, issn = {2574-3414}, abstract = {Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience.}, }
@article {pmid35943423, year = {2022}, author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV}, title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16642}, pmid = {35943423}, issn = {1365-294X}, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we leverage aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE - 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence ancient DNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.}, }
@article {pmid35910618, year = {2022}, author = {Vad, J and Duran Suja, L and Summers, S and Henry, TB and Roberts, JM}, title = {Marine Sponges in a Snowstorm - Extreme Sensitivity of a Sponge Holobiont to Marine Oil Snow and Chemically Dispersed Oil Pollution.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909853}, doi = {10.3389/fmicb.2022.909853}, pmid = {35910618}, issn = {1664-302X}, abstract = {Holobionts formed by a host organism and associated symbionts are key biological units in marine ecosystems where they are responsible for fundamental ecosystem services. Therefore, understanding anthropogenic impacts on holobionts is essential. Sponges (Phylum Porifera) are ideal holobiont models. They host a complex microbial community and provide ecosystem services including nutrient cycling. At bathyal depths, sponges can accumulate forming dense sponge ground habitats supporting biodiverse associated communities. However, the impacts of spilled oil and dispersants on sponge grounds cannot be understood without considering exposures mediated through sponge filtration of marine snow particles. To examine this, we exposed the model sponge Halichondria panicea to oil, dispersant and "marine oil snow" contaminated seawater and elucidate the complex molecular response of the holobiont through metatranscriptomics. While the host response included detoxification and immune response pathways, the bacterial symbiotic response differed and was at least partially the result of a change in the host environment rather than a direct response to hydrocarbon exposure. As the sponge host reduced its pumping activity and internal tissue oxygen levels declined, the symbionts changed their metabolism from aerobic to anaerobic pathways possibly via quorum sensing. Furthermore, we found evidence of hydrocarbon degradation by sponge symbionts, but sponge mortality (even when exposed to low concentrations of hydrocarbons) implied this may not provide the holobiont with sufficient resilience against contaminants. Given the continued proposed expansion of hydrocarbon production into deep continental shelf and slope settings where sponge grounds form significant habitats it is important that dispersant use is minimised and that environmental impact assessments carefully consider the vulnerability of sponge holobionts.}, }
@article {pmid35902906, year = {2022}, author = {Morrow, KM and Pankey, MS and Lesser, MP}, title = {Community structure of coral microbiomes is dependent on host morphology.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {113}, pmid = {35902906}, issn = {2049-2618}, support = {OCE 1437054/1638296//National Science Foundation/ ; OCE 1437054/1638296//National Science Foundation/ ; OCE 1437054/1638296//National Science Foundation/ ; }, abstract = {BACKGROUND: The importance of symbiosis has long been recognized on coral reefs, where the photosynthetic dinoflagellates of corals (Symbiodiniaceae) are the primary symbiont. Numerous studies have now shown that a diverse assemblage of prokaryotes also make-up part of the microbiome of corals. A subset of these prokaryotes is capable of fixing nitrogen, known as diazotrophs, and is also present in the microbiome of scleractinian corals where they have been shown to supplement the holobiont nitrogen budget. Here, an analysis of the microbiomes of 16 coral species collected from Australia, Curaçao, and Hawai'i using three different marker genes (16S rRNA, nifH, and ITS2) is presented. These data were used to examine the effects of biogeography, coral traits, and ecological life history characteristics on the composition and diversity of the microbiome in corals and their diazotrophic communities.<br><br>RESULTS: The prokaryotic microbiome community composition (i.e., beta diversity) based on the 16S rRNA gene varied between sites and ecological life history characteristics, but coral morphology was the most significant factor affecting the microbiome of the corals studied. For 15 of the corals studied, only two species Pocillopora acuta and Seriotopora hystrix, both brooders, showed a weak relationship between the 16S rRNA gene community structure and the diazotrophic members of the microbiome using the nifH marker gene, suggesting that many corals support a microbiome with diazotrophic capabilities. The order Rhizobiales, a taxon that contains primarily diazotrophs, are common members of the coral microbiome and were eight times greater in relative abundances in Hawai'i compared to corals from either Curacao or Australia. However, for the diazotrophic component of the coral microbiome, only host species significantly influenced the composition and diversity of the community.<br><br>CONCLUSIONS: The roles and interactions between members of the coral holobiont are still not well understood, especially critical functions provided by the coral microbiome (e.g., nitrogen fixation), and the variation of these functions across species. The findings presented here show the significant effect of morphology, a coral "super trait," on the overall community structure of the microbiome in corals and that there is a strong association of the diazotrophic community within the microbiome of corals. However, the underlying coral traits linking the effects of host species on diazotrophic communities remain unknown. Video Abstract.}, }
@article {pmid35895230, year = {2022}, author = {Xiang, X and Poli, D and Degnan, BM and Degnan, SM}, title = {Ribosomal RNA-Depletion Provides an Efficient Method for Successful Dual RNA-Seq Expression Profiling of a Marine Sponge Holobiont.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {}, number = {}, pages = {}, pmid = {35895230}, issn = {1436-2236}, support = {DP170102353//Australian Research Council/ ; DP170102353//Australian Research Council/ ; DP170102353//Australian Research Council/ ; DP170102353//Australian Research Council/ ; }, abstract = {Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. Here, we address this gap in knowledge with the aim of helping others to choose an appropriate RNA-Seq approach for analysis of animal host-bacterial symbiont transcriptomes. Specifically, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont. Annotated genomes of the sponge host and the three most abundant bacterial symbionts, which can comprise up to 95% of the adult microbiome, are available. Importantly, this allows for transcriptomes to be accurately mapped to these genomes, and thus quantitatively assessed and compared. The two strategies that we compare here are (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq) and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to simultaneously capture gene expression in host and symbionts and thus to analyse holobiont transcriptomes.}, }
@article {pmid35894614, year = {2022}, author = {Tanabe, N and Takasu, R and Hirose, Y and Kamei, Y and Kondo, M and Nakabachi, A}, title = {Diaphorin, a Polyketide Produced by a Bacterial Symbiont of the Asian Citrus Psyllid, Inhibits the Growth and Cell Division of Bacillus subtilis but Promotes the Growth and Metabolic Activity of Escherichia coli.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0175722}, doi = {10.1128/spectrum.01757-22}, pmid = {35894614}, issn = {2165-0497}, abstract = {Diaphorin is a polyketide produced by "Candidatus Profftella armatura" (Gammaproteobacteria: Burkholderiales), an obligate symbiont of a notorious agricultural pest, the Asian citrus psyllid Diaphorina citri (Hemiptera: Psyllidae). Diaphorin belongs to the pederin family of bioactive agents found in various host-symbiont systems, including beetles, lichens, and sponges, harboring phylogenetically diverse bacterial producers. Previous studies showed that diaphorin, which is present in D. citri at concentrations of 2 to 20 mM, has inhibitory effects on various eukaryotes, including the natural enemies of D. citri. However, little is known about its effects on prokaryotic organisms. To address this issue, the present study assessed the biological activities of diaphorin on two model prokaryotes, Escherichia coli (Gammaproteobacteria: Enterobacterales) and Bacillus subtilis (Firmicutes: Bacilli). Their growth and morphological features were analyzed using spectrophotometry, optical microscopy followed by image analysis, and transmission electron microscopy. The metabolic activity of E. coli was further assessed using the β-galactosidase assay. The results revealed that physiological concentrations of diaphorin inhibit the growth and cell division of B. subtilis but promote the growth and metabolic activity of E. coli. This finding implies that diaphorin functions as a defensive agent of the holobiont (host plus symbionts) against some bacterial lineages but is metabolically beneficial for others, which potentially include obligate symbionts of D. citri. IMPORTANCE Certain secondary metabolites, including antibiotics, evolve to mediate interactions among organisms. These molecules have distinct spectra for microorganisms and are often more effective against Gram-positive bacteria than Gram-negative ones. However, it is rare that a single molecule has completely opposite activities on distinct bacterial lineages. The present study revealed that a secondary metabolite synthesized by an organelle-like bacterial symbiont of psyllids inhibits the growth of Gram-positive Bacillus subtilis but promotes the growth of Gram-negative Escherichia coli. This finding not only provides insights into the evolution of microbiomes in animal hosts but also may potentially be exploited to promote the effectiveness of industrial material production by microorganisms.}, }
@article {pmid35884910, year = {2022}, author = {Amedei, A}, title = {Editorial of Special Issue "Pharmacomicrobiomics in Non-Communicable Disease".}, journal = {Biomedicines}, volume = {10}, number = {7}, pages = {}, doi = {10.3390/biomedicines10071605}, pmid = {35884910}, issn = {2227-9059}, abstract = {The human superorganism, also known as the human holobiont, is a complex organism made up of host body as well as the bacteria, archaea, viruses, and fungi that live inside it along with their genes [...].}, }
@article {pmid35881247, year = {2022}, author = {King, NG and Smale, DA and Thorpe, JM and McKeown, NJ and Andrews, AJ and Browne, R and Malham, SK}, title = {Core Community Persistence Despite Dynamic Spatiotemporal Responses in the Associated Bacterial Communities of Farmed Pacific Oysters.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35881247}, issn = {1432-184X}, abstract = {A breakdown in host-bacteria relationships has been associated with the progression of a number of marine diseases and subsequent mortality events. For the Pacific oyster, Crassostrea gigas, summer mortality syndrome (SMS) is one of the biggest constraints to the growth of the sector and is set to expand into temperate systems as ocean temperatures rise. Currently, a lack of understanding of natural spatiotemporal dynamics of the host-bacteria relationship limits our ability to develop microbially based monitoring approaches. Here, we characterised the associated bacterial community of C. gigas, at two Irish oyster farms, unaffected by SMS, over the course of a year. We found C. gigas harboured spatiotemporally variable bacterial communities that were distinct from bacterioplankton in surrounding seawater. Whilst the majority of bacteria-oyster associations were transient and highly variable, we observed clear patterns of stability in the form of a small core consisting of six persistent amplicon sequence variants (ASVs). This core made up a disproportionately large contribution to sample abundance (34 ± 0.14%), despite representing only 0.034% of species richness across the study, and has been associated with healthy oysters in other systems. Overall, our study demonstrates the consistent features of oyster bacterial communities across spatial and temporal scales and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35875588, year = {2022}, author = {Chun, SJ and Cui, Y and Yoo, SH and Lee, JR}, title = {Organic Connection of Holobiont Components and the Essential Roles of Core Microbes in the Holobiont Formation of Feral Brassica napus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {920759}, pmid = {35875588}, issn = {1664-302X}, abstract = {Brassica napus (Rapeseed) is an econfomically important oil-producing crop. The microbial interactions in the plant holobiont are fundamental to the understanding of plant growth and health. To investigate the microbial dynamics in the holobiont of feral B. napus, a total of 215 holobiont samples, comprised of bulk soil, primary root, lateral root, dead leaf, caulosphere, basal leaf, apical leaf, carposphere, and anthosphere, were collected from five different grassland sites in South Korea. The soil properties differed in different sampling sites, but prokaryotic communities were segregated according to plant holobiont components. The structures of the site-specific SparCC networks were similar across the regions. Recurrent patterns were found in the plant holobionts in the recurrent network. Ralstonia sp., Massilia sp., and Rhizobium clusters were observed consistently and were identified as core taxa in the phyllosphere, dead leaf microbiome, and rhizosphere, respectively. Arthropod-related microbes, such as Wolbachia sp., Gilliamella sp., and Corynebacteriales amplicon sequence variants, were found in the anthosphere. PICRUSt2 analysis revealed that microbes also possessed specific functions related to holobiont components, such as functions related to degradation pathways in the dead leaf microbiome. Structural equation modeling analysis showed the organic connections among holobiont components and the essential roles of the core microbes in the holobiont formations in natural ecosystem. Microbes coexisting in a specific plant showed relatively stable community structures, even though the regions and soil characteristics were different. Microbes in each plant component were organically connected to form their own plant holobiont. In addition, plant-related microbes, especially core microbes in each holobiont, showed recurrent interaction patterns that are essential to an understanding of the survival and coexistence of plant microbes in natural ecosystems.}, }
@article {pmid35864739, year = {2022}, author = {Martínez-Arias, C and Witzell, J and Solla, A and Martín, JA and Calcerrada, JR}, title = {Beneficial and pathogenic plant-microbe interactions during flooding stress.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14403}, pmid = {35864739}, issn = {1365-3040}, abstract = {The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favors the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behavior or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e. the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiraling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective. This article is protected by copyright. All rights reserved.}, }
@article {pmid35862823, year = {2022}, author = {Loureiro, C and Galani, A and Gavriilidou, A and Chaib de Mares, M and van der Oost, J and Medema, MH and Sipkema, D}, title = {Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035722}, doi = {10.1128/msystems.00357-22}, pmid = {35862823}, issn = {2379-5077}, abstract = {Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.}, }
@article {pmid35862808, year = {2022}, author = {Dove, NC and Carrell, AA and Engle, NL and Klingeman, DM and Rodriguez, M and Wahl, T and Tschaplinski, TJ and Muchero, W and Schadt, CW and Cregger, MA}, title = {Relationships between Sphaerulina musiva Infection and the Populus Microbiome and Metabolome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0012022}, doi = {10.1128/msystems.00120-22}, pmid = {35862808}, issn = {2379-5077}, abstract = {Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.}, }
@article {pmid35860838, year = {2022}, author = {Miral, A and Jargeat, P and Mambu, L and Rouaud, I and Tranchimand, S and Tomasi, S}, title = {Microbial community associated with the crustose lichen Rhizocarpon geographicum L. (DC.) living on oceanic seashore: A large source of diversity revealed by using multiple isolation methods.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13105}, pmid = {35860838}, issn = {1758-2229}, abstract = {Recently, the study of the interactions within a microcosm between hosts and their associated microbial communities drew an unprecedented interest arising from the holobiont concept. Lichens, a symbiotic association between a fungus and an alga, are redefined as complex ecosystems considering the tremendous array of associated microorganisms that satisfy this concept. The present study focuses on the diversity of the microbiota associated with the seashore located lichen Rhizocarpon geographicum, recovered by different culture-dependent methods. Samples harvested from two sites allowed the isolation and the molecular identification of 68 fungal isolates distributed in 43 phylogenetic groups, 15 bacterial isolates distributed in five taxonomic groups and three microalgae belonging to two species. Moreover, for 12 fungal isolates belonging to 10 different taxa, the genus was not described in GenBank. These fungal species have never been sequenced or described and therefore non-studied. All these findings highlight the novel and high diversity of the microflora associated with R. geographicum. While many species disappear every day, this work suggests that coastal and wild environments still contain an unrevealed variety to offer and that lichens constitute a great reservoir of new microbial taxa which can be recovered by multiplying the culture-dependent techniques.}, }
@article {pmid35857470, year = {2022}, author = {Wada, N and Hsu, MT and Tandon, K and Hsiao, SS and Chen, HJ and Chen, YH and Chiang, PW and Yu, SP and Lu, CY and Chiou, YJ and Tu, YC and Tian, X and Chen, BC and Lee, DC and Yamashiro, H and Bourne, DG and Tang, SL}, title = {High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata.}, journal = {Science advances}, volume = {8}, number = {27}, pages = {eabo2431}, doi = {10.1126/sciadv.abo2431}, pmid = {35857470}, issn = {2375-2548}, abstract = {Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.}, }
@article {pmid35847106, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Xu, K and Liu, J and Zhu, W and Zhu, J and He, C and Han, C and Qin, C and Luo, H and Chen, K and Zheng, Y and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Dynamics of Small Non-coding RNA Profiles and the Intestinal Microbiome of High and Low Weight Chickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916280}, pmid = {35847106}, issn = {1664-302X}, abstract = {The host and its symbiotic bacteria form a biological entity, holobiont, in which they share a dynamic connection characterized by symbiosis, co-metabolism, and coevolution. However, how these collaborative relationships were maintained over evolutionary time remains unclear. In this research, the small non-coding RNA (sncRNA) profiles of cecum and their bacteria contents were measured from lines of chickens that have undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. The results from these lines that originated from a common founder population and maintained under the same husbandry showed an association between host intestinal sncRNA expression profile (miRNA, lncRNA fragment, mRNA fragment, snoRNA, and snRNA) and intestinal microbiota. Correlation analyses suggested that some central miRNAs and mRNA fragments had interactions with the abundance of intestinal microbial species and microbiota functions. miR-6622-3p, a significantly differentially expressed (DE) miRNA was correlated with a body weight gain related bacterium, Alistipes putredinis. Our results showed that host sncRNAs may be mediators of interaction between the host and its intestinal microbiome. This provides additional clue for holobiont concepts.}, }
@article {pmid35832387, year = {2022}, author = {Hernández, M and Mayer, MPA and Santi-Rocca, J}, title = {Editorial: The Human Microbiota in Periodontitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {952205}, doi = {10.3389/fcimb.2022.952205}, pmid = {35832387}, issn = {2235-2988}, }
@article {pmid35816968, year = {2022}, author = {Griffin, ME and Hang, HC}, title = {Microbial mechanisms to improve immune checkpoint blockade responsiveness.}, journal = {Neoplasia (New York, N.Y.)}, volume = {31}, number = {}, pages = {100818}, doi = {10.1016/j.neo.2022.100818}, pmid = {35816968}, issn = {1476-5586}, abstract = {The human microbiota acts as a diverse source of molecular cues that influence the development and homeostasis of the immune system. Beyond endogenous roles in the human holobiont, host-microbial interactions also alter outcomes for immune-related diseases and treatment regimens. Over the past decade, sequencing analyses of cancer patients have revealed correlations between microbiota composition and the efficacy of cancer immunotherapies such as checkpoint inhibitors. However, very little is known about the exact mechanisms that link specific microbiota with patient responses, limiting our ability to exploit these microbial agents for improved oncology care. Here, we summarize current progress towards a molecular understanding of host-microbial interactions in the context of checkpoint inhibitor immunotherapies. By highlighting the successes of a limited number of studies focused on identifying specific, causal molecules, we underscore how the exploration of specific microbial features such as proteins, enzymes, and metabolites may translate into precise and actionable therapies for personalized patient care in the clinic.}, }
@article {pmid35783967, year = {2022}, author = {Plaszkó, T and Szűcs, Z and Cziáky, Z and Ács-Szabó, L and Csoma, H and Géczi, L and Vasas, G and Gonda, S}, title = {Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish (Armoracia rusticana, Brassicaceae) Roots.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {921008}, doi = {10.3389/fpls.2022.921008}, pmid = {35783967}, issn = {1664-462X}, abstract = {The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.}, }
@article {pmid35777916, year = {2022}, author = {Xu, P and Fan, X and Mao, Y and Cheng, H and Xu, A and Lai, W and Lv, T and Hu, Y and Nie, Y and Zheng, X and Meng, Q and Wang, Y and Cernava, T and Wang, M}, title = {Temporal metabolite responsiveness of microbiota in the tea plant phyllosphere promotes continuous suppression of fungal pathogens.}, journal = {Journal of advanced research}, volume = {39}, number = {}, pages = {49-60}, doi = {10.1016/j.jare.2021.10.003}, pmid = {35777916}, issn = {2090-1224}, abstract = {INTRODUCTION: A broad spectrum of rhizosphere bacteria and fungi were shown to play a central role for health, fitness and productivity of their host plants. However, implications of host metabolism on microbiota assembly in the phyllosphere and potential consequences for holobiont functioning were sparsely addressed. Previous observations indicated that tea plants might reduce disease occurrence in various forests located in their proximity; the underlying mechanisms and potential implications of the phyllosphere microbiota remained elusive.<br><br>OBJECTIVES: This study aimed atdeciphering microbiome assembly in the tea plant phyllosphere throughout shoot development as well as elucidating potential implications of host metabolites in this process. The main focus was to explore hidden interconnections between the homeostasis of the phyllosphere microbiome and resistance to fungal pathogens.<br><br>METHODS: Profiling of host metabolites and microbiome analyses based on high-throughput sequencing were integrated to identify drivers of microbiome assembly throughout shoot development in the phyllosphere of tea plants. This was complemented by tracking of beneficial microorganisms in all compartments of the plant. Synthetic assemblages (SynAss), bioassays and field surveys were implemented to verify functioning of the phyllosphere microbiota.<br><br>RESULTS: Theophylline and epigallocatechin gallate, two prevalent metabolites at the early and late shoot development stage respectively, were identified as the main drivers of microbial community assembly. Flavobacterium and Myriangium were distinct microbial responders at the early stage, while Parabacteroides and Mortierella were more enriched at the late stage. Reconstructed, stage-specific SynAss suppressed various tree phytopathogens by 13.0%-69.3% in vitro and reduced disease incidence by 8.24%-41.3% in vivo.<br><br>CONCLUSION: The findings indicate that a functional phyllosphere microbiota was assembled along with development-specific metabolites in tea plants, which continuously suppressed prevalent fungal pathogens. The insights gained into the temporally resolved metabolite response of the tea plant microbiota could provide novel solutions for disease management.}, }
@article {pmid35775576, year = {2022}, author = {Gilbert, SF and Hadfield, MG}, title = {Symbiosis of disciplines: how can developmental biologists join conservationists in sustaining and restoring earth's biodiversity?.}, journal = {Development (Cambridge, England)}, volume = {149}, number = {13}, pages = {}, doi = {10.1242/dev.199960}, pmid = {35775576}, issn = {1477-9129}, support = {//Swarthmore College/ ; //Office of Naval Research/ ; //Leidos/ ; }, abstract = {What can developmental biology contribute toward mitigating the consequences of anthropogenic assaults on the environment and climate change? In this Spotlight article, we advocate a developmental biology that takes seriously Lynn Margulis' claim that 'the environment is part of the body'. We believe this to be a pre-condition for developmental biology playing important roles in conservation and environmental restoration. We need to forge a developmental biology of the holobiont - the multi-genomic physiologically integrated organism that is also a functional biome. To this end, we highlight how developmental biology needs to explore more deeply the interactions between developing organisms, and their chemical, physical and biotic environments.}, }
@article {pmid35773344, year = {2022}, author = {Wang, W and Tang, K and Wang, P and Zeng, Z and Xu, T and Zhan, W and Liu, T and Wang, Y and Wang, X}, title = {The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {35773344}, issn = {2397-334X}, abstract = {The coral reef microbiome is central to reef health and resilience. Competitive interactions between opportunistic coral pathogens and other commensal microbes affect the health of coral. Despite great advances over the years in sequencing-based microbial profiling of healthy and diseased coral, the molecular mechanism underlying colonization competition has been much less explored. In this study, by examining the culturable bacteria inhabiting the gastric cavity of healthy Galaxea fascicularis, a scleractinian coral, we found that temperate phages played a major role in mediating colonization competition in the coral microbiota. Specifically, the non-toxigenic Vibrio sp. inhabiting the healthy coral had a much higher colonization capacity than the coral pathogen Vibrio coralliilyticus, yet this advantage was diminished by the latter killing the former. Pathogen-encoded LodAB, which produces hydrogen peroxide, triggers the lytic cycle of prophage in the non-toxicogenic Vibrio sp. Importantly, V. coralliilyticus could outcompete other coral symbiotic bacteria (for example, Endozoicomonas sp.) through LodAB-dependent prophage induction. Overall, we reveal that LodAB can be used by pathogens as an important weapon to gain a competitive advantage over lysogenic competitors when colonizing corals.}, }
@article {pmid35767862, year = {2022}, author = {Bendová, B and Mikula, O and Bímová, BV and Čížková, D and Daniszová, K and Ďureje, Ľ and Hiadlovská, Z and Macholán, M and Martin, JF and Piálek, J and Schmiedová, L and Kreisinger, J}, title = {Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiac078}, pmid = {35767862}, issn = {1574-6941}, abstract = {The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are therefore an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under semi-natural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of co-divergence with their hosts. Helicobacters represent promising candidates for studying GM-host co-adaptations and the fitness effects of their interactions.}, }
@article {pmid35748637, year = {2022}, author = {Poulin, R and Jorge, F and Salloum, PM}, title = {Inter-individual variation in parasite manipulation of host phenotype: a role for parasite microbiomes?.}, journal = {The Journal of animal ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1365-2656.13764}, pmid = {35748637}, issn = {1365-2656}, abstract = {Alterations in host phenotype induced by metazoan parasites are widespread in nature, yet the underlying mechanisms and the sources of intraspecific variation in the extent of those alterations remain poorly understood. In light of the microbiome revolution sweeping through ecology and evolutionary biology, we hypothesise that the composition of symbiotic microbial communities living within individual parasites influences the nature and extent of their effect on host phenotype. The interests of both the parasite and its symbionts are aligned through the latter's vertical transmission, favouring joint contributions to the manipulation of host phenotype. Our hypothesis can explain the variation in the extent to which parasites alter host phenotype, as microbiome composition varies among individual parasites. We propose two non-exclusive approaches to test the hypothesis, furthering the integration of microbiomes into studies of host-parasite interactions.}, }
@article {pmid35746877, year = {2022}, author = {Roik, A and Reverter, M and Pogoreutz, C}, title = {A roadmap to understanding diversity and function of coral reef-associated fungi.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuac028}, pmid = {35746877}, issn = {1574-6976}, abstract = {Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.}, }
@article {pmid35729906, year = {2022}, author = {Williams, SD and Klinges, JG and Zinman, S and Clark, AS and Bartels, E and Villoch Diaz Maurino, M and Muller, EM}, title = {Geographically driven differences in microbiomes of Acropora cervicornis originating from different regions of Florida's Coral Reef.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13574}, doi = {10.7717/peerj.13574}, pmid = {35729906}, issn = {2167-8359}, abstract = {Effective coral restoration must include comprehensive investigations of the targeted coral community that consider all aspects of the coral holobiont-the coral host, symbiotic algae, and microbiome. For example, the richness and composition of microorganisms associated with corals may be indicative of the corals' health status and thus help guide restoration activities. Potential differences in microbiomes of restoration corals due to differences in host genetics, environmental condition, or geographic location, may then influence outplant success. The objective of the present study was to characterize and compare the microbiomes of apparently healthy Acropora cervicornis genotypes that were originally collected from environmentally distinct regions of Florida's Coral Reef and sampled after residing within Mote Marine Laboratory's in situ nursery near Looe Key, FL (USA) for multiple years. By using 16S rRNA high-throughput sequencing, we described the microbial communities of 74 A. cervicornis genotypes originating from the Lower Florida Keys (n = 40 genotypes), the Middle Florida Keys (n = 15 genotypes), and the Upper Florida Keys (n = 19 genotypes). Our findings demonstrated that the bacterial communities of A. cervicornis originating from the Lower Keys were significantly different from the bacterial communities of those originating from the Upper and Middle Keys even after these corals were held within the same common garden nursery for an average of 3.4 years. However, the bacterial communities of corals originating in the Upper Keys were not significantly different from those in the Middle Keys. The majority of the genotypes, regardless of collection region, were dominated by Alphaproteobacteria, namely an obligate intracellular parasite of the genus Ca. Aquarickettsia. Genotypes from the Upper and Middle Keys also had high relative abundances of Spirochaeta bacteria. Several genotypes originating from both the Lower and Upper Keys had lower abundances of Aquarickettsia, resulting in significantly higher species richness and diversity. Low abundance of Aquarickettsia has been previously identified as a signature of disease resistance. While the low-Aquarickettsia corals from both the Upper and Lower Keys had high abundances of an unclassified Proteobacteria, the genotypes in the Upper Keys were also dominated by Spirochaeta. The results of this study suggest that the abundance of Aquarickettsia and Spirochaeta may play an important role in distinguishing bacterial communities among A. cervicornis populations and compositional differences of these bacterial communities may be driven by regional processes that are influenced by both the environmental history and genetic relatedness of the host. Additionally, the high microbial diversity of low-Aquarickettsia genotypes may provide resilience to their hosts, and these genotypes may be a potential resource for restoration practices and management.}, }
@article {pmid35715703, year = {2022}, author = {Lan, Y and Sun, J and Chen, C and Wang, H and Xiao, Y and Perez, M and Yang, Y and Kwan, YH and Sun, Y and Zhou, Y and Han, X and Miyazaki, J and Watsuji, TO and Bissessur, D and Qiu, JW and Takai, K and Qian, PY}, title = {Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35715703}, issn = {1751-7370}, support = {42176110//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18K06401//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.}, }
@article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, support = {9659-15//National Geographic Society/ ; }, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, }
@article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, }
@article {pmid35718641, year = {2022}, author = {Ricci, F and Leggat, W and Page, CE and Ainsworth, TD}, title = {Coral growth anomalies, neoplasms, and tumors in the Anthropocene.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2022.05.013}, pmid = {35718641}, issn = {1878-4380}, abstract = {One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.}, }
@article {pmid35714829, year = {2022}, author = {Zhu, Y and Liao, X and Han, T and Chen, JY and He, C and Lu, Z}, title = {Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration.}, journal = {Genomics}, volume = {114}, number = {4}, pages = {110404}, doi = {10.1016/j.ygeno.2022.110404}, pmid = {35714829}, issn = {1089-8646}, abstract = {Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel. This work provides evidence for the early origin of cross-kingdom regulation as a mechanism of self-defense autotrophs can use against heterotrophs, sheds more light on coral-Symbiodiniaceae holobionts, and contributes valuable data for further coral research.}, }
@article {pmid35322689, year = {2022}, author = {Omae, N and Tsuda, K}, title = {Plant-Microbiota Interactions in Abiotic Stress Environments.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {}, number = {}, pages = {MPMI11210281FI}, doi = {10.1094/MPMI-11-21-0281-FI}, pmid = {35322689}, issn = {0894-0282}, abstract = {Abiotic stress adversely affects cellular homeostasis and ultimately impairs plant growth, posing a serious threat to agriculture. Climate change modeling predicts increasing occurrences of abiotic stresses such as drought and extreme temperature, resulting in decreasing the yields of major crops such as rice, wheat, and maize, which endangers food security for human populations. Plants are associated with diverse and taxonomically structured microbial communities that are called the plant microbiota. Plant microbiota often assist plant growth and abiotic stress tolerance by providing water and nutrients to plants and modulating plant metabolism and physiology and, thus, offer the potential to increase crop production under abiotic stress. In this review, we summarize recent progress on how abiotic stress affects plants, microbiota, plant-microbe interactions, and microbe-microbe interactions, and how microbes affect plant metabolism and physiology under abiotic stress conditions, with a focus on drought, salt, and temperature stress. We also discuss important steps to utilize plant microbiota in agriculture under abiotic stress.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, }
@article {pmid35698170, year = {2022}, author = {Wang, K and Gao, P and Geng, L and Liu, C and Zhang, J and Shu, C}, title = {Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {90}, pmid = {35698170}, issn = {2049-2618}, support = {32070511//National Natural Science Foundation of China/ ; 31972336//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.<br><br>RESULTS: Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.<br><br>CONCLUSIONS: This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.}, }
@article {pmid35674443, year = {2022}, author = {Low, A and Soh, M and Miyake, S and Seedorf, H}, title = {Host Age Prediction from Fecal Microbiota Composition in Male C57BL/6J Mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0073522}, doi = {10.1128/spectrum.00735-22}, pmid = {35674443}, issn = {2165-0497}, abstract = {The lifelong relationship between microorganisms and hosts has a profound impact on the overall health and physiology of the holobiont. Microbiome composition throughout the life span of a host remains largely understudied. Here, the fecal microbiota of conventionally raised C57BL/6J male mice was characterized throughout almost the entire adult life span, from "maturing" (9 weeks) until "very old" (112 weeks) age. Our results suggest that microbiota changes occur throughout life but are more pronounced in maturing to middle-age mice than in mice later in life. Phylum-level analysis indicates a shift of the Bacteroidota-to-Firmicutes ratio in favor of Firmicutes in old and very old mice. More Firmicutes amplicon sequence variants (ASVs) were transient with varying successional patterns than Bacteroidota ASVs, which varied primarily during maturation. Microbiota configurations from five defined life phases were used as training sets in a Bayesian model, which effectively enabled the prediction of host age. These results suggest that age-associated compositional differences may have considerable implications for the interpretation and comparability of animal model-based microbiome studies. The sensitivity of the age prediction to dietary perturbations was tested by applying this approach to two age-matched groups of C57BL/6J mice that were fed either a standard or western diet. The predicted age for the western diet-fed animals was on average 27 ± 11 (mean ± standard deviation) weeks older than that of standard diet-fed animals. This indicates that the fecal microbiota-based predicted age may be influenced not only by the host age and physiology but also potentially by other factors such as diet. IMPORTANCE The gut microbiome of a host changes with age. Cross-sectional studies demonstrate that microbiota of different age groups are distinct but do not demonstrate the temporal change that a longitudinal study is able to show. Here, we performed a longitudinal study of adult mice for over 2 years. We identified life stages where compositional changes were more dynamic and showed temporal changes for the more abundant species. Using a Bayesian model, we could reliably predict the life stages of the mice. Application of the same training set to mice fed different dietary regimens revealed that life-stage age predictions were possible for mice fed the same diet but less so for mice fed different diets. This study sheds light on the temporal changes that occur within the gut microbiota of laboratory mice over their life span and may inform researchers on the appropriate mouse age for their research.}, }
@article {pmid35630391, year = {2022}, author = {Hernandez, J and Rhimi, S and Kriaa, A and Mariaule, V and Boudaya, H and Drut, A and Jablaoui, A and Mkaouar, H and Saidi, A and Biourge, V and Borgi, MA and Rhimi, M and Maguin, E}, title = {Domestic Environment and Gut Microbiota: Lessons from Pet Dogs.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/microorganisms10050949}, pmid = {35630391}, issn = {2076-2607}, support = {PS-Com-Pro Project//Royal Canin/ ; 41786NC//Campus France/ ; MICAfrica 952583//European Commission/ ; }, abstract = {Accumulating data show the involvement of intestinal microbiota in the development and maintenance of numerous diseases. Many environmental factors influence the composition and function of the gut microbiota. An animal model subjected to the same environmental constraints that will allow better characterization of the microbiota-host dialogue is awaited. The domestic dog has physiological, dietary and pathological characteristics similar to those of humans and shares the domestic environment and lifestyle of its owner. This review exposes how the domestication of dogs has brought them closer to humans based on their intrinsic and extrinsic similarities which were discerned through examining and comparing the current knowledge and data on the intestinal microbiota of humans and canines in the context of several spontaneous pathologies, including inflammatory bowel disease, obesity and diabetes mellitus.}, }
@article {pmid35620601, year = {2022}, author = {Lin, S and Yu, K and Zhou, Z}, title = {Editorial: Physiological Regulation and Homeostasis Among Coral Holobiont Partners.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {921401}, doi = {10.3389/fphys.2022.921401}, pmid = {35620601}, issn = {1664-042X}, }
@article {pmid35619157, year = {2022}, author = {Sahu, KP and Kumar, A and Sakthivel, K and Reddy, B and Kumar, M and Patel, A and Sheoran, N and Gopalakrishnan, S and Prakash, G and Rathour, R and Gautam, RK}, title = {Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {28}, pmid = {35619157}, issn = {2524-6372}, support = {File No: 09/083(0367)/2016-EMR-I//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future.<br><br>RESULTS: The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings.<br><br>CONCLUSIONS: PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.}, }
@article {pmid35604874, year = {2022}, author = {Snelders, NC and Rovenich, H and Thomma, BPHJ}, title = {Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom.}, journal = {FEMS microbiology reviews}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsre/fuac022}, pmid = {35604874}, issn = {1574-6976}, abstract = {Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.}, }
@article {pmid35602056, year = {2022}, author = {Ren, CG and Kong, CC and Liu, ZY and Zhong, ZH and Yang, JC and Wang, XL and Qin, S}, title = {A Perspective on Developing a Plant 'Holobiont' for Future Saline Agriculture.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {763014}, doi = {10.3389/fmicb.2022.763014}, pmid = {35602056}, issn = {1664-302X}, abstract = {Soil salinity adversely affects plant growth and has become a major limiting factor for agricultural development worldwide. There is a continuing demand for sustainable technology innovation in saline agriculture. Among various bio-techniques being used to reduce the salinity hazard, symbiotic microorganisms such as rhizobia and arbuscular mycorrhizal (AM) fungi have proved to be efficient. These symbiotic associations each deploy an array of well-tuned mechanisms to provide salinity tolerance for the plant. In this review, we first comprehensively cover major research advances in symbiont-induced salinity tolerance in plants. Second, we describe the common signaling process used by legumes to control symbiosis establishment with rhizobia and AM fungi. Multi-omics technologies have enabled us to identify and characterize more genes involved in symbiosis, and eventually, map out the key signaling pathways. These developments have laid the foundation for technological innovations that use symbiotic microorganisms to improve crop salt tolerance on a larger scale. Thus, with the aim of better utilizing symbiotic microorganisms in saline agriculture, we propose the possibility of developing non-legume 'holobionts' by taking advantage of newly developed genome editing technology. This will open a new avenue for capitalizing on symbiotic microorganisms to enhance plant saline tolerance for increased sustainability and yields in saline agriculture.}, }
@article {pmid35590396, year = {2022}, author = {Unzueta-Martínez, A and Scanes, E and Parker, LM and Ross, PM and O'Connor, W and Bowen, JL}, title = {Microbiomes of the Sydney Rock Oyster are acquired through both vertical and horizontal transmission.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {32}, pmid = {35590396}, issn = {2524-4671}, support = {1938052//National Science Foundation/ ; 1451070//National Science Foundation/ ; }, abstract = {BACKGROUND: The term holobiont is widely accepted to describe animal hosts and their associated microorganisms. The genomes of all that the holobiont encompasses, are termed the hologenome and it has been proposed as a unit of selection in evolution. To demonstrate that natural selection acts on the hologenome, a significant portion of the associated microbial genomes should be transferred between generations. Using the Sydney Rock Oyster (Saccostrea glomerata) as a model, we tested if the microbes of this broadcast spawning species could be passed down to the next generation by conducting single parent crosses and tracking the microbiome from parent to offspring and throughout early larval stages using 16S rRNA gene amplicon sequencing. From each cross, we sampled adult tissues (mantle, gill, stomach, gonad, eggs or sperm), larvae (D-veliger, umbo, eyed pediveliger, and spat), and the surrounding environment (water and algae feed) for microbial community analysis.<br><br>RESULTS: We found that each larval stage has a distinct microbiome that is partially influenced by their parental microbiome, particularly the maternal egg microbiome. We also demonstrate the presence of core microbes that are consistent across all families, persist throughout early life stages (from eggs to spat), and are not detected in the microbiomes of the surrounding environment. In addition to the core microbiomes that span all life cycle stages, there is also evidence of environmentally acquired microbial communities, with earlier larval stages (D-veliger and umbo), more influenced by seawater microbiomes, and later larval stages (eyed pediveliger and spat) dominated by microbial members that are specific to oysters and not detected in the surrounding environment.<br><br>CONCLUSION: Our study characterized the succession of oyster larvae microbiomes from gametes to spat and tracked selected members that persisted across multiple life stages. Overall our findings suggest that both horizontal and vertical transmission routes are possible for the complex microbial communities associated with a broadcast spawning marine invertebrate. We demonstrate that not all members of oyster-associated microbiomes are governed by the same ecological dynamics, which is critical for determining what constitutes a hologenome.}, }
@article {pmid35589992, year = {2022}, author = {King, NG and Moore, PJ and Thorpe, JM and Smale, DA}, title = {Consistency and Variation in the Kelp Microbiota: Patterns of Bacterial Community Structure Across Spatial Scales.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35589992}, issn = {1432-184X}, support = {MR/S032827/1//UKRI/ ; NE/S011692/1//Natural Environment Research Council/ ; }, abstract = {Kelp species are distributed along ~ 25% of the world's coastlines and the forests they form represent some of the world's most productive and diverse ecosystems. Like other marine habitat-formers, the associated microbial community is fundamental for host and, in turn, wider ecosystem functioning. Given there are thousands of bacteria-host associations, determining which relationships are important remains a major challenge. We characterised the associated bacteria of two habitat-forming kelp species, Laminaria hyperborea and Saccharina latissima, from eight sites across a range of spatial scales (10 s of metres to 100 s of km) in the northeast Atlantic. We found no difference in diversity or community structure between the two kelps, but there was evidence of regional structuring (across 100 s km) and considerable variation between individuals (10 s of metres). Within sites, individuals shared few amplicon sequence variants (ASVs) and supported a very small proportion of diversity found across the wider study area. However, consistent characteristics between individuals were observed with individual host communities containing a small conserved "core" (8-11 ASVs comprising 25 and 32% of sample abundances for L. hyperborea and S. latissima, respectively). At a coarser taxonomic resolution, communities were dominated by four classes (Planctomycetes, Gammaproteobacteria, Alphaproteobacteria and Bacteroidia) that made up ~ 84% of sample abundances. Remaining taxa (47 classes) made up very little contribution to overall abundance but the majority of taxonomic diversity. Overall, our study demonstrates the consistent features of kelp bacterial communities across large spatial scales and environmental gradients and provides an ecologically meaningful baseline to track environmental change.}, }
@article {pmid35588270, year = {2022}, author = {Bashir, F and Kovács, S and Ábrahám, Á and Nagy, K and Ayaydin, F and Valkony-Kelemen, I and Ferenc, G and Galajda, P and Tóth, SZ and Sass, L and Kós, PB and Vass, I and Szabó, M}, title = {Viable protoplast formation of the coral endosymbiont alga Symbiodinium spp. in a microfluidics platform.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d2lc00130f}, pmid = {35588270}, issn = {1473-0189}, abstract = {Symbiodiniaceae is an important dinoflagellate family which lives in endosymbiosis with reef invertebrates, including coral polyps, making them central to the holobiont. With coral reefs currently under extreme threat from climate change, there is a pressing need to improve our understanding on the stress tolerance and stress avoidance mechanisms of Symbiodinium spp. Reactive oxygen species (ROS) such as singlet oxygen are central players in mediating various stress responses; however, the detection of ROS using specific dyes is still far from definitive in intact Symbiodinium cells due to the hindrance of uptake of certain fluorescent dyes because of the presence of the cell wall. Protoplast technology provides a promising platform for studying oxidative stress with the main advantage of removed cell wall, however the preparation of viable protoplasts remains a significant challenge. Previous studies have successfully applied cellulose-based protoplast preparation in Symbiodiniaceae; however, the protoplast formation and regeneration process was found to be suboptimal. Here, we present a microfluidics-based platform which allowed protoplast isolation from individually trapped Symbiodinium cells, by using a precisely adjusted flow of cell wall digestion enzymes (cellulase and macerozyme). Trapped single cells exhibited characteristic changes in their morphology, cessation of cell division and a slight decrease in photosynthetic activity during protoplast formation. Following digestion and transfer to regeneration medium, protoplasts remained photosynthetically active, regrew cell walls, regained motility, and entered exponential growth. Elevated flow rates in the microfluidic chambers resulted in somewhat faster protoplast formation; however, cell wall digestion at higher flow rates partially compromised photosynthetic activity. Physiologically competent protoplasts prepared from trapped cells in microfluidic chambers allowed for the first time the visualization of the intracellular localization of singlet oxygen (using Singlet Oxygen Sensor Green dye) in Symbiodiniaceae, potentially opening new avenues for studying oxidative stress.}, }
@article {pmid35579919, year = {2022}, author = {Soldan, R and Fusi, M and Preston, GM}, title = {Approaching the domesticated plant holobiont from a community evolution perspective.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {5}, pages = {}, doi = {10.1099/mic.0.001188}, pmid = {35579919}, issn = {1465-2080}, abstract = {Plants establish a pivotal relationship with their microbiome and are often conceptualized as holobionts. Nonetheless, holobiont theories have attracted much criticism, especially concerning the fact that the holobiont is rarely a unit of selection. In previous work, we discussed how the plant microbiome can be considered to be an 'ecosystem on a leash', which is subject to the influence of natural selection acting on plant traits. We proposed that in domesticated plants the assembly of the plant microbiome can usefully be conceptualized as being subject to a 'double leash', which encompasses both the effect of artificial selection imposed by the domesticator on plant traits and the leash from the plant to the microbiome. Here we approach the domesticated plant holobiont, simply defined as a community of organisms, from a community evolution point of view, and show how community heritability (a measure of community selection) complements the 'double-leash' framework in providing a community-level view of plant domestication and its impact on plant-microbe interactions. We also propose simple experiments that could be performed to investigate whether plant domestication has altered the potential for community selection at the holobiont level.}, }
@article {pmid35578838, year = {2022}, author = {de Oliveira, BFR and Freitas-Silva, J and Canellas, ALB and Costa, WF and Laport, MS}, title = {Time for a change! A spotlight on the many neglected facets of sponge microbial biotechnology.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/1389201023666220516103715}, pmid = {35578838}, issn = {1873-4316}, abstract = {The sponge-microorganism partnership is one the most successful symbiotic associations exploited under a biotechnological perspective. During the last thirty years, sponge-associated bacteria have been increasingly harnessed for bioactive molecules, notably antimicrobials and cytotoxic compounds. Unfortunately, there are gaps in sponge microbial biotechnology, with a multitude of applications being little investigated or even unregarded. In this context, the current Perspective aims to shed light on these underrated facets of sponge microbial biotechnology with a balance of existent reports and proposals for further research in the field. Our overview has showcased that the members of the sponge microbiome produce biomolecules which usage can be valuable for several economically-relevant and demanding sectors. Outside the exhaustive search for antimicrobial secondary metabolites, sponge-associated microorganisms are gifted producers of antibiofilm, antivirulence and chronic diseases-attenuating substances highly envisaged by the pharmaceutical industry. Despite still at an infant stage of research, anti-ageing enzymes and pigments of special interest for the cosmetic and cosmeceutical sectors have also been reported from the sponge microbial symbionts. In a world urging for sustainability, sponge-associated microorganisms have been proven as fruitful resources for bioremediation, including recovery of heavy-metal contaminated areas, bioleaching processes, and as bioindicators of environmental pollution. In conclusion, we propose alternatives to better assess these neglected biotechnological applications of the sponge microbiome in the hope of sparking the interest of the scientific community towards their deserved exploitation.}, }
@article {pmid35537882, year = {2022}, author = {Oláh, P and Szlávicz, E and Kuchner, M and Nemmer, J and Zeeuwen, P and Lefèvre-Utile, A and Fyhrquist, N and Prast-Nielsen, S and Skoog, T and Serra, A and Rodríguez, E and Raap, U and Meller, S and Gyulai, R and Hupé, P and Kere, J and Levi-Schaffer, F and Tsoka, S and Alexander, H and Nestle, FO and Schröder, JM and Weidinger, S and van den Bogaard, E and Soumelis, V and Greco, D and Barker, J and Lauerma, A and Ranki, A and Andersson, B and Alenius, H and Homey, B}, title = {Influence of FLG loss-of-function mutations in host-microbe interactions during atopic skin inflammation.}, journal = {Journal of dermatological science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jdermsci.2022.04.007}, pmid = {35537882}, issn = {1873-569X}, abstract = {BACKGROUND: Loss-of-function mutations in the filaggrin (FLG) gene directly alter skin barrier function and critically influence atopic inflammation. While skin barrier dysfunction, Th2-associated inflammation and bacterial dysbiosis are well-known characteristics of atopic dermatitis (AD), the mechanisms interconnecting genotype, transcriptome and microbiome remain largely elusive.<br><br>OBJECTIVE: In-depth analysis of FLG genotype-associated skin gene expression alterations and host-microbe interactions in AD.<br><br>METHODS: Multi-omics characterization of a cohort of AD patients carrying heterozygous loss-of-function mutations in the FLG gene (ADMut) (n = 15), along with matched wild-type (ADWt) patients and healthy controls. Detailed clinical characterization, microarray gene expression and 16 S rRNA-based microbial marker gene data were generated and analyzed.<br><br>RESULTS: In the context of filaggrin dysfunction, the transcriptome was characterized by dysregulation of barrier function and water homeostasis, while the lesional skin of ADWt demonstrated the specific upregulation of pro-inflammatory cytokines and T-cell proliferation. S. aureus dominated the microbiome in both patient groups, however, shifting microbial communities could be observed when comparing healthy with non-lesional ADWt or ADMut skin, offering the opportunity to identify microbe-associated transcriptomic signatures. Moreover, an AD core signature with 28 genes, including CCL13, CCL18, BTC, SCIN, RAB31 and PCLO was identified.<br><br>CONCLUSIONS: Our integrative approach provides molecular insights for the concept that FLG loss-of-function mutations are a genetic shortcut to atopic inflammation and unravels the complex interplay between genotype, transcriptome and microbiome in the human holobiont.}, }
@article {pmid35524305, year = {2022}, author = {Carrier, TJ and Maldonado, M and Schmittmann, L and Pita, L and Bosch, TCG and Hentschel, U}, title = {Symbiont transmission in marine sponges: reproduction, development, and metamorphosis.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {100}, pmid = {35524305}, issn = {1741-7007}, mesh = {Animals ; *Microbiota ; Phylogeny ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S ; Reproduction ; Symbiosis ; }, abstract = {Marine sponges (phylum Porifera) form symbioses with diverse microbial communities that can be transmitted between generations through their developmental stages. Here, we integrate embryology and microbiology to review how symbiotic microorganisms are transmitted in this early-diverging lineage. We describe that vertical transmission is widespread but not universal, that microbes are vertically transmitted during a select developmental window, and that properties of the developmental microbiome depends on whether a species is a high or low microbial abundance sponge. Reproduction, development, and symbiosis are thus deeply rooted, but why these partnerships form remains the central and elusive tenet of these developmental symbioses.}, }
@article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {}, number = {}, pages = {e0067922}, doi = {10.1128/mbio.00679-22}, pmid = {35502903}, issn = {2150-7511}, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, }
@article {pmid35482345, year = {2022}, author = {Gennery, AR}, title = {Seek and you shall find: immune lymphoid cells in holobiont health.}, journal = {Blood}, volume = {139}, number = {17}, pages = {2577-2578}, doi = {10.1182/blood.2022015801}, pmid = {35482345}, issn = {1528-0020}, mesh = {*Dysbiosis ; Humans ; Immunity, Mucosal ; Interleukin Receptor Common gamma Subunit ; Janus Kinase 3 ; Lymphocytes ; Severe Combined Immunodeficiency ; *Transplants ; }, }
@article {pmid35481756, year = {2022}, author = {Bell, JK and Mamet, SD and Helgason, B and Siciliano, SD}, title = {Brassica napus Bacterial Assembly Processes Vary with Plant Compartment and Growth Stage but Not between Lines.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0027322}, doi = {10.1128/aem.00273-22}, pmid = {35481756}, issn = {1098-5336}, abstract = {Holobiont bacterial community assembly processes are an essential element to understanding the plant microbiome. To elucidate these processes, leaf, root, and rhizosphere samples were collected from eight lines of Brassica napus in Saskatchewan over the course of 10 weeks. We then used ecological null modeling to disentangle the community assembly processes over the growing season in each plant part. The root was primarily dominated by stochastic community assembly processes, which is inconsistent with previous studies that suggest of a highly selective root environment. Leaf assembly processes were primarily stochastic as well. In contrast, the rhizosphere was a highly selective environment. The dominant rhizosphere selection process leads to more similar communities. Assembly processes in all plant compartments were dependent on plant growth stage with little line effect on community assembly. The foundations of assembly in the leaf were due to the harsh environment, leading to dominance of stochastic effects, whereas the stochastic effects in the root interior likely arise due to competitive exclusion or priority effects. Engineering canola microbiomes should occur during periods of strong selection assuming strong selection could promote beneficial bacteria. For example, engineering the microbiome to resist pathogens, which are typically aerially born, should focus on the flowering period, whereas microbiomes to enhance yield should likely be engineered postflowering as the rhizosphere is undergoing strong selection. IMPORTANCE In order to harness the microbiome for more sustainable crop production, we must first have a better understanding of microbial community assembly processes that occurring during plant development. This study examines the bacterial community assembly processes of the leaf, root, and rhizosphere of eight different lines of Brassica napus over the growing season. The influence of growth stage and B. napus line were examined in conjunction with the assembly processes. Understanding what influences the assembly processes of crops might allow for more targeted breeding efforts by working with the plant to manipulate the microbiome when it is undergoing the strongest selection pressure.}, }
@article {pmid35476981, year = {2022}, author = {Weagley, JS and Zaydman, M and Venkatesh, S and Sasaki, Y and Damaraju, N and Yenkin, A and Buchser, W and Rodionov, DA and Osterman, A and Ahmed, T and Barratt, MJ and DiAntonio, A and Milbrandt, J and Gordon, JI}, title = {Products of gut microbial Toll/interleukin-1 receptor domain NADase activities in gnotobiotic mice and Bangladeshi children with malnutrition.}, journal = {Cell reports}, volume = {39}, number = {4}, pages = {110738}, doi = {10.1016/j.celrep.2022.110738}, pmid = {35476981}, issn = {2211-1247}, support = {R01 NS119812/NS/NINDS NIH HHS/United States ; RF1 AG013730/AG/NIA NIH HHS/United States ; U2C DK119886/DK/NIDDK NIH HHS/United States ; R37 NS065053/NS/NINDS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/metabolism ; Child ; Cyclic ADP-Ribose ; *Gastrointestinal Microbiome ; Germ-Free Life ; Humans ; *Malnutrition ; Mice ; NAD/metabolism ; NAD+ Nucleosidase/metabolism ; Receptors, Interleukin-1 ; }, abstract = {Perturbed gut microbiome development has been linked to childhood malnutrition. Here, we characterize bacterial Toll/interleukin-1 receptor (TIR) protein domains that metabolize nicotinamide adenine dinucleotide (NAD), a co-enzyme with far-reaching effects on human physiology. A consortium of 26 human gut bacterial strains, representing the diversity of TIRs observed in the microbiome and the NAD hydrolase (NADase) activities of a subset of 152 bacterial TIRs assayed in vitro, was introduced into germ-free mice. Integrating mass spectrometry and microbial RNA sequencing (RNA-seq) with consortium membership manipulation disclosed that a variant of cyclic-ADPR (v-cADPR-x) is a specific product of TIR NADase activity and a prominent, colonization-discriminatory, taxon-specific metabolite. Guided by bioinformatic analyses of biochemically validated TIRs, we find that acute malnutrition is associated with decreased fecal levels of genes encoding TIRs known or predicted to generate v-cADPR-x, as well as decreased levels of the metabolite itself. These results underscore the need to consider microbiome TIR NADases when evaluating NAD metabolism in the human holobiont.}, }
@article {pmid35444618, year = {2022}, author = {Happel, L and Rondon, R and Font, A and González-Aravena, M and Cárdenas, CA}, title = {Stability of the Microbiome of the Sponge Mycale (Oxymycale) acerata in the Western Antarctic Peninsula.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {827863}, pmid = {35444618}, issn = {1664-302X}, abstract = {The sponge microbiome, especially in Low Microbial Abundance (LMA) species, is expected to be influenced by the local environment; however, contrasting results exist with evidence showing that host specificity is also important, hence suggesting that the microbiome is influenced by host-specific and environmental factors. Despite sponges being important members of Southern Ocean benthic communities, their relationships with the microbial communities they host remain poorly studied. Here, we studied the spatial and temporal patterns of the microbiota associated with the ecologically important LMA sponge M. acerata at sites along ∼400 km of the Western Antarctic Peninsula (WAP) to assess patterns in the core and variable microbial components of the symbiont communities of this sponge species. The analyses of 31 samples revealed that the microbiome of M. acerata is composed of 35 prokaryotic phyla (3 Archaea, 31 Bacteria, and one unaffiliated), being mainly dominated by Proteobacteria with Gammaproteobacteria as the most dominant class. The core community was composed of six prokaryotic OTUs, with gammaproteobacterial OTU (EC94 Family), showing a mean abundance over 65% of the total abundance. Despite some differences in rare OTUs, the core community did not show clear patterns in diversity and abundance associated with specific sites/environmental conditions, confirming a low variability in community structure of this species along the WAP. The analysis at small scale (Doumer Island, Palmer Archipelago) showed no differences in space and time in the microbiome M. acerata collected at sites around the island, sampled in three consecutive years (2016-2018). Our results highlight the existence of a low spatial and temporal variability in the microbiome of M. acerata, supporting previous suggestions based on limited studies on this and other Antarctic sponges.}, }
@article {pmid35444262, year = {2022}, author = {Pogoreutz, C and Oakley, CA and Rädecker, N and Cárdenas, A and Perna, G and Xiang, N and Peng, L and Davy, SK and Ngugi, DK and Voolstra, CR}, title = {Coral holobiont cues prime Endozoicomonas for a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, pmid = {35444262}, issn = {1751-7370}, support = {URF/1/3400-01-01//King Abdullah University of Science and Technology (KAUST)/ ; 15902919 FP 029/19//Universität Konstanz (University of Konstanz)/ ; 19-VUW-086//Royal Marsden NHS Foundation Trust (Royal Marsden)/ ; 201807565016//China Scholarship Council (CSC)/ ; }, abstract = {Endozoicomonas are prevalent, abundant bacterial associates of marine animals, including corals. Their role in holobiont health and functioning, however, remains poorly understood. To identify potential interactions within the coral holobiont, we characterized the novel isolate Endozoicomonas marisrubri sp. nov. 6c and assessed its transcriptomic and proteomic response to tissue extracts of its native host, the Red Sea coral Acropora humilis. We show that coral tissue extracts stimulated differential expression of genes putatively involved in symbiosis establishment via the modulation of the host immune response by E. marisrubri 6c, such as genes for flagellar assembly, ankyrins, ephrins, and serpins. Proteome analyses revealed that E. marisrubri 6c upregulated vitamin B1 and B6 biosynthesis and glycolytic processes in response to holobiont cues. Our results suggest that the priming of Endozoicomonas for a symbiotic lifestyle involves the modulation of host immunity and the exchange of essential metabolites with other holobiont members. Consequently, Endozoicomonas may play an important role in holobiont nutrient cycling and may therefore contribute to coral health, acclimatization, and adaptation.}, }
@article {pmid35432258, year = {2022}, author = {Zhu, W and Liu, X and Zhu, M and Li, X and Yin, H and Huang, J and Wang, A and Li, X}, title = {Responses of Symbiodiniaceae Shuffling and Microbial Community Assembly in Thermally Stressed Acropora hyacinthus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {832081}, pmid = {35432258}, issn = {1664-302X}, abstract = {Although the importance of coral holobionts is widely accepted, the relationship between the flexibility of the microbial structure and the coral host is very complicated. Particularly, the community dynamics of holobionts and the stability of host-microbe interactions under different thermal stresses remain largely unknown. In the present study, we holistically explored the physiology and growth of Acropora hyacinthus in response to increased temperatures (from 26 to 33°C). We observed that bleaching corals with loss of algal symbionts reduced lipids and proteins to maintain their survival, leading to decreased tissue biomass and retarded growth. The diversity of Symbiodiniaceae and symbiont shuffling in the community structure was mainly caused by alterations in the relative abundance of the thermally sensitive but dominant clade C symbionts and low abundance of "background types." Bacterial diversity showed a decreasing trend with increasing temperature, whereas no significant shifts were observed in the bacterial community structure. This finding might be attributed to the local adjustment of specific microbial community members that did not affect the overall metabolic state of the coral holobiont, and there was no increase in the proportion of sequences identified as typically pathogenic or opportunistic taxa. The Sloan neutral community model showed that neutral processes could explain 42.37-58.43% of bacterial community variation. The Stegen null model analysis indicates that the stochastic processes explain a significantly higher proportion of community assembly than deterministic processes when the temperature was elevated. The weak effect of temperature on the bacterial community structure and assembly might be related to an increase in stochastic dominance. The interaction of bacterial communities exhibits a fluctuating and simplistic trend with increasing temperature. Moreover, temperature increases were sufficient to establish the high stability of bacterial networks, and a non-linear response was found between the complexity and stability of the networks. Our findings collectively provide new insights into successive changes in the scleractinian coral host and holobionts in response to elevated seawater temperatures, especially the contribution of the community assembly process and species coexistence patterns to the maintenance of the coral-associated bacterial community.}, }
@article {pmid35432234, year = {2022}, author = {Quintanilla, E and Rodrigues, CF and Henriques, I and Hilário, A}, title = {Microbial Associations of Abyssal Gorgonians and Anemones (&gt;4,000 m Depth) at the Clarion-Clipperton Fracture Zone.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828469}, pmid = {35432234}, issn = {1664-302X}, abstract = {Deep coral-dominated communities play paramount roles in benthic environments by increasing their complexity and biodiversity. Coral-associated microbes are crucial to maintain fitness and homeostasis at the holobiont level. However, deep-sea coral biology and their associated microbiomes remain largely understudied, and less from remote and abyssal environments such as those in the Clarion-Clipperton Fracture Zone (CCZ) in the tropical Northeast (NE) Pacific Ocean. Here, we study microbial-associated communities of abyssal gorgonian corals and anemones (>4,000 m depth) in the CCZ; an area harboring the largest known global reserve of polymetallic nodules that are commercially interesting for the deep-sea nodule mining. Coral samples (n = 25) belonged to Isididae and Primnoidae families, while anemones (n = 4) to Actinostolidae family. Significant differences in bacterial community compositions were obtained between these three families, despite sharing similar habitats. Anemones harbored bacterial microbiomes composed mainly of Hyphomicrobiaceae, Parvibaculales, and Pelagibius members. Core microbiomes of corals were mainly dominated by different Spongiibacteraceae and Terasakiellaceae bacterial members, depending on corals' taxonomy. Moreover, the predicted functional profiling suggests that deep-sea corals harbor bacterial communities that allow obtaining additional energy due to the scarce availability of nutrients. This study presents the first report of microbiomes associated with abyssal gorgonians and anemones and will serve as baseline data and crucial insights to evaluate and provide guidance on the impacts of deep-sea mining on these key abyssal communities.}, }
@article {pmid35428831, year = {2022}, author = {Berlinghof, J and Peiffer, F and Marzocchi, U and Munari, M and Quero, GM and Dennis, L and Wild, C and Cardini, U}, title = {The role of epiphytes in seagrass productivity under ocean acidification.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6249}, pmid = {35428831}, issn = {2045-2322}, mesh = {*Alismatales/physiology ; Carbon Dioxide ; Hydrogen-Ion Concentration ; Plant Leaves ; *Seawater/chemistry ; }, abstract = {Ocean Acidification (OA), due to rising atmospheric CO2, can affect the seagrass holobiont by changing the plant's ecophysiology and the composition and functioning of its epiphytic community. However, our knowledge of the role of epiphytes in the productivity of the seagrass holobiont in response to environmental changes is still very limited. CO2 vents off Ischia Island (Italy) naturally reduce seawater pH, allowing to investigate the adaptation of the seagrass Posidonia oceanica L. (Delile) to OA. Here, we analyzed the percent cover of different epiphytic groups and the epiphytic biomass of P. oceanica leaves, collected inside (pH 6.9-7.9) and outside (pH 8.1-8.2) the CO2 vents. We estimated the contribution of epiphytes to net primary production (NPP) and respiration (R) of leaf sections collected from the vent and ambient pH sites in laboratory incubations. Additionally, we quantified net community production (NCP) and community respiration (CR) of seagrass communities in situ at vent and ambient pH sites using benthic chambers. Leaves at ambient pH sites had a 25% higher total epiphytic cover with encrusting red algae (32%) dominating the community, while leaves at vent pH sites were dominated by hydrozoans (21%). Leaf sections with and without epiphytes from the vent pH site produced and respired significantly more oxygen than leaf sections from the ambient pH site, showing an average increase of 47 ± 21% (mean ± SE) in NPP and 50 ± 4% in R, respectively. Epiphytes contributed little to the increase in R; however, their contribution to NPP was important (56 ± 6% of the total flux). The increase in productivity of seagrass leaves adapted to OA was only marginally reflected by the results from the in situ benthic chambers, underlining the complexity of the seagrass community response to naturally occurring OA conditions.}, }
@article {pmid35428367, year = {2022}, author = {Szitenberg, A and Beca-Carretero, P and Azcárate-García, T and Yergaliyev, T and Alexander-Shani, R and Winters, G}, title = {Teasing apart the host-related, nutrient-related and temperature-related effects shaping the phenology and microbiome of the tropical seagrass Halophila stipulacea.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {18}, pmid = {35428367}, issn = {2524-6372}, support = {3-15152//Italy-Israel binational fund/ ; 03-16-06a//ICA in Israel/ ; }, abstract = {BACKGROUND: Halophila stipulacea seagrass meadows are an ecologically important and threatened component of the ecosystem in the Gulf of Aqaba. Recent studies have demonstrated correlated geographic patterns for leaf epiphytic community composition and leaf morphology, also coinciding with different levels of water turbidity and nutrient concentrations. Based on these observations, workers have suggested an environmental microbial fingerprint, which may reflect various environmental stress factors seagrasses have experienced, and may add a holobiont level of plasticity to seagrasses, assisting their acclimation to changing environments and through range expansion. However, it is difficult to tease apart environmental effects from host-diversity dependent effects, which have covaried in field studies, although this is required in order to establish that differences in microbial community compositions among sites are driven by environmental conditions rather than by features governed by the host.<br><br>RESULTS: In this study we carried out a mesocosm experiment, in which we studied the effects of warming and nutrient stress on the composition of epiphytic bacterial communities and on some phenological traits. We studied H. stipulacea collected from two different meadows in the Gulf of Aqaba, representing differences in the host and the environment alike. We found that the source site from which seagrasses were collected was the major factor governing seagrass phenology, although heat increased shoot mortality and nutrient loading delayed new shoot emergence. Bacterial diversity, however, mostly depended on the environmental conditions. The most prominent pattern was the increase in Rhodobacteraceae under nutrient stress without heat stress, along with an increase in Microtrichaceae. Together, the two taxa have the potential to maintain nitrate reduction followed by an anammox process, which can together buffer the increase in nutrient concentrations across the leaf surface.<br><br>CONCLUSIONS: Our results thus corroborate the existence of environmental microbial fingerprints, which are independent from the host diversity, and support the notion of a holobiont level plasticity, both important to understand and monitor H. stipulacea ecology under the changing climate.}, }
@article {pmid35418670, year = {2022}, author = {Titus, BM and Daly, M}, title = {Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes?.}, journal = {Heredity}, volume = {128}, number = {5}, pages = {338-351}, pmid = {35418670}, issn = {1365-2540}, support = {1601645//NSF | BIO | Division of Environmental Biology (DEB)/ ; Lewis and Clark Fund//American Philosophical Society (APS)/ ; Lerner Gray Fund//American Museum of Natural History (AMNH)/ ; Trautman Fund//Ohio State University (OSU)/ ; }, mesh = {Animals ; Genome/genetics ; Genomics/methods ; Humans ; *Metagenomics/methods ; Phylogeny ; *Sea Anemones/genetics ; Sequence Analysis, DNA ; }, abstract = {Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.}, }
@article {pmid35398946, year = {2022}, author = {Rolshausen, G and Dal Grande, F and Otte, J and Schmitt, I}, title = {Lichen holobionts show compositional structure along elevation.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.16471}, pmid = {35398946}, issn = {1365-294X}, abstract = {Holobionts are dynamic ecosystems that may respond to abiotic drivers with compositional changes. Uncovering elevational diversity patterns within these microecosystems can further our understanding of community-environment interactions. Here, we assess how the major components of lichen holobionts-fungal hosts, green algal symbionts, and the bacterial community-collectively respond to an elevational gradient. We analyse populations of two lichen symbioses, Umbilicaria pustulata and U. hispanica, along an elevational gradient spanning 2100 altitudinal metres and covering three major biomes. Our study shows (i) discontinuous genomic variation in fungal hosts with one abrupt genomic differentiation within each of the two host species, (ii) altitudinally structured bacterial communities with pronounced turnover within and between hosts, and (iii) altitude-specific presence of algal symbionts. Alpha diversity of bacterial communities decreased with increasing elevation. A marked turnover in holobiont diversity occurred across two altitudinal belts: at 11°C-13°C average annual temperature (here: 800-1200 m a.s.l.), and at 7°C-9°C average annual temperature (here: 1500-1800 m a.s.l.). The two observed zones mark a clustering of distribution limits and community shifts. The three ensuing altitudinal classes, that is, the most frequent combinations of species in holobionts, approximately correspond to the Mediterranean, cool-temperate, and alpine climate zones. We conclude that multitrophic microecosystems, such as lichen holobionts, respond with concerted compositional changes to climatic factors that also structure communities of macroorganisms, for example, vascular plants.}, }
@article {pmid35397610, year = {2022}, author = {Strehlow, BW and Schuster, A and Francis, WR and Canfield, DE}, title = {Metagenomic data for Halichondria panicea from Illumina and nanopore sequencing and preliminary genome assemblies for the sponge and two microbial symbionts.}, journal = {BMC research notes}, volume = {15}, number = {1}, pages = {135}, pmid = {35397610}, issn = {1756-0500}, support = {16518//Villum Fonden/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; *Microbiota ; *Nanopore Sequencing ; *Porifera/genetics ; Sequence Analysis, DNA ; }, abstract = {OBJECTIVES: These data were collected to generate a novel reference metagenome for the sponge Halichondria panicea and its microbiome for subsequent differential expression analyses.<br><br>DATA DESCRIPTION: These data include raw sequences from four separate sequencing runs of the metagenome of a single individual of Halichondria panicea-one Illumina MiSeq (2 × 300 bp, paired-end) run and three Oxford Nanopore Technologies (ONT) long-read sequencing runs, generating 53.8 and 7.42 Gbp respectively. Comparing assemblies of Illumina, ONT and an Illumina-ONT hybrid revealed the hybrid to be the 'best' assembly, comprising 163 Mbp in 63,555 scaffolds (N50: 3084). This assembly, however, was still highly fragmented and only contained 52% of core metazoan genes (with 77.9% partial genes), so it was also not complete. However, this sponge is an emerging model species for field and laboratory work, and there is considerable interest in genomic sequencing of this species. Although the resultant assemblies from the data presented here are suboptimal, this data note can inform future studies by providing an estimated genome size and coverage requirements for future sequencing, sharing additional data to potentially improve other suboptimal assemblies of this species, and outlining potential limitations and pitfalls of the combined Illumina and ONT approach to novel genome sequencing.}, }
@article {pmid35393600, year = {2022}, author = {Sabrina Pankey, M and Plachetzki, DC and Macartney, KJ and Gastaldi, M and Slattery, M and Gochfeld, DJ and Lesser, MP}, title = {Cophylogeny and convergence shape holobiont evolution in sponge-microbe symbioses.}, journal = {Nature ecology &amp; evolution}, volume = {}, number = {}, pages = {}, pmid = {35393600}, issn = {2397-334X}, support = {OCE-1638296//NSF | GEO | Division of Ocean Sciences (OCE)/ ; OCE-1638289//NSF | GEO | Division of Ocean Sciences (OCE)/ ; }, abstract = {Symbiotic microbial communities of sponges serve critical functions that have shaped the evolution of reef ecosystems since their origins. Symbiont abundance varies tremendously among sponges, with many species classified as either low microbial abundance (LMA) or high microbial abundance (HMA), but the evolutionary dynamics of these symbiotic states remain unknown. This study examines the LMA/HMA dichotomy across an exhaustive sampling of Caribbean sponge biodiversity and predicts that the LMA symbiotic state is the ancestral state among sponges. Conversely, HMA symbioses, consisting of more specialized microorganisms, have evolved multiple times by recruiting similar assemblages, mostly since the rise of scleractinian-dominated reefs. Additionally, HMA symbioses show stronger signals of phylosymbiosis and cophylogeny, consistent with stronger co-evolutionary interaction in these complex holobionts. These results indicate that HMA holobionts are characterized by increased endemism, metabolic dependence and chemical defences. The selective forces driving these patterns may include the concurrent increase in dissolved organic matter in reef ecosystems or the diversification of spongivorous fishes.}, }
@article {pmid35365219, year = {2022}, author = {Marasco, R and Fusi, M and Mosqueira, M and Booth, JM and Rossi, F and Cardinale, M and Michoud, G and Rolli, E and Mugnai, G and Vergani, L and Borin, S and De Philippis, R and Cherif, A and Daffonchio, D}, title = {Rhizosheath-root system changes exopolysaccharide content but stabilizes bacterial community across contrasting seasons in a desert environment.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {14}, pmid = {35365219}, issn = {2524-6372}, support = {CSA-SA REGPOT-2008-2//seventh framework programme/ ; Baseline research funds//king abdullah university of science and technology/ ; 841317//horizon 2020 framework programme/ ; 841317//horizon 2020 framework programme/ ; }, abstract = {BACKGROUND: In hot deserts daily/seasonal fluctuations pose great challenges to the resident organisms. However, these extreme ecosystems host unique microenvironments, such as the rhizosheath-root system of desert speargrasses in which biological activities and interactions are facilitated by milder conditions and reduced fluctuations. Here, we examined the bacterial microbiota associated with this structure and its surrounding sand in the desert speargrass Stipagrostis pungens under the contrasting environmental conditions of summer and winter in the Sahara Desert.<br><br>RESULTS: The belowground rhizosheath-root system has higher nutrient and humidity contents, and cooler temperatures than the surrounding sand. The plant responds to the harsh environmental conditions of the summer by increasing the abundance and diversity of extracellular polymeric substances (EPS) compared to the winter. On the contrary, the bacterial community associated with the rhizosheath-root system and its interactome remain stable and, unlike the bulk sand, are unaffected by the seasonal environmental variations. The rhizosheath-root system bacterial communities are consistently dominated by Actinobacteria and Alphaproteobacteria and form distinct bacteria communities from those of bulk sand in the two seasons. The microbiome-stabilization mediated by the plant host acts to consistently retain beneficial bacteria with multiple plant growth promoting functions, including those capable to produce EPS, which increase the sand water holding capacity ameliorating the rhizosheath micro-environment.<br><br>CONCLUSIONS: Our results reveal the capability of plants in desert ecosystems to stabilize their below ground microbial community under seasonal contrasting environmental conditions, minimizing the heterogeneity of the surrounding bulk sand and contributing to the overall holobiont resilience under poly-extreme conditions.}, }
@article {pmid35342582, year = {2022}, author = {Herrán, N and Narayan, GR and Doo, SS and Klicpera, A and Freiwald, A and Westphal, H}, title = {High-resolution imaging sheds new light on a multi-tier symbiotic partnership between a "walking" solitary coral, a sipunculan, and a bivalve from East Africa.}, journal = {Ecology and evolution}, volume = {12}, number = {3}, pages = {e8633}, pmid = {35342582}, issn = {2045-7758}, abstract = {Marine symbioses are integral to the persistence of ecosystem functioning in coral reefs. Solitary corals of the species Heteropsammia cochlea and Heterocyathus aequicostatus have been observed to live in symbiosis with the sipunculan worm Aspidosiphon muelleri muelleri, which inhabits a cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these photosymbiotic corals enables the coral holobiont to move, in fine to coarse unconsolidated substrata, a process termed as "walking." This allows the coral to escape sediment cover in turbid conditions which is crucial for these light-dependent species. An additional commensalistic symbiosis of this coral-worm holobiont is found between the Aspidosiphon worm and the cryptoendolithic bivalve Jousseaumiella sp., which resides within the cavity of the coral skeleton. To understand the morphological alterations caused by these symbioses, interspecific relationships, with respect to the carbonate structures between these three organisms, are documented using high-resolution imaging techniques (scanning electron microscopy and µCT scanning). Documenting multi-layered symbioses can shed light on how morphological plasticity interacts with environmental conditions to contribute to species persistence.}, }
@article {pmid35341677, year = {2022}, author = {Tandon, K and Pasella, MM and Iha, C and Ricci, F and Hu, J and O'Kelly, CJ and Medina, M and Kühl, M and Verbruggen, H}, title = {Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business.}, journal = {Seminars in cell &amp; developmental biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcdb.2022.03.010}, pmid = {35341677}, issn = {1096-3634}, abstract = {Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.}, }
@article {pmid35336242, year = {2022}, author = {Ratiner, K and Abdeen, SK and Goldenberg, K and Elinav, E}, title = {Utilization of Host and Microbiome Features in Determination of Biological Aging.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336242}, issn = {2076-2607}, abstract = {The term 'old age' generally refers to a period characterized by profound changes in human physiological functions and susceptibility to disease that accompanies the final years of a person's life. Despite the conventional definition of old age as exceeding the age of 65 years old, quantifying aging as a function of life years does not necessarily reflect how the human body ages. In contrast, characterizing biological (or physiological) aging based on functional parameters may better reflect a person's temporal physiological status and associated disease susceptibility state. As such, differentiating 'chronological aging' from 'biological aging' holds the key to identifying individuals featuring accelerated aging processes despite having a young chronological age and stratifying them to tailored surveillance, diagnosis, prevention, and treatment. Emerging evidence suggests that the gut microbiome changes along with physiological aging and may play a pivotal role in a variety of age-related diseases, in a manner that does not necessarily correlate with chronological age. Harnessing of individualized gut microbiome data and integration of host and microbiome parameters using artificial intelligence and machine learning pipelines may enable us to more accurately define aging clocks. Such holobiont-based estimates of a person's physiological age may facilitate prediction of age-related physiological status and risk of development of age-associated diseases.}, }
@article {pmid35336184, year = {2022}, author = {Ducousso-Détrez, A and Fontaine, J and Lounès-Hadj Sahraoui, A and Hijri, M}, title = {Diversity of Phosphate Chemical Forms in Soils and Their Contributions on Soil Microbial Community Structure Changes.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336184}, issn = {2076-2607}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council/ ; Support for the A.D-D. Ph.D. thesis//Région des Hauts de France/ ; }, abstract = {In many soils, the bioavailability of Phosphorus (P), an essential macronutrient is a limiting factor for crop production. Among the mechanisms developed to facilitate the absorption of phosphorus, the plant, as a holobiont, can rely on its rhizospheric microbial partners. Therefore, microbial P-solubilizing inoculants are proposed to improve soil P fertility in agriculture. However, a better understanding of the interactions of the soil-plant-microorganism continuum with the phosphorus cycle is needed to propose efficient inoculants. Before proposing further methods of research, we carried out a critical review of the literature in two parts. First, we focused on the diversity of P-chemical forms. After a review of P forms in soils, we describe multiple factors that shape these forms in soil and their turnover. Second, we provide an analysis of P as a driver of microbial community diversity in soil. Even if no rule enabling to explain the changes in the composition of microbial communities according to phosphorus has been shown, this element has been perfectly targeted as linked to the presence/absence and/or abundance of particular bacterial taxa. In conclusion, we point out the need to link soil phosphorus chemistry with soil microbiology in order to understand the variations in the composition of microbial communities as a function of P bioavailability. This knowledge will make it possible to propose advanced microbial-based inoculant engineering for the improvement of bioavailable P for plants in sustainable agriculture.}, }
@article {pmid35336179, year = {2022}, author = {Zommiti, M and Chevalier, S and Feuilloley, MGJ and Connil, N}, title = {Special Issue "Enterococci for Probiotic Use: Safety and Risk": Editorial.}, journal = {Microorganisms}, volume = {10}, number = {3}, pages = {}, pmid = {35336179}, issn = {2076-2607}, abstract = {Microorganisms, their activity, and metabolites are now considered as intrinsic elements of the human body and this awareness gave was leading to the concept of holobiont [...].}, }
@article {pmid35310651, year = {2022}, author = {Chen, P and He, W and Shen, Y and Zhu, L and Yao, X and Sun, R and Dai, C and Sun, B and Chen, Y}, title = {Interspecific Neighbor Stimulates Peanut Growth Through Modulating Root Endophytic Microbial Community Construction.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {830666}, pmid = {35310651}, issn = {1664-462X}, abstract = {Plants have evolved the capability to respond to interspecific neighbors by changing morphological performance and reshaping belowground microbiota. However, whether neighboring plants influence the microbial colonization of the host's root and further affect host performance is less understood. In this study, using 16S rRNA high-throughput sequencing of peanut (Arachis hypogaea L.) roots from over 5 years of mono- and intercropping field systems, we found that neighbor maize can alter the peanut root microbial composition and re-shape microbial community assembly. Interspecific maize coexistence increased the colonization of genera Bradyrhizobium and Streptomyces in intercropped peanut roots. Through endophytic bacterial isolation and isolate back inoculation experiments, we demonstrated that the functional potentials of available nutrient accumulation and phytohormones production from Bradyrhizobium and Streptomyces endowed them with the ability to act as keystones in the microbial network to benefit peanut growth and production with neighbor competition. Our results support the idea that plants establish a plant-endophytic microbial holobiont through root selective filtration to enhance host competitive dominance, and provide a promising direction to develop modern diversified planting for harnessing crop microbiomes for the promotion of crop growth and productivity in sustainable agriculture.}, }
@article {pmid35308397, year = {2022}, author = {Taubenheim, J and Miklós, M and Tökölyi, J and Fraune, S}, title = {Population Differences and Host Species Predict Variation in the Diversity of Host-Associated Microbes in Hydra.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {799333}, pmid = {35308397}, issn = {1664-302X}, abstract = {Most animals co-exist with diverse host-associated microbial organisms that often form complex communities varying between individuals, habitats, species and higher taxonomic levels. Factors driving variation in the diversity of host-associated microbes are complex and still poorly understood. Here, we describe the bacterial composition of field-collected Hydra, a freshwater cnidarian that forms stable associations with microbial species in the laboratory and displays complex interactions with components of the microbiota. We sampled Hydra polyps from 21 Central European water bodies and identified bacterial taxa through 16S rRNA sequencing. We asked whether diversity and taxonomic composition of host-associated bacteria depends on sampling location, habitat type, host species or host reproductive mode (sexual vs. asexual). Bacterial diversity was most strongly explained by sampling location, suggesting that the source environment plays an important role in the assembly of bacterial communities associated with Hydra polyps. We also found significant differences between host species in their bacterial composition that partly mirrored variations observed in lab strains. Furthermore, we detected a minor effect of host reproductive mode on bacterial diversity. Overall, our results suggest that extrinsic (habitat identity) factors predict the diversity of host-associated bacterial communities more strongly than intrinsic (species identity) factors, however, only a combination of both factors determines microbiota composition in Hydra.}, }
@article {pmid35303955, year = {2022}, author = {Cambon-Bonavita, MA and Aubé, J and Cueff-Gauchard, V and Reveillaud, J}, title = {Correction to: Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {51}, pmid = {35303955}, issn = {2049-2618}, }
@article {pmid35299055, year = {2022}, author = {Burgunter-Delamare, B and Tanguy, G and Legeay, E and Boyen, C and Dittami, SM}, title = {Effects of sampling and storage procedures on 16S rDNA amplicon sequencing results of kelp microbiomes.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100944}, doi = {10.1016/j.margen.2022.100944}, pmid = {35299055}, issn = {1876-7478}, mesh = {DNA, Ribosomal ; *Kelp/genetics ; *Microbiota ; Nitrogen ; RNA ; RNA, Ribosomal, 16S/genetics ; *Seaweed ; Silica Gel ; }, abstract = {Brown macroalgae, including the kelp Saccharina latissima, are of both ecological and increasing economic interest. Together with their microbiota, these organisms form a singular entity, the holobiont. Sampling campaigns are required to study the microbiome of algae in natural populations, but freezing samples in liquid nitrogen is complex in the field, particularly at remote locations. Here we tested two simple alternative methods for sampling the microbial diversity associated with the kelp S. latissima: silica gel conservation of tissue and swab samples preserved in DNA/RNA shield solution. We used these techniques to compare apex and meristem samples from Roscoff (Brittany, France) and evaluated their impact on the results of 16S rDNA metabarcoding experiments. Both methods were able to separate apex and meristem microbiomes, and the results were concordant with results obtained for flash-frozen samples. However, differences were observed for several rare genera and ASVs, and the detection of contaminant sequences in the silica gel-preserved samples underline the importance of including blank samples for this method. Globally, our results confirm that the silica gel technique and swabbing combined with DNA/RNA shield preservation are valid alternatives to liquid nitrogen preservation when sampling brown macroalgae in the field. However, they also underline that, regardless of the method, caution should be taken when interpreting data on rare sequences.}, }
@article {pmid35276225, year = {2022}, author = {Detmer, AR and Cunning, R and Pfab, F and Brown, AL and Stier, AC and Nisbet, RM and Moeller, HV}, title = {Fertilization by coral-dwelling fish promotes coral growth but can exacerbate bleaching response.}, journal = {Journal of theoretical biology}, volume = {541}, number = {}, pages = {111087}, doi = {10.1016/j.jtbi.2022.111087}, pmid = {35276225}, issn = {1095-8541}, mesh = {Animals ; *Anthozoa ; Carbon ; Coral Reefs ; Fertilization ; Fishes ; Nitrogen ; Symbiosis/physiology ; }, abstract = {Many corals form close associations with a diverse assortment of coral-dwelling fishes and other fauna. As coral reefs around the world are increasingly threatened by mass bleaching events, it is important to understand how these biotic interactions influence corals' susceptibility to bleaching. We used dynamic energy budget modeling to explore how nitrogen excreted by coral-dwelling fish affects the physiological performance of host corals. In our model, fish presence influenced the functioning of the coral-Symbiodiniaceae symbiosis by altering nitrogen availability, and the magnitude and sign of these effects depended on environmental conditions. Although our model predicted that fish-derived nitrogen can promote coral growth, the relationship between fish presence and coral tolerance of photo-oxidative stress was non-linear. Fish excretions supported denser symbiont populations that provided protection from incident light through self-shading. However, these symbionts also used more of their photosynthetic products for their own growth, rather than sharing with the coral host, putting the coral holobiont at a higher risk of becoming carbon-limited and bleaching. The balance between the benefits of increased symbiont shading and costs of reduced carbon sharing depended on environmental conditions. Thus, while there were some scenarios under which fish presence increased corals' tolerance of light stress, fish could also exacerbate bleaching and slow or prevent subsequent recovery. We discuss how the contrast between the potentially harmful effects of fish predicted by our model and results of empirical studies may relate to key model assumptions that warrant further investigation. Overall, this study provides a foundation for future work on how coral-associated fauna influence the bioenergetics of their host corals, which in turn has implications for how these corals respond to bleaching-inducing stressors.}, }
@article {pmid35273199, year = {2022}, author = {McLachlan, RH and Price, JT and Muñoz-Garcia, A and Weisleder, NL and Levas, SJ and Jury, CP and Toonen, RJ and Grottoli, AG}, title = {Physiological acclimatization in Hawaiian corals following a 22-month shift in baseline seawater temperature and pH.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {3712}, pmid = {35273199}, issn = {2045-2322}, mesh = {Acclimatization ; Animals ; *Anthozoa/physiology ; Coral Reefs ; Ecosystem ; Hawaii ; Hydrogen-Ion Concentration ; Lipids ; Seawater ; Temperature ; }, abstract = {Climate change poses a major threat to coral reefs. We conducted an outdoor 22-month experiment to investigate if coral could not just survive, but also physiologically cope, with chronic ocean warming and acidification conditions expected later this century under the Paris Climate Agreement. We recorded survivorship and measured eleven phenotypic traits to evaluate the holobiont responses of Hawaiian coral: color, Symbiodiniaceae density, calcification, photosynthesis, respiration, total organic carbon flux, carbon budget, biomass, lipids, protein, and maximum Artemia capture rate. Survivorship was lowest in Montipora capitata and only some survivors were able to meet metabolic demand and physiologically cope with future ocean conditions. Most M. capitata survivors bleached through loss of chlorophyll pigments and simultaneously experienced increased respiration rates and negative carbon budgets due to a 236% increase in total organic carbon losses under combined future ocean conditions. Porites compressa and Porites lobata had the highest survivorship and coped well under future ocean conditions with positive calcification and increased biomass, maintenance of lipids, and the capacity to exceed their metabolic demand through photosynthesis and heterotrophy. Thus, our findings show that significant biological diversity within resilient corals like Porites, and some genotypes of sensitive species, will persist this century provided atmospheric carbon dioxide levels are controlled. Since Porites corals are ubiquitous throughout the world's oceans and often major reef builders, the persistence of this resilient genus provides hope for future reef ecosystem function globally.}, }
@article {pmid35269523, year = {2022}, author = {Kriaa, A and Mariaule, V and Jablaoui, A and Rhimi, S and Mkaouar, H and Hernandez, J and Korkmaz, B and Lesner, A and Maguin, E and Aghdassi, A and Rhimi, M}, title = {Bile Acids: Key Players in Inflammatory Bowel Diseases?.}, journal = {Cells}, volume = {11}, number = {5}, pages = {}, pmid = {35269523}, issn = {2073-4409}, support = {MICA department//National Research Institute for Agriculture, Food and Environment/ ; Animal microbiota analysis project//Oniris/ ; MICAfrica//European Commission/ ; }, mesh = {Bile Acids and Salts ; *Gastrointestinal Microbiome ; Homeostasis ; Humans ; Inflammation ; *Inflammatory Bowel Diseases ; }, abstract = {Inflammatory bowel diseases (IBDs) have emerged as a public health problem worldwide with a limited number of efficient therapeutic options despite advances in medical therapy. Although changes in the gut microbiota composition are recognized as key drivers of dysregulated intestinal immunity, alterations in bile acids (BAs) have been shown to influence gut homeostasis and contribute to the pathogenesis of the disease. In this review, we explore the interactions involving BAs and gut microbiota in IBDs, and discuss how the gut microbiota-BA-host axis may influence digestive inflammation.}, }
@article {pmid35261041, year = {2022}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Paus, R and Bosch, TCG}, title = {Hydra and the hair follicle - An unconventional comparative biology approach to exploring the human holobiont.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {44}, number = {5}, pages = {e2100233}, doi = {10.1002/bies.202100233}, pmid = {35261041}, issn = {1521-1878}, support = {//Monasterium Laboratory GmbH/ ; //Deutsche Forschungsgemeinschaft/ ; //Canadian Institute for Advanced Research/ ; //Giuliani Spa/ ; }, mesh = {Animals ; Biology ; Hair Follicle ; Humans ; *Hydra/physiology ; Microbial Interactions ; *Microbiota/physiology ; }, abstract = {The microbiome of human hair follicles (HFs) has emerged as an important player in different HF and skin pathologies, yet awaits in-depth exploration. This raises questions regarding the tightly linked interactions between host environment, nutrient dependency of host-associated microbes, microbial metabolism, microbe-microbe interactions and host immunity. The use of simple model systems facilitates addressing generally important questions and testing overarching, therapeutically relevant principles that likely transcend obvious interspecies differences. Here, we evaluate the potential of the freshwater polyp Hydra, to dissect fundamental principles of microbiome regulation by the host, that is the human HF. In particular, we focus on therapeutically targetable host-microbiome interactions, such as nutrient dependency, microbial interactions and host defence. Offering a new lens into the study of HF - microbiota interactions, we argue that general principles of how Hydra manages its microbiota can inform the development of novel, microbiome-targeting therapeutic interventions in human skin disease.}, }
@article {pmid35253476, year = {2022}, author = {Ricci, F and Tandon, K and Black, JR and Lê Cao, KA and Blackall, LL and Verbruggen, H}, title = {Host Traits and Phylogeny Contribute to Shaping Coral-Bacterial Symbioses.}, journal = {mSystems}, volume = {7}, number = {2}, pages = {e0004422}, pmid = {35253476}, issn = {2379-5077}, support = {DP200101613//Australian Research Council/ ; GNT1159458//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, abstract = {The success of tropical scleractinian corals depends on their ability to establish symbioses with microbial partners. Host phylogeny and traits are known to shape the coral microbiome, but to what extent they affect its composition remains unclear. Here, by using 12 coral species representing the complex and robust clades, we explored the influence of host phylogeny, skeletal architecture, and reproductive mode on the microbiome composition, and further investigated the structure of the tissue and skeleton bacterial communities. Our results show that host phylogeny and traits explained 14% of the tissue and 13% of the skeletal microbiome composition, providing evidence that these predictors contributed to shaping the holobiont in terms of presence and relative abundance of bacterial symbionts. Based on our data, we conclude that host phylogeny affects the presence of specific microbial lineages, reproductive mode predictably influences the microbiome composition, and skeletal architecture works like a filter that affects bacterial relative abundance. We show that the β-diversity of coral tissue and skeleton microbiomes differed, but we found that a large overlapping fraction of bacterial sequences were recovered from both anatomical compartments, supporting the hypothesis that the skeleton can function as a microbial reservoir. Additionally, our analysis of the microbiome structure shows that 99.6% of tissue and 99.7% of skeletal amplicon sequence variants (ASVs) were not consistently present in at least 30% of the samples, suggesting that the coral tissue and skeleton are dominated by rare bacteria. Together, these results provide novel insights into the processes driving coral-bacterial symbioses, along with an improved understanding of the scleractinian microbiome.}, }
@article {pmid35242117, year = {2022}, author = {Gómez-Lama Cabanás, C and Wentzien, NM and Zorrilla-Fontanesi, Y and Valverde-Corredor, A and Fernández-González, AJ and Fernández-López, M and Mercado-Blanco, J}, title = {Impacts of the Biocontrol Strain Pseudomonas simiae PICF7 on the Banana Holobiont: Alteration of Root Microbial Co-occurrence Networks and Effect on Host Defense Responses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {809126}, pmid = {35242117}, issn = {1664-302X}, abstract = {The impact of the versatile biocontrol and plant-growth-promoting rhizobacteria Pseudomonas simiae PICF7 on the banana holobiont under controlled conditions was investigated. We examine the fate of this biological control agent (BCA) upon introduction in the soil, the effect on the banana root microbiota, and the influence on specific host genetic defense responses. While the presence of strain PICF7 significantly altered neither the composition nor the structure of the root microbiota, a significant shift in microbial community interactions through co-occurrence network analysis was observed. Despite the fact that PICF7 did not constitute a keystone, the topology of this network was significantly modified-the BCA being identified as a constituent of one of the main network modules in bacterized plants. Gene expression analysis showed the early suppression of several systemic acquired resistance and induced systemic resistance (ISR) markers. This outcome occurred at the time in which the highest relative abundance of PICF7 was detected. The absence of major and permanent changes on the banana holobiont upon PICF7 introduction poses advantages regarding the use of this beneficial rhizobacteria under field conditions. Indeed a BCA able to control the target pathogen while altering as little as possible the natural host-associated microbiome should be a requisite when developing effective bio-inoculants.}, }
@article {pmid35237241, year = {2021}, author = {Li, J and Wei, X and Huang, D and Xiao, J}, title = {The Phylosymbiosis Pattern Between the Fig Wasps of the Same Genus and Their Associated Microbiota.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {800190}, pmid = {35237241}, issn = {1664-302X}, abstract = {Microbial communities can be critical for many metazoans, which can lead to the observation of phylosymbiosis with phylogenetically related species sharing similar microbial communities. Most of the previous studies on phylosymbiosis were conducted across the host families or genera. However, it is unclear whether the phylosymbiosis signal is still prevalent at lower taxonomic levels. In this study, 54 individuals from six species of the fig wasp genus Ceratosolen (Hymenoptera: Agaonidae) collected from nine natural populations and their associated microbiota were investigated. The fig wasp species were morphologically identified and further determined by mitochondrial CO1 gene fragments and nuclear ITS2 sequences, and the V4 region of 16S rRNA gene was sequenced to analyze the bacterial communities. The results suggest a significant positive correlation between host genetic characteristics and microbial diversity characteristics, indicating the phylosymbiosis signal between the phylogeny of insect hosts and the associated microbiota in the lower classification level within a genus. Moreover, we found that the endosymbiotic Wolbachia carried by fig wasps led to a decrease in bacterial diversity of host-associated microbial communities. This study contributes to our understanding of the role of host phylogeny, as well as the role of endosymbionts in shaping the host-associated microbial community.}, }
@article {pmid35229422, year = {2022}, author = {Taylor, JA and Díez-Vives, C and Nielsen, S and Wemheuer, B and Thomas, T}, title = {Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15962}, pmid = {35229422}, issn = {1462-2920}, support = {//Bioplatforms Australia/ ; //Integrated Marine Observing System/ ; }, abstract = {The diversity and function of sponge-associated symbionts is now increasingly understood; however, we lack an understanding of how they dynamically behave to ensure holobiont stability in the face of environmental variation. Here, we performed a metatransciptomic analysis on three microbial symbionts of the sponge Cymbastela concentrica in situ over 14 months and through differential gene expression and correlation analysis to environmental variables uncovered differences that speak to their metabolic activities and level of symbiotic and environmental interactions. The nitrite-oxidizing Ca. Porinitrospira cymbastela maintained a seemingly stable metabolism, with the few differentially expressed genes related only to stress responses. The heterotrophic Ca. Porivivens multivorans displayed differential use of holobiont-derived compounds and respiration modes, while the ammonium-oxidizing archaeon Ca. Nitrosopumilus cymbastelus differentially expressed genes related to phosphate metabolism and symbiosis effectors. One striking similarity between the symbionts was their similar variation in expression of stress-related genes. Our time-series study showed that the microbial community of C. concentrica undertakes dynamic gene expression adjustments in response to the surroundings, tuned to deal with general stress and metabolic interactions between holobiont members. The success of these dynamic adjustments likely underpins the stability of the sponge holobiont and may provide resilience against environmental change.}, }
@article {pmid35222085, year = {2022}, author = {Cotinat, P and Fricano, C and Toullec, G and Röttinger, E and Barnay-Verdier, S and Furla, P}, title = {Intrinsically High Capacity of Animal Cells From a Symbiotic Cnidarian to Deal With Pro-Oxidative Conditions.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {819111}, pmid = {35222085}, issn = {1664-042X}, abstract = {The cnidarian-dinoflagellate symbiosis is a mutualistic intracellular association based on the photosynthetic activity of the endosymbiont. This relationship involves significant constraints and requires co-evolution processes, such as an extensive capacity of the holobiont to counteract pro-oxidative conditions induced by hyperoxia generated during photosynthesis. In this study, we analyzed the capacity of Anemonia viridis cells to deal with pro-oxidative conditions by in vivo and in vitro approaches. Whole specimens and animal primary cell cultures were submitted to 200 and 500 μM of H2O2 during 7 days. Then, we monitored global health parameters (symbiotic state, viability, and cell growth) and stress biomarkers (global antioxidant capacity, oxidative protein damages, and protein ubiquitination). In animal primary cell cultures, the intracellular reactive oxygen species (ROS) levels were also evaluated under H2O2 treatments. At the whole organism scale, both H2O2 concentrations didn't affect the survival and animal tissues exhibited a high resistance to H2O2 treatments. Moreover, no bleaching has been observed, even at high H2O2 concentration and after long exposure (7 days). Although, the community has suggested the role of ROS as the cause of bleaching, our results indicating the absence of bleaching under high H2O2 concentration may exculpate this specific ROS from being involved in the molecular processes inducing bleaching. However, counterintuitively, the symbiont compartment appeared sensitive to an H2O2 burst as it displayed oxidative protein damages, despite an enhancement of antioxidant capacity. The in vitro assays allowed highlighting an intrinsic high capacity of isolated animal cells to deal with pro-oxidative conditions, although we observed differences on tolerance between H2O2 treatments. The 200 μM H2O2 concentration appeared to correspond to the tolerance threshold of animal cells. Indeed, no disequilibrium on redox state was observed and only a cell growth decrease was measured. Contrarily, the 500 μM H2O2 concentration induced a stress state, characterized by a cell viability decrease from 1 day and a drastic cell growth arrest after 7 days leading to an uncomplete recovery after treatment. In conclusion, this study highlights the overall high capacity of cnidarian cells to cope with H2O2 and opens new perspective to investigate the molecular mechanisms involved in this peculiar resistance.}, }
@article {pmid35218086, year = {2022}, author = {Rosenberg, Y and Simon-Blecher, N and Lalzar, M and Yam, R and Shemesh, A and Alon, S and Perna, G and Cárdenas, A and Voolstra, CR and Miller, DJ and Levy, O}, title = {Urbanization comprehensively impairs biological rhythms in coral holobionts.}, journal = {Global change biology}, volume = {28}, number = {10}, pages = {3349-3364}, doi = {10.1111/gcb.16144}, pmid = {35218086}, issn = {1365-2486}, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Microbiota ; Periodicity ; Urbanization ; }, abstract = {Coral reefs are in global decline due to climate change and anthropogenic influences (Hughes et al., Conservation Biology, 27: 261-269, 2013). Near coastal cities or other densely populated areas, coral reefs face a range of additional challenges. While considerable progress has been made in understanding coral responses to acute individual stressors (Dominoni et al., Nature Ecology &amp; Evolution, 4: 502-511, 2020), the impacts of chronic exposure to varying combinations of sensory pollutants are largely unknown. To investigate the impacts of urban proximity on corals, we conducted a year-long in-natura study-incorporating sampling at diel, monthly, and seasonal time points-in which we compared corals from an urban area to corals from a proximal non-urban area. Here we reveal that despite appearing relatively healthy, natural biorhythms and environmental sensory systems were extensively disturbed in corals from the urban environment. Transcriptomic data indicated poor symbiont performance, disturbance to gametogenic cycles, and loss or shifted seasonality of vital biological processes. Altered seasonality patterns were also observed in the microbiomes of the urban coral population, signifying the impact of urbanization on the holobiont, rather than the coral host alone. These results should raise alarm regarding the largely unknown long-term impacts of sensory pollution on the resilience and survival of coral reefs close to coastal communities.}, }
@article {pmid35208935, year = {2022}, author = {Butina, TV and Petrushin, IS and Khanaev, IV and Bukin, YS}, title = {Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208935}, issn = {2076-2607}, support = {17-44-388080//Russian Foundation for Basic Research/ ; }, abstract = {Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.}, }
@article {pmid35208684, year = {2022}, author = {Dietert, RR and Dietert, JM}, title = {Using Microbiome-Based Approaches to Deprogram Chronic Disorders and Extend the Healthspan following Adverse Childhood Experiences.}, journal = {Microorganisms}, volume = {10}, number = {2}, pages = {}, pmid = {35208684}, issn = {2076-2607}, abstract = {Adverse childhood experiences (ACEs), which can include child trafficking, are known to program children for disrupted biological cycles, premature aging, microbiome dysbiosis, immune-inflammatory misregulation, and chronic disease multimorbidity. To date, the microbiome has not been a major focus of deprogramming efforts despite its emerging role in every aspect of ACE-related dysbiosis and dysfunction. This article examines: (1) the utility of incorporating microorganism-based, anti-aging approaches to combat ACE-programmed chronic diseases (also known as noncommunicable diseases and conditions, NCDs) and (2) microbiome regulation of core systems biology cycles that affect NCD comorbid risk. In this review, microbiota influence over three key cyclic rhythms (circadian cycles, the sleep cycle, and the lifespan/longevity cycle) as well as tissue inflammation and oxidative stress are discussed as an opportunity to deprogram ACE-driven chronic disorders. Microbiota, particularly those in the gut, have been shown to affect host-microbe interactions regulating the circadian clock, sleep quality, as well as immune function/senescence, and regulation of tissue inflammation. The microimmunosome is one of several systems biology targets of gut microbiota regulation. Furthermore, correcting misregulated inflammation and increased oxidative stress is key to protecting telomere length and lifespan/longevity and extending what has become known as the healthspan. This review article concludes that to reverse the tragedy of ACE-programmed NCDs and premature aging, managing the human holobiont microbiome should become a routine part of healthcare and preventative medicine across the life course.}, }
@article {pmid35202673, year = {2022}, author = {Tougeron, K}, title = {Homeostasis theory: What can we learn from dormancy and symbiotic associations?.}, journal = {Physiology &amp; behavior}, volume = {249}, number = {}, pages = {113749}, doi = {10.1016/j.physbeh.2022.113749}, pmid = {35202673}, issn = {1873-507X}, mesh = {Animals ; *Diapause/physiology ; Homeostasis ; *Symbiosis ; }, abstract = {In this letter, I discuss the notion of dormancy that De Luca Jr. relies on to criticize the theory of homeostasis. In particular, I try to qualify the issues related to the fact that dormancy is not always a free behavior but is in most situations under the influence of environmental factors. To this end, I discuss diapause in arthropods, which can be obligatory (under the influence of endogenous commands) but which is in most cases facultative (under external command). I emphasize that the notion of stability of a dormant organism must be taken with caution. I briefly mention what the study of sleep in animals can contribute to the notion of homeostasis. Finally, I focus on the role of microbial symbionts and the notion of holobiont. Through this, I question the future of the notions of internal environment and homeostasis and I propose to revisit them in the context of the effects of species interactions on the physiology of organisms.}, }
@article {pmid35187610, year = {2022}, author = {Roggatz, CC and Hardege, JD and Saha, M}, title = {Modelling Antifouling compounds of Macroalgal Holobionts in Current and Future pH Conditions.}, journal = {Journal of chemical ecology}, volume = {48}, number = {4}, pages = {455-473}, pmid = {35187610}, issn = {1573-1561}, support = {PML Fellowship//Plymouth Marine Laboratory/ ; ERC-2016-COG GEOSTICK/ERC_/European Research Council/International ; }, mesh = {Bacteria/metabolism ; *Biofouling/prevention &amp; control ; Ecosystem ; Hydrogen-Ion Concentration ; Phylogeny ; Seawater/chemistry ; *Seaweed/microbiology ; }, abstract = {Marine macroalgae are important ecosystem engineers in marine coastal habitats. Macroalgae can be negatively impacted through excessive colonization by harmful bacteria, fungi, microalgae, and macro-colonisers and thus employ a range of chemical compounds to minimize such colonization. Recent research suggests that environmental pH conditions potentially impact the functionality of such chemical compounds. Here we predict if and how naturally fluctuating pH conditions and future conditions caused by ocean acidification will affect macroalgal (antifouling) compounds and thereby potentially alter the chemical defence mediated by these compounds. We defined the relevant ecological pH range, analysed and scored the pH-sensitivity of compounds with antifouling functions based on their modelled chemical properties before assessing their distribution across the phylogenetic macroalgal groups, and the proportion of sensitive compounds for each investigated function. For some key compounds, we also predicted in detail how the associated ecological function may develop across the pH range. The majority of compounds were unaffected by pH, but compounds containing phenolic and amine groups were found to be particularly sensitive to pH. Future pH changes due to predicted average open ocean acidification pH were found to have little effect. Compounds from Rhodophyta were mainly pH-stable. However, key algal species amongst Phaeophyceae and Chlorophyta were found to rely on highly pH-sensitive compounds for their chemical defence against harmful bacteria, microalgae, fungi, and biofouling by macro-organisms. All quorum sensing disruptive compounds were found the be unaffected by pH, but the other ecological functions were all conveyed in part by pH-sensitive compounds. For some ecological keystone species, all of their compounds mediating defence functions were found to be pH-sensitive based on our calculations, which may not only affect the health and fitness of the host alga resulting in host breakdown but also alter the associated ecological interactions of the macroalgal holobiont with micro and macrocolonisers, eventually causing ecosystem restructuring and the functions (e.g. habitat provision) provided by macroalgal hosts. Our study investigates a question of fundamental importance because environments with fluctuating or changing pH are common and apply not only to coastal marine habitats and estuaries but also to freshwater environments or terrestrial systems that are subject to acid rain. Hence, whilst warranting experimental validation, this investigation with macroalgae as model organisms can serve as a basis for future investigations in other aquatic or even terrestrial systems.}, }
@article {pmid35182319, year = {2022}, author = {Ünüvar, ÖC and Zencirci, N and Ünlü, ES}, title = {Bacteria isolated from Triticum monococcum ssp. monococcum roots can improve wheat hologenome in agriculture.}, journal = {Molecular biology reports}, volume = {}, number = {}, pages = {}, pmid = {35182319}, issn = {1573-4978}, support = {2180200//TÜBİTAK (TEYDEB)/ ; }, abstract = {BACKGROUND: Triticum monococcum ssp. monococcum is an ancestral wheat species originated from Karacadağ Mountain of Turkey more than ten thousand years ago. Because of environmental and anthropogenic effects, food supply and demand are not balanced. Agricultural activities such as breeding, and fertilization are important to sustain the balance. Conventional breeding and fertilization applications usually neglect contribution of plant related hologenomes in agricultural yield. The disruption of plant growth promoting microorganisms results in intensive usage of chemical fertilizers. The harmony between plant and plant-associated microorganisms is important for sustainability. In this study, isolation, biochemical characterization, and impact on plant growth parameters of natural bacteria associated with Triticum monococcum ssp. monococcum hologenome were aimed.<br><br>METHODS AND RESULTS: The collection of root samples and isolations of the root-associated bacterial species were carried out from local wheat lands. According to interpretation of three identification methods (MALDI-TOF, 16S rDNA, 16S-23S rDNA) eight isolates are Arthrobacter spp. ESU164, Arthrobacter spp. ESU193, Pseudomonas spp. ESU131, Pseudomonas spp. ESU141, Pseudomonas poae strain ESU182, Pseudomonas thivervalensis strain ESU192, Pseudomonas spp. ESU1531, Bacillus subtilis strain ESU181. For each isolate we investigated biochemical properties especially nitrogen fixation, phosphate solubilization, and indole-3-acetic acid production abilities. The results show that all isolates are nitrogen fixers and the best phosphate solubilizer have been reported as Pseudomonas spp. ESU131 with 2.805 ± 0.439.<br><br>CONCLUSIONS: All isolates are indole-3-acetic acid productors. 2 isolates affected the coleoptile lengths, 7 bacterial isolates showed statistically positive effect on root number, and 5 isolates promote the root lengths and the root fresh weights.}, }
@article {pmid35153869, year = {2021}, author = {Martínez, M and Postolache, TT and García-Bueno, B and Leza, JC and Figuero, E and Lowry, CA and Malan-Müller, S}, title = {The Role of the Oral Microbiota Related to Periodontal Diseases in Anxiety, Mood and Trauma- and Stress-Related Disorders.}, journal = {Frontiers in psychiatry}, volume = {12}, number = {}, pages = {814177}, pmid = {35153869}, issn = {1664-0640}, abstract = {The prevalence of anxiety, mood and trauma- and stress-related disorders are on the rise; however, efforts to develop new and effective treatment strategies have had limited success. To identify novel therapeutic targets, a comprehensive understanding of the disease etiology is needed, especially in the context of the holobiont, i.e., the superorganism consisting of a human and its microbiotas. Much emphasis has been placed on the role of the gut microbiota in the development, exacerbation, and persistence of psychiatric disorders; however, data for the oral microbiota are limited. The oral cavity houses the second most diverse microbial community in the body, with over 700 bacterial species that colonize the soft and hard tissues. Periodontal diseases encompass a group of infectious and inflammatory diseases that affect the periodontium. Among them, periodontitis is defined as a chronic, multi-bacterial infection that elicits low-grade systemic inflammation via the release of pro-inflammatory cytokines, as well as local invasion and long-distance translocation of periodontal pathogens. Periodontitis can also induce or exacerbate other chronic systemic inflammatory diseases such as atherosclerosis and diabetes and can lead to adverse pregnancy outcomes. Recently, periodontal pathogens have been implicated in the etiology and pathophysiology of neuropsychiatric disorders (such as depression and schizophrenia), especially as dysregulation of the immune system also plays an integral role in the etiology and pathophysiology of these disorders. This review will discuss the role of the oral microbiota associated with periodontal diseases in anxiety, mood and trauma- and stress-related disorders. Epidemiological data of periodontal diseases in individuals with these disorders will be presented, followed by a discussion of the microbiological and immunological links between the oral microbiota and the central nervous system. Pre-clinical and clinical findings on the oral microbiota related to periodontal diseases in anxiety, mood and trauma- and stress-related phenotypes will be reviewed, followed by a discussion on the bi-directionality of the oral-brain axis. Lastly, we will focus on the oral microbiota associated with periodontal diseases as a target for future therapeutic interventions to alleviate symptoms of these debilitating psychiatric disorders.}, }
@article {pmid35147188, year = {2022}, author = {Zouache, K and Martin, E and Rahola, N and Gangue, MF and Minard, G and Dubost, A and Van, VT and Dickson, L and Ayala, D and Lambrechts, L and Moro, CV}, title = {Larval habitat determines the bacterial and fungal microbiota of the mosquito vector Aedes aegypti.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {1}, pages = {}, doi = {10.1093/femsec/fiac016}, pmid = {35147188}, issn = {1574-6941}, mesh = {*Aedes/microbiology ; Animals ; Bacteria/genetics ; Larva/microbiology ; *Microbiota ; Mosquito Vectors/microbiology ; *Mycobiome ; Plant Breeding ; }, abstract = {Mosquito larvae are naturally exposed to microbial communities present in a variety of larval development sites. Several earlier studies have highlighted that the larval habitat influences the composition of the larval bacterial microbiota. However, little information is available on their fungal microbiota, i.e. the mycobiota. In this study, we provide the first simultaneous characterization of the bacterial and fungal microbiota in field-collected Aedes aegypti larvae and their respective aquatic habitats. We evaluated whether the microbial communities associated with the breeding site may affect the composition of both the bacterial and fungal communities in Ae. aegypti larvae. Our results show a higher similarity in microbial community structure for both bacteria and fungi between larvae and the water in which larvae develop than between larvae from different breeding sites. This supports the hypothesis that larval habitat is a major factor driving microbial composition in mosquito larvae. Since the microbiota plays an important role in mosquito biology, unravelling the network of interactions that operate between bacteria and fungi is essential to better understand the functioning of the mosquito holobiont.}, }
@article {pmid35138928, year = {2022}, author = {Riva, V and Mapelli, F and Bagnasco, A and Mengoni, A and Borin, S}, title = {A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0253721}, pmid = {35138928}, issn = {1098-5336}, mesh = {*Bacteria ; Endophytes ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S ; }, abstract = {Endophytic bacteria are key members of the plant microbiome, which phylogenetic diversity has been widely described through next-generation sequencing technologies in the last decades. On the other side, a synopsis of culturable plant endophytic bacteria is still lacking in the literature. However, culturability is necessary for biotechnology innovations related to sustainable agriculture, such as biofertilizer and biostimulant agents' development. In this review, 148 scientific papers were analyzed to establish a large data set of cultured endophytic bacteria, reported at the genus level, inhabiting different compartments of wild and farmed plants, sampled around the world from different soil types and isolated using various growth media. To the best of our knowledge, this work provides the first overview of the current repertoire of cultured plant endophytic bacteria. Results indicate the presence of a recurrent set of culturable bacterial genera regardless of factors known to influence the plant bacterial community composition and the growth media used for the bacterial isolation. Moreover, a wide variety of bacterial genera that are currently rarely isolated from the plant endosphere was identified, demonstrating that culturomics can catch previously uncultured bacteria from the plant microbiome, widening the panorama of strains exploitable to support plant holobiont health and production.}, }
@article {pmid35137526, year = {2022}, author = {Ren, CG and Liu, ZY and Wang, XL and Qin, S}, title = {The seaweed holobiont: from microecology to biotechnological applications.}, journal = {Microbial biotechnology}, volume = {15}, number = {3}, pages = {738-754}, pmid = {35137526}, issn = {1751-7915}, mesh = {*Seaweed/chemistry ; }, abstract = {In the ocean, seaweed and microorganisms have coexisted since the earliest stages of evolution and formed an inextricable relationship. Recently, seaweed has attracted extensive attention worldwide for ecological and industrial purposes, but the function of its closely related microbes is often ignored. Microbes play an indispensable role in different stages of seaweed growth, development and maturity. A very diverse group of seaweed-associated microbes have important functions and are dynamically reconstructed as the marine environment fluctuates, forming an inseparable 'holobiont' with their host. To further understand the function and significance of holobionts, this review first reports on recent advances in revealing seaweed-associated microbe spatial and temporal distribution. Then, this review discusses the microbe and seaweed interactions and their ecological significance, and summarizes the current applications of the seaweed-microbe relationship in various environmental and biological technologies. Sustainable industries based on seaweed holobionts could become an integral part of the future bioeconomy because they can provide more resource-efficient food, high-value chemicals and medical materials. Moreover, holobionts may provide a new approach to marine environment restoration.}, }
@article {pmid35119475, year = {2022}, author = {Tran, C}, title = {Coral-microbe interactions: their importance to reef function and survival.}, journal = {Emerging topics in life sciences}, volume = {6}, number = {1}, pages = {33-44}, doi = {10.1042/ETLS20210229}, pmid = {35119475}, issn = {2397-8554}, mesh = {*Anemone ; Animals ; *Anthozoa ; Host Microbial Interactions ; Hypochlorous Acid ; *Microbiota ; *Scyphozoa ; Sodium Compounds ; }, abstract = {Many different microorganisms associate with the coral host in a single entity known as the holobiont, and their interactions with the host contribute to coral health, thereby making them a fundamental part of reef function, survival, and conservation. As corals continue to be susceptible to bleaching due to environmental stress, coral-associated bacteria may have a potential role in alleviating bleaching. This review provides a synthesis of the various roles bacteria have in coral physiology and development, and explores the possibility that changes in the microbiome with environmental stress could have major implications in how corals acclimatize and survive. Recent studies on the interactions between the coral's algal and bacterial symbionts elucidate how bacteria may stabilize algal health and, therefore, mitigate bleaching. A summary of the innovative tools and experiments to examine host-microbe interactions in other cnidarians (a temperate coral, a jellyfish, two anemones, and a freshwater hydroid) is offered in this review to delineate our current knowledge of mechanisms underlying microbial establishment and maintenance in the animal host. A better understanding of these mechanisms may enhance the success of maintaining probiotics long-term in corals as a conservation strategy.}, }
@article {pmid35112871, year = {2022}, author = {Deutsch, JM and Mandelare-Ruiz, P and Yang, Y and Foster, G and Routhu, A and Houk, J and De La Flor, YT and Ushijima, B and Meyer, JL and Paul, VJ and Garg, N}, title = {Metabolomics Approaches to Dereplicate Natural Products from Coral-Derived Bioactive Bacteria.}, journal = {Journal of natural products}, volume = {85}, number = {3}, pages = {462-478}, doi = {10.1021/acs.jnatprod.1c01110}, pmid = {35112871}, issn = {1520-6025}, mesh = {Animals ; *Anthozoa/microbiology ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/genetics ; *Biological Products/metabolism/pharmacology ; Metabolomics ; Symbiosis ; }, abstract = {Stony corals (Scleractinia) are invertebrates that form symbiotic relationships with eukaryotic algal endosymbionts and the prokaryotic microbiome. The microbiome has the potential to produce bioactive natural products providing defense and resilience to the coral host against pathogenic microorganisms, but this potential has not been extensively explored. Bacterial pathogens can pose a significant threat to corals, with some species implicated in primary and opportunistic infections of various corals. In response, probiotics have been proposed as a potential strategy to protect corals in the face of increased incidence of disease outbreaks. In this study, we screened bacterial isolates from healthy and diseased corals for antibacterial activity. The bioactive extracts were analyzed using untargeted metabolomics. Herein, an UpSet plot and hierarchical clustering analyses were performed to identify isolates with the largest number of unique metabolites. These isolates also displayed different antibacterial activities. Through application of in silico and experimental approaches coupled with genome analysis, we dereplicated natural products from these coral-derived bacteria from Florida's coral reef environments. The metabolomics approach highlighted in this study serves as a useful resource to select probiotic candidates and enables insights into natural product-mediated chemical ecology in holobiont symbiosis.}, }
@article {pmid35108095, year = {2022}, author = {Tignat-Perrier, R and van de Water, JAJM and Guillemain, D and Aurelle, D and Allemand, D and Ferrier-Pagès, C}, title = {The Effect of Thermal Stress on the Physiology and Bacterial Communities of Two Key Mediterranean Gorgonians.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {6}, pages = {e0234021}, pmid = {35108095}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Mediterranean Sea ; *Microbiota ; Seawater/microbiology ; }, abstract = {Gorgonians are important habitat-providing species in the Mediterranean Sea, but their populations are declining due to microbial diseases and repeated mass mortality events caused by summer heat waves. Elevated seawater temperatures may impact the stress tolerance and disease resistance of gorgonians and lead to disturbances in their microbiota. However, our knowledge of the biological response of the gorgonian holobiont (i.e., the host and its microbiota) to thermal stress remains limited. Here, we investigated how the holobiont of two gorgonian species (Paramuricea clavata and Eunicella cavolini) are affected throughout a 7-week thermal stress event by following both the corals' physiology and the composition of their bacterial communities. We found that P. clavata was more sensitive to elevated seawater temperatures than E. cavolini, showing a greater loss in energy reserves, reduced feeding ability, and partial mortality. This lower thermotolerance may be linked to the ∼20× lower antioxidant defense capacity in P. clavata compared with E. cavolini. In the first 4 weeks of thermal stress, we also observed minor shifts in the microbiota of both species, suggesting that the microbiota likely plays a limited role in thermal acclimation of the holobiont. However, major stochastic changes occurred later on in some colonies, which were of a transient nature in E. cavolini, but were linked to partial colony mortality in P. clavata. Overall, our results show significant, but differential, effects of thermal stress on the holobionts of both E. cavolini and P. clavata and predict potentially severe impacts on gorgonian populations under future climate scenarios. IMPORTANCE In the Mediterranean Sea, the tree-shaped gorgonian corals form large forests that provide a place to live for many species. Because of this important ecological role, it is crucial to understand how common habitat-forming gorgonians, like Eunicella cavolini and Paramuricea clavata, are affected by high seawater temperatures that are expected in the future due to climate change. We found that both species lost biomass, but P. clavata was more affected, being also unable to feed and showing signs of mortality. The microbiota of both gorgonians also changed substantively under high temperatures. Although this could be linked to partial colony mortality in P. clavata, the changes were temporary in E. cavolini. The overall higher resistance of E. cavolini may be related to its much higher antioxidant defense levels than P. clavata. Climate change may thus have severe impacts on gorgonian populations and the habitats they provide.}, }
@article {pmid35106548, year = {2022}, author = {Nerva, L and Garcia, JF and Favaretto, F and Giudice, G and Moffa, L and Sandrini, M and Cantu, D and Zanzotto, A and Gardiman, M and Velasco, R and Gambino, G and Chitarra, W}, title = {The hidden world within plants: metatranscriptomics unveils the complexity of wood microbiomes.}, journal = {Journal of experimental botany}, volume = {73}, number = {8}, pages = {2682-2697}, doi = {10.1093/jxb/erac032}, pmid = {35106548}, issn = {1460-2431}, support = {C94E19000770008//Italian Ministry for Agriculture and Forestry/ ; }, mesh = {Bacteria/genetics ; *Endophytes ; *Microbiota ; Plants ; Wood ; }, abstract = {The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.}, }
@article {pmid35105377, year = {2022}, author = {Zhang, S and Song, W and Nothias, LF and Couvillion, SP and Webster, N and Thomas, T}, title = {Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {22}, pmid = {35105377}, issn = {2049-2618}, mesh = {Chromatography, Liquid ; *Metabolomics ; *Tandem Mass Spectrometry ; }, abstract = {BACKGROUND: Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species.<br><br>RESULTS: Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms.<br><br>CONCLUSIONS: This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts. Video abstract.}, }
@article {pmid35104474, year = {2022}, author = {Yoksan, R and Boontanimitr, A and Klompong, N and Phothongsurakun, T}, title = {Poly(lactic acid)/thermoplastic cassava starch blends filled with duckweed biomass.}, journal = {International journal of biological macromolecules}, volume = {203}, number = {}, pages = {369-378}, doi = {10.1016/j.ijbiomac.2022.01.159}, pmid = {35104474}, issn = {1879-0003}, mesh = {*Araceae ; Biomass ; *Manihot/metabolism ; Polyesters ; Starch/metabolism ; }, abstract = {Duckweed (DW) is a highly small, free-floating aquatic plant. It grows and reproduces rapidly, comprises mainly protein and carbohydrate, and has substantial potential as a feedstock to produce bioplastics due to its renewability and having very little impact on the food chain. The aim of this work was to analyze the effect of DW biomass on the characteristics and properties of bio-based and biodegradable plastics based on a poly(lactic acid)/thermoplastic cassava starch (PLA/TPS) blend. Various amounts of DW biomass were compounded with PLA and TPS in a twin-screw extruder and then converted into dumbbell-shaped specimens using an injection molding machine. The obtained PLA/TPS blends filled with DW biomass exhibited a lower melt flow ability, higher moisture content, and increased surface hydrophilicity than the neat PLA/TPS blend. Incorporation of DW with low concentrations of 2.3 and 4.6 wt% increased the tensile strength, Young's modulus, and hardness of the PLA/TPS blend. Moisture and glycerol from DW and TPS played important roles in reducing the Tg, Tcc, Tm, and Td of PLA in the blends. The current work demonstrated that DW could be used as a biofiller for PLA/TPS blends, and the resulting PLA/TPS blends filled with DW biomass have potential in manufacturing injection-molded articles for sustainable, biodegradable, and short-term use.}, }
@article {pmid35104027, year = {2022}, author = {Dungan, AM and Hartman, LM and Blackall, LL and van Oppen, MJH}, title = {Exploring microbiome engineering as a strategy for improved thermal tolerance in Exaiptasia diaphana.}, journal = {Journal of applied microbiology}, volume = {132}, number = {4}, pages = {2940-2956}, doi = {10.1111/jam.15465}, pmid = {35104027}, issn = {1365-2672}, support = {DP160101468//Australian Research Council/ ; FL180100036//Australian Research Council/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Coral Reefs ; *Microbiota ; *Rhodobacteraceae ; Seawater/microbiology ; }, abstract = {AIMS: Fourteen percent of all living coral, equivalent to more than all the coral on the Great Barrier Reef, has died in the past decade as a result of climate change-driven bleaching. Inspired by the 'oxidative stress theory of coral bleaching', we investigated whether a bacterial consortium designed to scavenge free radicals could integrate into the host microbiome and improve thermal tolerance of the coral model, Exaiptasia diaphana.<br><br>METHODS AND RESULTS: E. diaphana anemones were inoculated with a consortium of high free radical scavenging (FRS) bacteria, a consortium of congeneric low FRS bacteria, or sterile seawater as a control, then exposed to elevated temperature. Increases in the relative abundance of Labrenzia during the first 2 weeks following the last inoculation provided evidence for temporary inoculum integration into the E. diaphana microbiome. Initial uptake of other consortium members was inconsistent, and these bacteria did not persist either in E. diaphana's microbiome over time. Given their non-integration into the host microbiome, the ability of the FRS consortium to mitigate thermal stress could not be assessed. Importantly, there were no physiological impacts (negative or positive) of the bacterial inoculations on the holobiont.<br><br>CONCLUSIONS: The introduced bacteria were not maintained in the anemone microbiome over time, thus, their protective effect is unknown. Achieving long-term integration of bacteria into cnidarian microbiomes remains a research priority.<br><br>Microbiome engineering strategies to mitigate coral bleaching may assist coral reefs in their persistence until climate change has been curbed. This study provides insights that will inform microbiome manipulation approaches in coral bleaching mitigation research.}, }
@article {pmid35104026, year = {2022}, author = {Wood, G and Steinberg, PD and Campbell, AH and Vergés, A and Coleman, MA and Marzinelli, EM}, title = {Host genetics, phenotype and geography structure the microbiome of a foundational seaweed.}, journal = {Molecular ecology}, volume = {31}, number = {7}, pages = {2189-2206}, doi = {10.1111/mec.16378}, pmid = {35104026}, issn = {1365-294X}, mesh = {Geography ; *Microbiota/genetics ; *Phaeophyta/genetics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; *Seaweed/genetics ; }, abstract = {Interactions between hosts and their microbiota are vital to the functioning and resilience of macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives host-microbiota interactions is essential for informing ecosystem restoration and conservation. We investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We quantified 16 morphological and functional phenotypic traits, including host genetics (using 354 single nucleotide polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1,300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e., present on all Phyllospora individuals sampled) exhibited slightly higher associations with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defence, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of how "holobionts" (hosts plus their microbiota) are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.}, }
@article {pmid35095978, year = {2021}, author = {Abdullaeva, Y and Ratering, S and Ambika Manirajan, B and Rosado-Porto, D and Schnell, S and Cardinale, M}, title = {Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {806915}, pmid = {35095978}, issn = {1664-462X}, abstract = {The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.}, }
@article {pmid35090190, year = {2022}, author = {Bonthond, G and Barilo, A and Allen, RJ and Cunliffe, M and Krueger-Hadfield, SA}, title = {Fungal endophytes vary by species, tissue type, and life cycle stage in intertidal macroalgae.}, journal = {Journal of phycology}, volume = {58}, number = {2}, pages = {330-342}, doi = {10.1111/jpy.13237}, pmid = {35090190}, issn = {1529-8817}, support = {772584//H2020 European Research Council/ ; //start-up funds from the University of Alabama at Birmingham/ ; //ASSEMBLE Plus Infrastructure Access/ ; 32830//PADI Foundation/ ; }, mesh = {Animals ; *Chondrus ; Ecosystem ; Endophytes ; Life Cycle Stages ; *Seaweed ; }, abstract = {Fungal symbionts of terrestrial plants are among the most widespread and well-studied symbioses, relatively little is known about fungi that are associated with macroalgae. To fill the gap in marine fungal taxonomy, we combined simple culture methods with amplicon sequencing to characterize the fungal communities associated with three brown (Sargassum muticum, Pelvetia canaliculata, and Himanthalia elongata) and two red (Mastocarpus stellatus and Chondrus crispus) macroalgae from one intertidal zone. In addition to characterizing novel fungal diversity, we tested three hypotheses: fungal diversity and community composition vary (i) among species distributed at different tidal heights, (ii) among tissue types (apices, mid-thallus, and stipe), and (iii) among "isomorphic" C. crispus life cycle stages. Almost 70% of our reads were classified as Ascomycota, 29% as Basidiomycota, and 1% that could not be classified to a phylum. Thirty fungal isolates were obtained, 18 of which were also detected with amplicon sequencing. Fungal communities differed by host and tissue type. Interestingly, P. canaliculata, a fucoid at the extreme high intertidal, did not show differences in fungal diversity across the thallus. As found in filamentous algal endophytes, fungal diversity varied among the three life cycle stages in C. crispus. Female gametophytes were also compositionally more dispersed as compared to the fewer variable tetrasporophytes and male gametophytes. We demonstrate the utility of combining relatively simple cultivation and sequencing approaches to characterize and study macroalgal-fungal associations and highlight the need to understand the role of fungi in near-shore marine ecosystems.}, }
@article {pmid35056519, year = {2021}, author = {Rosenberg, E and Zilber-Rosenberg, I}, title = {Reconstitution and Transmission of Gut Microbiomes and Their Genes between Generations.}, journal = {Microorganisms}, volume = {10}, number = {1}, pages = {}, pmid = {35056519}, issn = {2076-2607}, abstract = {Microbiomes are transmitted between generations by a variety of different vertical and/or horizontal modes, including vegetative reproduction (vertical), via female germ cells (vertical), coprophagy and regurgitation (vertical and horizontal), physical contact starting at birth (vertical and horizontal), breast-feeding (vertical), and via the environment (horizontal). Analyses of vertical transmission can result in false negatives (failure to detect rare microbes) and false positives (strain variants). In humans, offspring receive most of their initial gut microbiota vertically from mothers during birth, via breast-feeding and close contact. Horizontal transmission is common in marine organisms and involves selectivity in determining which environmental microbes can colonize the organism's microbiome. The following arguments are put forth concerning accurate microbial transmission: First, the transmission may be of functions, not necessarily of species; second, horizontal transmission may be as accurate as vertical transmission; third, detection techniques may fail to detect rare microbes; lastly, microbiomes develop and reach maturity with their hosts. In spite of the great variation in means of transmission discussed in this paper, microbiomes and their functions are transferred from one generation of holobionts to the next with fidelity. This provides a strong basis for each holobiont to be considered a unique biological entity and a level of selection in evolution, largely maintaining the uniqueness of the entity and conserving the species from one generation to the next.}, }
@article {pmid35054418, year = {2021}, author = {Rusanova, A and Fedorchuk, V and Toshchakov, S and Dubiley, S and Sutormin, D}, title = {An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {35054418}, issn = {2075-1729}, abstract = {Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus-host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.}, }
@article {pmid35050172, year = {2022}, author = {Ortega, MA and Alvarez-Mon, MA and García-Montero, C and Fraile-Martinez, O and Guijarro, LG and Lahera, G and Monserrat, J and Valls, P and Mora, F and Rodríguez-Jiménez, R and Quintero, J and Álvarez-Mon, M}, title = {Gut Microbiota Metabolites in Major Depressive Disorder-Deep Insights into Their Pathophysiological Role and Potential Translational Applications.}, journal = {Metabolites}, volume = {12}, number = {1}, pages = {}, pmid = {35050172}, issn = {2218-1989}, support = {B2017/BMD3804//Comunidad de Madrid/ ; }, abstract = {The gut microbiota is a complex and dynamic ecosystem essential for the proper functioning of the organism, affecting the health and disease status of the individuals. There is continuous and bidirectional communication between gut microbiota and the host, conforming to a unique entity known as "holobiont". Among these crosstalk mechanisms, the gut microbiota synthesizes a broad spectrum of bioactive compounds or metabolites which exert pleiotropic effects on the human organism. Many of these microbial metabolites can cross the blood-brain barrier (BBB) or have significant effects on the brain, playing a key role in the so-called microbiota-gut-brain axis. An altered microbiota-gut-brain (MGB) axis is a major characteristic of many neuropsychiatric disorders, including major depressive disorder (MDD). Significative differences between gut eubiosis and dysbiosis in mental disorders like MDD with their different metabolite composition and concentrations are being discussed. In the present review, the main microbial metabolites (short-chain fatty acids -SCFAs-, bile acids, amino acids, tryptophan -trp- derivatives, and more), their signaling pathways and functions will be summarized to explain part of MDD pathophysiology. Conclusions from promising translational approaches related to microbial metabolome will be addressed in more depth to discuss their possible clinical value in the management of MDD patients.}, }
@article {pmid35050140, year = {2021}, author = {Liang, J and Luo, W and Yu, K and Xu, Y and Chen, J and Deng, C and Ge, R and Su, H and Huang, W and Wang, G}, title = {Multi-Omics Revealing the Response Patterns of Symbiotic Microorganisms and Host Metabolism in Scleractinian Coral Pavona minuta to Temperature Stresses.}, journal = {Metabolites}, volume = {12}, number = {1}, pages = {}, pmid = {35050140}, issn = {2218-1989}, support = {42030502//National Natural Science Foundation of China/ ; }, abstract = {Global climate change has resulted in large-scale coral reef decline worldwide, for which the ocean warming has paid more attention. Coral is a typical mutually beneficial symbiotic organism with diverse symbiotic microorganisms, which maintain the stability of physiological functions. This study compared the responses of symbiotic microorganisms and host metabolism in a common coral species, Pavona minuta, under indoor simulated thermal and cold temperatures. The results showed that abnormal temperature stresses had unfavorable impact on the phenotypes of corals, resulting in bleaching and color change. The compositions of symbiotic bacteria and dinoflagellate communities only presented tiny changes under temperature stresses. However, some rare symbiotic members have been showed to be significantly influenced by water temperatures. Finally, by using ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS) method, we found that different temperature stresses had very different impacts on the metabolism of coral holobiont. The thermal and cold stresses induced the decrease of anti-oxidation metabolites, several monogalactosyldiacylglycerols (MGDGs), and the increase of lipotoxic metabolite, 10-oxo-nonadecanoic acid, in the coral holobiont, respectively. Our study indicated the response patterns of symbiotic microorganisms and host metabolism in coral to the thermal and cold stresses, providing theoretical data for the adaptation and evolution of coral to a different climate in the future.}, }
@article {pmid35043221, year = {2022}, author = {Kanisan, DP and Quek, ZBR and Oh, RM and Afiq-Rosli, L and Lee, JN and Huang, D and Wainwright, BJ}, title = {Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {35043221}, issn = {1432-184X}, abstract = {Coral-associated bacteria play critical roles in the regulation of coral health and function. Environmental perturbations that alter the bacterial community structure can render the coral holobiont more susceptible and less resilient to disease. Understanding the natural variation of the coral microbiome across space and host species provides a baseline that can be used to distinguish shifts in community structure. Using a 16S rRNA gene metabarcoding approach, this study examines bacterial community structure across three scleractinian coral hosts. Our results show that corals of three regions-eastern and western Peninsular Malaysia and Singapore-host distinct bacterial communities; despite these differences, we were able to identify a core microbiome shared across all three species. This core microbiome was also present in samples previously collected in Thailand, suggesting that these core microbes play an important role in promoting and maintaining host health. For example, several have been identified as dimethylsulfoniopropionate (DMSP) metabolizers that have roles in sulfur cycling and the suppression of bacterial pathogens. Pachyseris speciosa has the most variable microbiome, followed by Porites lutea, with the composition of the Diploastrea heliopora microbiome the least variable throughout all locations. Microbial taxa associated with each region or site are likely shaped by local environmental conditions. Taken together, host identity is a major driver of differences in microbial community structure, while environmental heterogeneity shapes communities at finer scales.}, }
@article {pmid35042418, year = {2022}, author = {Kriefall, NG and Kanke, MR and Aglyamova, GV and Davies, SW}, title = {Reef environments shape microbial partners in a highly connected coral population.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1967}, pages = {20212459}, pmid = {35042418}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/genetics/microbiology ; Bacteria/genetics ; Coral Reefs ; Polynesia ; }, abstract = {Evidence is mounting that composition of microorganisms within a host can play an essential role in total holobiont health. In corals, for instance, studies have identified algal and bacterial taxa that can significantly influence coral host function and these communities depend on environmental context. However, few studies have linked host genetics to algal and microbial partners across environments within a single coral population. Here, using 2b-RAD sequencing of corals and metabarcoding of their associated algal (ITS2) and bacterial (16S) communities, we show evidence that reef zones (locales that differ in proximity to shore and other environmental characteristics) structure algal and bacterial communities at different scales in a highly connected coral population (Acropora hyacinthus) in French Polynesia. Fore reef (FR) algal communities in Mo'orea were more diverse than back reef (BR) communities, suggesting that these BR conditions constrain diversity. Interestingly, in FR corals, host genetic diversity correlated with bacterial diversity, which could imply genotype by genotype interactions between these holobiont members. Our results illuminate that local reef conditions play an important role in shaping unique host-microbial partner combinations, which may have fitness consequences for dispersive coral populations arriving in novel environments.}, }
@article {pmid35014869, year = {2022}, author = {Zhou, H and Yang, L and Ding, J and Dai, R and He, C and Xu, K and Luo, L and Xiao, L and Zheng, Y and Han, C and Akinyemi, FT and Honaker, CF and Zhang, Y and Siegel, PB and Meng, H}, title = {Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome.}, journal = {mSystems}, volume = {7}, number = {1}, pages = {e0126121}, pmid = {35014869}, issn = {2379-5077}, support = {31572384//National Science Foundation of China/ ; }, abstract = {Multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts and variation in DNA methylation, mRNA expression, and microRNA profiles in the ceca. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by the upregulation of expression of gga-miR-2128 and a methylated region near its transcription start site (388 bp). Correlation analysis showed that IGF2BP1 expression was associated with an abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in adapting to long-term artificial selection for body weight. Our study provides evidence that adaptation of the holobiont can occur in the microbiome as well as in the epigenetic profile of the host. IMPORTANCE The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts, and variation in DNA methylation, mRNA expression, and microRNA profiles in ceca. The insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) was the most upregulated gene in HWS ceca with its expression likely affected by a methylated region near its transcription start site and the upregulation of expression of gga-miR-2128. Correlation analysis also showed that IGF2BP1 expression was associated with the abundance of microbes, such as Lactobacillus and Methanocorpusculum. These findings suggest that IGF2BP1 was regulated in the hologenome in response to long-term artificial selection for body weight. Our study shows that the holobiont may adapt in both the microbiome and the host's epigenetic profile.}, }
@article {pmid34987542, year = {2021}, author = {Lombardi, N and Woo, SL and Vinale, F and Turrà, D and Marra, R}, title = {Editorial: The Plant Holobiont Volume II: Impacts of the Rhizosphere on Plant Health.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {809291}, pmid = {34987542}, issn = {1664-462X}, }
@article {pmid34985334, year = {2022}, author = {Marasco, R and Fusi, M and Callegari, M and Jucker, C and Mapelli, F and Borin, S and Savoldelli, S and Daffonchio, D and Crotti, E}, title = {Destabilization of the Bacterial Interactome Identifies Nutrient Restriction-Induced Dysbiosis in Insect Guts.}, journal = {Microbiology spectrum}, volume = {10}, number = {1}, pages = {e0158021}, pmid = {34985334}, issn = {2165-0497}, mesh = {Animal Feed/*analysis ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; *Gastrointestinal Microbiome ; Nutrients/analysis/*metabolism ; Simuliidae/growth &amp; development/metabolism/*microbiology ; }, abstract = {Stress-associated dysbiosis of microbiome can have several configurations that, under an energy landscape conceptual framework, can change from one configuration to another due to different alternating selective forces. It has been proposed-according to the Anna Karenina Principle-that in stressed individuals the microbiome are more dispersed (i.e., with a higher within-beta diversity), evidencing the grade of dispersion as indicator of microbiome dysbiosis. We hypothesize that although dysbiosis leads to different microbial communities in terms of beta diversity, these are not necessarily differently dispersed (within-beta diversity), but they form disrupted networks that make them less resilient to stress. To test our hypothesis, we select nutrient restriction (NR) stress that impairs host fitness but does not introduce overt microbiome selectors, such as toxic compounds and pathogens. We fed the polyphagous black soldier fly, Hermetia illucens, with two NR diets and a control full-nutrient (FN) diet. NR diets were dysbiotic because they strongly affected insect growth and development, inducing significant microscale changes in physiochemical conditions of the gut compartments. NR diets established new configurations of the gut microbiome compared to FN-fed guts but with similar dispersion. However, these new configurations driven by the deterministic changes induced by NR diets were reflected in rarefied, less structured, and less connected bacterial interactomes. These results suggested that while the dispersion cannot be considered a consistent indicator of the unhealthy state of dysbiotic microbiomes, the capacity of the community members to maintain network connections and stability can be an indicator of the microbial dysbiotic conditions and their incapacity to sustain the holobiont resilience and host homeostasis. IMPORTANCE Changes in diet play a role in reshaping the gut microbiome in animals, inducing dysbiotic configurations of the associated microbiome. Although studies have reported on the effects of specific nutrient contents on the diet, studies regarding the conditions altering the microbiome configurations and networking in response to diet changes are limited. Our results showed that nutrient poor diets determine dysbiotic states of the host with reduction of insect weight and size, and increase of the times for developmental stage. Moreover, the poor nutrient diets lead to changes in the compositional diversity and network interaction properties of the gut microbial communities. Our study adds a new component to the understanding of the ecological processes associated with dysbiosis, by disentangling consequences of diets on microbiome dysbiosis that is manifested with the disruption of microbiome networking properties rather than changes in microbiome dispersion and beta diversity.}, }
@article {pmid34977575, year = {2021}, author = {Jomori, T and Matsuda, K and Egami, Y and Abe, I and Takai, A and Wakimoto, T}, title = {Insights into phosphatase-activated chemical defense in a marine sponge holobiont.}, journal = {RSC chemical biology}, volume = {2}, number = {6}, pages = {1600-1607}, pmid = {34977575}, issn = {2633-0679}, abstract = {Marine sponges often contain potent cytotoxic compounds, which in turn evokes the principle question of how marine sponges avoid self-toxicity. In a marine sponge Discodermia calyx, the highly toxic calyculin A is detoxified by the phosphorylation, which is catalyzed by the phosphotransferase CalQ of a producer symbiont, "Candidatus Entotheonella" sp. Here we show the activating mechanism to dephosphorylate the stored phosphocalyculin A protoxin. The phosphatase specific to phosphocalyculin A is CalL, which is also encoded in the calyculin biosynthetic gene cluster. CalL represents a new clade and unprecedently coordinates the heteronuclear metals Cu and Zn. CalL is localized in the periplasmic space of the sponge symbiont, where it is ready for the on-demand production of calyculin A in response to sponge tissue disruption.}, }
@article {pmid34975794, year = {2021}, author = {Ge, R and Liang, J and Yu, K and Chen, B and Yu, X and Deng, C and Chen, J and Xu, Y and Qin, L}, title = {Regulation of the Coral-Associated Bacteria and Symbiodiniaceae in Acropora valida Under Ocean Acidification.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {767174}, pmid = {34975794}, issn = {1664-302X}, abstract = {Ocean acidification is one of many stressors that coral reef ecosystems are currently contending with. Thus, understanding the response of key symbiotic microbes to ocean acidification is of great significance for understanding the adaptation mechanism and development trend of coral holobionts. Here, high-throughput sequencing technology was employed to investigate the coral-associated bacteria and Symbiodiniaceae of the ecologically important coral Acropora valida exposed to different pH gradients. After 30 days of acclimatization, we set four acidification gradients (pH 8.2, 7.8, 7.4, and 7.2, respectively), and each pH condition was applied for 10 days, with the whole experiment lasting for 70 days. Although the Symbiodiniaceae density decreased significantly, the coral did not appear to be bleached, and the real-time photosynthetic rate did not change significantly, indicating that A. valida has strong tolerance to acidification. Moreover, the Symbiodiniaceae community composition was hardly affected by ocean acidification, with the C1 subclade (Cladocopium goreaui) being dominant among the Symbiodiniaceae dominant types. The relative abundance of the Symbiodiniaceae background types was significantly higher at pH 7.2, indicating that ocean acidification might increase the stability of the community composition by regulating the Symbiodiniaceae rare biosphere. Furthermore, the stable symbiosis between the C1 subclade and coral host may contribute to the stability of the real-time photosynthetic efficiency. Finally, concerning the coral-associated bacteria, the stable symbiosis between Endozoicomonas and coral host is likely to help them adapt to ocean acidification. The significant increase in the relative abundance of Cyanobacteria at pH 7.2 may also compensate for the photosynthesis efficiency of a coral holobiont. In summary, this study suggests that the combined response of key symbiotic microbes helps the whole coral host resist the threats of ocean acidification.}, }
@article {pmid34959516, year = {2021}, author = {Hartmann, A and Klink, S and Rothballer, M}, title = {Importance of N-Acyl-Homoserine Lactone-Based Quorum Sensing and Quorum Quenching in Pathogen Control and Plant Growth Promotion.}, journal = {Pathogens (Basel, Switzerland)}, volume = {10}, number = {12}, pages = {}, pmid = {34959516}, issn = {2076-0817}, support = {RO 2340/4-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The biological control of plant pathogens is linked to the composition and activity of the plant microbiome. Plant-associated microbiomes co-evolved with land plants, leading to plant holobionts with plant-beneficial microbes but also with plant pathogens. A diverse range of plant-beneficial microbes assists plants to reach their optimal development and growth under both abiotic and biotic stress conditions. Communication within the plant holobiont plays an important role, and besides plant hormonal interactions, quorum-sensing signalling of plant-associated microbes plays a central role. Quorum-sensing (QS) autoinducers, such as N-acyl-homoserine lactones (AHL) of Gram-negative bacteria, cause a pronounced interkingdom signalling effect on plants, provoking priming processes of pathogen defence and insect pest control. However, plant pathogenic bacteria also use QS signalling to optimise their virulence; these QS activities can be controlled by quorum quenching (QQ) and quorum-sensing inhibition (QSI) approaches by accompanying microbes and also by plants. Plant growth-promoting bacteria (PGPB) have also been shown to demonstrate QQ activity. In addition, some PGPB only harbour genes for AHL receptors, so-called luxR-solo genes, which can contribute to plant growth promotion and biological control. The presence of autoinducer solo receptors may reflect ongoing microevolution processes in microbe-plant interactions. Different aspects of QS systems in bacteria-plant interactions of plant-beneficial and pathogenic bacteria will be discussed, and practical applications of bacteria with AHL-producing or -quenching activity; QS signal molecules stimulating pathogen control and plant growth promotion will also be presented.}, }
@article {pmid34951090, year = {2022}, author = {Rolli, E and de Zélicourt, A and Alzubaidy, H and Karampelias, M and Parween, S and Rayapuram, N and Han, B and Froehlich, K and Abulfaraj, AA and Alhoraibi, H and Mariappan, K and Andrés-Barrao, C and Colcombet, J and Hirt, H}, title = {The Lys-motif receptor LYK4 mediates Enterobacter sp. SA187 triggered salt tolerance in Arabidopsis thaliana.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {223-239}, doi = {10.1111/1462-2920.15839}, pmid = {34951090}, issn = {1462-2920}, mesh = {*Arabidopsis/genetics/microbiology ; *Arabidopsis Proteins/genetics ; Enterobacter/genetics ; Plant Immunity ; Salt Tolerance ; }, abstract = {Root endophytes establish beneficial interactions with plants, improving holobiont resilience and fitness, but how plant immunity accommodates beneficial microbes is poorly understood. The multi-stress tolerance-inducing endophyte Enterobacter sp. SA187 triggers a canonical immune response in Arabidopsis only at high bacterial dosage (>108 CFUs ml-1), suggesting that SA187 is able to evade or suppress the plant defence system at lower titres. Although SA187 flagellin epitopes are recognized by the FLS2 receptor, SA187-triggered salt tolerance functions independently of the FLS2 system. In contrast, overexpression of the chitin receptor components LYK4 and LYK5 compromised the beneficial effect of SA187 on Arabidopsis, while it was enhanced in lyk4 mutant plants. Transcriptome analysis revealed that the role of LYK4 is intertwined with a function in remodelling defence responses with growth and root developmental processes. LYK4 interferes with modification of plant ethylene homeostasis by Enterobacter SA187 to boost salt stress resistance. Collectively, these results contribute to unlock the crosstalk between components of the plant immune system and beneficial microbes and point to a new role for the Lys-motif receptor LYK4 in beneficial plant-microbe interaction.}, }
@article {pmid34950234, year = {2021}, author = {Iannello, M and Mezzelani, M and Dalla Rovere, G and Smits, M and Patarnello, T and Ciofi, C and Carraro, L and Boffo, L and Ferraresso, S and Babbucci, M and Mazzariol, S and Centelleghe, C and Cardazzo, B and Carrer, C and Varagnolo, M and Nardi, A and Pittura, L and Benedetti, M and Fattorini, D and Regoli, F and Ghiselli, F and Gorbi, S and Bargelloni, L and Milan, M}, title = {Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam.}, journal = {Evolutionary applications}, volume = {14}, number = {12}, pages = {2864-2880}, pmid = {34950234}, issn = {1752-4571}, abstract = {Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post-transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas-associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long-lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species.}, }
@article {pmid34946024, year = {2021}, author = {Singh, S and Singh, A and Baweja, V and Roy, A and Chakraborty, A and Singh, IK}, title = {Molecular Rationale of Insect-Microbes Symbiosis-From Insect Behaviour to Mechanism.}, journal = {Microorganisms}, volume = {9}, number = {12}, pages = {}, pmid = {34946024}, issn = {2076-2607}, abstract = {Insects nurture a panoply of microbial populations that are often obligatory and exist mutually with their hosts. Symbionts not only impact their host fitness but also shape the trajectory of their phenotype. This co-constructed niche successfully evolved long in the past to mark advanced ecological specialization. The resident microbes regulate insect nutrition by controlling their host plant specialization and immunity. It enhances the host fitness and performance by detoxifying toxins secreted by the predators and abstains them. The profound effect of a microbial population on insect physiology and behaviour is exploited to understand the host-microbial system in diverse taxa. Emergent research of insect-associated microbes has revealed their potential to modulate insect brain functions and, ultimately, control their behaviours, including social interactions. The revelation of the gut microbiota-brain axis has now unravelled insects as a cost-effective potential model to study neurodegenerative disorders and behavioural dysfunctions in humans. This article reviewed our knowledge about the insect-microbial system, an exquisite network of interactions operating between insects and microbes, its mechanistic insight that holds intricate multi-organismal systems in harmony, and its future perspectives. The demystification of molecular networks governing insect-microbial symbiosis will reveal the perplexing behaviours of insects that could be utilized in managing insect pests.}, }
@article {pmid34943189, year = {2021}, author = {Liu, Y and Liao, X and Han, T and Su, A and Guo, Z and Lu, N and He, C and Lu, Z}, title = {Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont.}, journal = {Biology}, volume = {10}, number = {12}, pages = {}, pmid = {34943189}, issn = {2079-7737}, abstract = {Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.}, }
@article {pmid34932575, year = {2021}, author = {Maltseva, AL and Varfolomeeva, MA and Gafarova, ER and Panova, MAZ and Mikhailova, NA and Granovitch, AI}, title = {Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species.}, journal = {PloS one}, volume = {16}, number = {12}, pages = {e0260792}, pmid = {34932575}, issn = {1932-6203}, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Environmental Microbiology ; *Genetic Variation ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/classification/*microbiology ; Species Specificity ; }, abstract = {Any multicellular organism during its life is involved in relatively stable interactions with microorganisms. The organism and its microbiome make up a holobiont, possessing a unique set of characteristics and evolving as a whole system. This study aimed to evaluate the degree of the conservativeness of microbiomes associated with intertidal gastropods. We studied the composition and the geographic and phylogenetic variability of the gut and body surface microbiomes of five closely related sympatric Littorina (Neritrema) spp. and a more distant species, L. littorea, from the sister subgenus Littorina (Littorina). Although snail-associated microbiomes included many lineages (207-603), they were dominated by a small number of OTUs of the genera Psychromonas, Vibrio, and Psychrilyobacter. The geographic variability was greater than the interspecific differences at the same collection site. While the microbiomes of the six Littorina spp. did not differ at the high taxonomic level, the OTU composition differed between groups of cryptic species and subgenera. A few species-specific OTUs were detected within the collection sites; notably, such OTUs never dominated microbiomes. We conclude that the composition of the high-rank taxa of the associated microbiome ("scaffolding enterotype") is more evolutionarily conserved than the composition of the low-rank individual OTUs, which may be site- and / or species-specific.}, }
@article {pmid34922182, year = {2022}, author = {Formosinho, J and Bencard, A and Whiteley, L}, title = {Environmentality in biomedicine: microbiome research and the perspectival body.}, journal = {Studies in history and philosophy of science}, volume = {91}, number = {}, pages = {148-158}, doi = {10.1016/j.shpsa.2021.11.005}, pmid = {34922182}, issn = {0039-3681}, mesh = {Causality ; Ecology ; Humans ; *Microbiota ; }, abstract = {Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool - environmentality - to think through this problem. Environmentality is the state or quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health.}, }
@article {pmid34917118, year = {2021}, author = {Cesaro, P and Gamalero, E and Zhang, J and Pivato, B}, title = {Editorial: The Plant Holobiont Volume I: Microbiota as Part of the Holobiont; Challenges for Agriculture.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {799168}, pmid = {34917118}, issn = {1664-462X}, }
@article {pmid34912564, year = {2021}, author = {Watson, SA and Neo, ML}, title = {Conserving threatened species during rapid environmental change: using biological responses to inform management strategies of giant clams.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coab082}, pmid = {34912564}, issn = {2051-1434}, abstract = {Giant clams are threatened by overexploitation for human consumption, their valuable shells and the aquarium trade. Consequently, these iconic coral reef megafauna are extinct in some former areas of their range and are included in the International Union for Conservation of Nature (IUCN) Red List of Threatened Species and Convention on International Trade in Endangered Species of Wild Fauna and Flora. Now, giant clams are also threatened by rapid environmental change from both a suite of local and regional scale stressors and global change, including climate change, global warming, marine heatwaves and ocean acidification. The interplay between local- to regional-scale and global-scale drivers is likely to cause an array of lethal and sub-lethal effects on giant clams, potentially limiting their depth distribution on coral reefs and decreasing suitable habitat area within natural ranges of species. Global change stressors, pervasive both in unprotected and protected areas, threaten to diminish conservation efforts to date. International efforts urgently need to reduce carbon dioxide emissions to avoid lethal and sub-lethal effects of global change on giant clams. Meanwhile, knowledge of giant clam physiological and ecological responses to local-regional and global stressors could play a critical role in conservation strategies of these threatened species through rapid environmental change. Further work on how biological responses translate into habitat requirements as global change progresses, selective breeding for resilience, the capacity for rapid adaptive responses of the giant clam holobiont and valuing tourism potential, including recognizing giant clams as a flagship species for coral reefs, may help improve the prospects of these charismatic megafauna over the coming decades.}, }
@article {pmid34899619, year = {2021}, author = {Barreto, MM and Ziegler, M and Venn, A and Tambutté, E and Zoccola, D and Tambutté, S and Allemand, D and Antony, CP and Voolstra, CR and Aranda, M}, title = {Effects of Ocean Acidification on Resident and Active Microbial Communities of Stylophora pistillata.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {707674}, pmid = {34899619}, issn = {1664-302X}, abstract = {Ocean warming and ocean acidification (OA) are direct consequences of climate change and affect coral reefs worldwide. While the effect of ocean warming manifests itself in increased frequency and severity of coral bleaching, the effects of ocean acidification on corals are less clear. In particular, long-term effects of OA on the bacterial communities associated with corals are largely unknown. In this study, we investigated the effects of ocean acidification on the resident and active microbiome of long-term aquaria-maintained Stylophora pistillata colonies by assessing 16S rRNA gene diversity on the DNA (resident community) and RNA level (active community). Coral colony fragments of S. pistillata were kept in aquaria for 2 years at four different pCO2 levels ranging from current pH conditions to increased acidification scenarios (i.e., pH 7.2, 7.4, 7.8, and 8). We identified 154 bacterial families encompassing 2,047 taxa (OTUs) in the resident and 89 bacterial families including 1,659 OTUs in the active communities. Resident communities were dominated by members of Alteromonadaceae, Flavobacteriaceae, and Colwelliaceae, while active communities were dominated by families Cyclobacteriacea and Amoebophilaceae. Besides the overall differences between resident and active community composition, significant differences were seen between the control (pH 8) and the two lower pH treatments (7.2 and 7.4) in the active community, but only between pH 8 and 7.2 in the resident community. Our analyses revealed profound differences between the resident and active microbial communities, and we found that OA exerted stronger effects on the active community. Further, our results suggest that rDNA- and rRNA-based sequencing should be considered complementary tools to investigate the effects of environmental change on microbial assemblage structure and activity.}, }
@article {pmid34896508, year = {2022}, author = {Lin, Z and Wang, L and Chen, M and Zheng, X and Chen, J}, title = {Proteome and microbiota analyses characterizing dynamic coral-algae-microbe tripartite interactions under simulated rapid ocean acidification.}, journal = {The Science of the total environment}, volume = {810}, number = {}, pages = {152266}, doi = {10.1016/j.scitotenv.2021.152266}, pmid = {34896508}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Homeostasis ; Hydrogen-Ion Concentration ; *Microbiota ; Oceans and Seas ; Proteome ; Seawater ; }, abstract = {Ocean acidification (OA) is a pressing issue currently and in the future for coral reefs. The importance of maintenance interactions among partners of the holobiont association in the stress response is well appreciated; however, the candidate molecular and microbial mechanisms that underlie holobiont stress resilience or susceptibility remain unclear. Here, to assess the effects of rapid pH change on coral holobionts at both the protein and microbe levels, combined proteomics and microbiota analyses of the scleractinian coral Galaxea fascicularis exposed to three relevant OA scenarios, including current (pHT = 8.15), preindustrial (pHT = 8.45) and future IPCC-2100 scenarios (pHT = 7.85), were conducted. The results demonstrated that pH changes had no significant effect on the physiological calcification rate of G. fascicularis in a 10-day experiment; however, significant differences were recorded in the proteome and 16S profiling. Proteome variance analysis identified some of the core biological pathways in coral holobionts, including coral host infection and immune defence, and maintaining metabolic compatibility involved in energy homeostasis, nutrient cycling, antibiotic activity and carbon budgets of coral-Symbiodiniaceae interactions were key mechanisms in the early OA stress response. Furthermore, microbiota changes indicate substantial microbial community and functional disturbances in response to OA stress, potentially compromising holobiont health and fitness. Our results may help to elucidate many complex mechanisms to describe scleractinian coral holobiont responses to OA and raise interesting questions for future studies.}, }
@article {pmid34861071, year = {2022}, author = {Armstrong, EE and Perez-Lamarque, B and Bi, K and Chen, C and Becking, LE and Lim, JY and Linderoth, T and Krehenwinkel, H and Gillespie, RG}, title = {A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates.}, journal = {Molecular ecology}, volume = {31}, number = {4}, pages = {1299-1316}, doi = {10.1111/mec.16301}, pmid = {34861071}, issn = {1365-294X}, mesh = {Animals ; Geography ; Hawaii ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Spiders/genetics ; }, abstract = {The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawai'i, and outgroup taxa on older islands, we tested whether each component of the "holobiont" (spider hosts, intracellular endosymbionts and gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. To investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. The results showed that the host A. waikula is indeed structured by geographical isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawai'i. Conversely, the gut microbiota, which we suspect is generally environmentally derived, was largely conserved across all populations and species. Our results show that different components of the holobiont respond in distinct ways to the dynamic environment of the volcanic archipelago. This highlights the necessity of understanding the interplay between different components of the holobiont, to properly characterize its evolution.}, }
@article {pmid34857934, year = {2022}, author = {Rädecker, N and Pogoreutz, C and Gegner, HM and Cárdenas, A and Perna, G and Geißler, L and Roth, F and Bougoure, J and Guagliardo, P and Struck, U and Wild, C and Pernice, M and Raina, JB and Meibom, A and Voolstra, CR}, title = {Heat stress reduces the contribution of diazotrophs to coral holobiont nitrogen cycling.}, journal = {The ISME journal}, volume = {16}, number = {4}, pages = {1110-1118}, pmid = {34857934}, issn = {1751-7370}, support = {200021_179092//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 433042944//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 458901010//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Anthozoa/metabolism ; Coral Reefs ; Heat-Shock Response ; Nitrogen/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Symbiosis ; }, abstract = {Efficient nutrient cycling in the coral-algal symbiosis requires constant but limited nitrogen availability. Coral-associated diazotrophs, i.e., prokaryotes capable of fixing dinitrogen, may thus support productivity in a stable coral-algal symbiosis but could contribute to its breakdown when overstimulated. However, the effects of environmental conditions on diazotroph communities and their interaction with other members of the coral holobiont remain poorly understood. Here we assessed the effects of heat stress on diazotroph diversity and their contribution to holobiont nutrient cycling in the reef-building coral Stylophora pistillata from the central Red Sea. In a stable symbiotic state, we found that nitrogen fixation by coral-associated diazotrophs constitutes a source of nitrogen to the algal symbionts. Heat stress caused an increase in nitrogen fixation concomitant with a change in diazotroph communities. Yet, this additional fixed nitrogen was not assimilated by the coral tissue or the algal symbionts. We conclude that although diazotrophs may support coral holobiont functioning under low nitrogen availability, altered nutrient cycling during heat stress abates the dependence of the coral host and its algal symbionts on diazotroph-derived nitrogen. Consequently, the role of nitrogen fixation in the coral holobiont is strongly dependent on its nutritional status and varies dynamically with environmental conditions.}, }
@article {pmid34853170, year = {2021}, author = {Wolinska, KW and Vannier, N and Thiergart, T and Pickel, B and Gremmen, S and Piasecka, A and Piślewska-Bednarek, M and Nakano, RT and Belkhadir, Y and Bednarek, P and Hacquard, S}, title = {Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {49}, pages = {}, pmid = {34853170}, issn = {1091-6490}, mesh = {Arabidopsis/*metabolism/microbiology ; Arabidopsis Proteins/metabolism ; Bacteria/metabolism ; Dysbiosis/metabolism ; Fungi/metabolism ; Microbiota/genetics/physiology ; Mycoses/metabolism ; Oomycetes/metabolism ; Plant Development ; Plant Roots/*growth &amp; development/metabolism/microbiology ; Soil Microbiology ; Symbiosis/physiology ; Tryptophan/*metabolism ; }, abstract = {In nature, roots of healthy plants are colonized by multikingdom microbial communities that include bacteria, fungi, and oomycetes. A key question is how plants control the assembly of these diverse microbes in roots to maintain host-microbe homeostasis and health. Using microbiota reconstitution experiments with a set of immunocompromised Arabidopsis thaliana mutants and a multikingdom synthetic microbial community (SynCom) representative of the natural A. thaliana root microbiota, we observed that microbiota-mediated plant growth promotion was abolished in most of the tested immunocompromised mutants. Notably, more than 40% of between-genotype variation in these microbiota-induced growth differences was explained by fungal but not bacterial or oomycete load in roots. Extensive fungal overgrowth in roots and altered plant growth was evident at both vegetative and reproductive stages for a mutant impaired in the production of tryptophan-derived, specialized metabolites (cyp79b2/b3). Microbiota manipulation experiments with single- and multikingdom microbial SynComs further demonstrated that 1) the presence of fungi in the multikingdom SynCom was the direct cause of the dysbiotic phenotype in the cyp79b2/b3 mutant and 2) bacterial commensals and host tryptophan metabolism are both necessary to control fungal load, thereby promoting A. thaliana growth and survival. Our results indicate that protective activities of bacterial root commensals are as critical as the host tryptophan metabolic pathway in preventing fungal dysbiosis in the A. thaliana root endosphere.}, }
@article {pmid34821475, year = {2021}, author = {Kopprio, GA and Luyen, ND and Cuong, LH and Duc, TM and Fricke, A and Kunzmann, A and Huong, LM and Gärdes, A}, title = {Insights into the bacterial community composition of farmed Caulerpa lentillifera: A comparison between contrasting health states.}, journal = {MicrobiologyOpen}, volume = {10}, number = {6}, pages = {e1253}, doi = {10.1002/mbo3.1253}, pmid = {34821475}, issn = {2045-8827}, mesh = {Bacteria/classification ; *Bacterial Physiological Phenomena ; Caulerpa/*microbiology/physiology ; Host Microbial Interactions ; *Microbiota ; Plant Diseases/*microbiology ; }, abstract = {The bacterial communities of Caulerpa lentillifera were studied during an outbreak of an unknown disease in a sea grape farm from Vietnam. Clear differences between healthy and diseased cases were observed at the order, genus, and Operational Taxonomic Unit (OTU) level. A richer diversity was detected in the diseased thalli of C. lentillifera, as well as the dominance of the orders Flavobacteriales (phylum Bacteroidetes) and Phycisphaerales (Planctomycetes). Aquibacter, Winogradskyella, and other OTUs of the family Flavobacteriaceae were hypothesized as detrimental bacteria, this family comprises some well-known seaweed pathogens. Phycisphaera together with other Planctomycetes and Woeseia were probably saprophytes of C. lentillifera. The Rhodobacteraceae and Rhodovulum dominated the bacterial community composition of healthy C. lentillifera. The likely beneficial role of Bradyrhizobium, Paracoccus, and Brevundimonas strains on nutrient cycling and phytohormone production was discussed. The bleaching of diseased C. lentillifera might not only be associated with pathogens but also with an oxidative response. This study offers pioneering insights on the co-occurrence of C. lentillifera-attached bacteria, potential detrimental or beneficial microbes, and a baseline for understanding the C. lentillifera holobiont. Further applied and basic research is urgently needed on C. lentillifera microbiome, shotgun metagenomic, metatranscriptomic, and metabolomic studies as well as bioactivity assays are recommended.}, }
@article {pmid34820166, year = {2021}, author = {Price, DC and Brennan, JR and Wagner, NE and Egizi, AM}, title = {Comparative hologenomics of two Ixodes scapularis tick populations in New Jersey.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12313}, pmid = {34820166}, issn = {2167-8359}, abstract = {Tick-borne diseases, such as those transmitted by the blacklegged tick Ixodes scapularis, are a significant and growing public health problem in the US. There is mounting evidence that co-occurring non-pathogenic microbes can also impact tick-borne disease transmission. Shotgun metagenome sequencing enables sampling of the complete tick hologenome-the collective genomes of the tick and all of the microbial species contained therein, whether pathogenic, commensal or symbiotic. This approach simultaneously uncovers taxonomic composition and allows the detection of intraspecific genetic variation, making it a useful tool to compare spatial differences across tick populations. We evaluated this approach by comparing hologenome data from two tick samples (N = 6 ticks per location) collected at a relatively fine spatial scale, approximately 23 km apart, within a single US county. Several intriguing variants in the data between the two sites were detected, including polymorphisms in both in the tick's own mitochondrial DNA and that of a rickettsial endosymbiont. The two samples were broadly similar in terms of the microbial species present, including multiple known tick-borne pathogens (Borrelia burgdorferi, Babesia microti, and Anaplasma phagocytophilum), filarial nematodes, and Wolbachia and Babesia species. We assembled the complete genome of the rickettsial endosymbiont (most likely Rickettsia buchneri) from both populations. Our results provide further evidence for the use of shotgun metagenome sequencing as a tool to compare tick hologenomes and differentiate tick populations across localized spatial scales.}, }
@article {pmid34820163, year = {2021}, author = {Liu, S and Zhang, SM and Buddenborg, SK and Loker, ES and Bonning, BC}, title = {Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e12290}, pmid = {34820163}, issn = {2167-8359}, abstract = {Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world's most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.}, }
@article {pmid34800848, year = {2022}, author = {Cerrano, C and Giovine, M and Steindler, L}, title = {Petrosia ficiformis (Poiret, 1789): an excellent model for holobiont and biotechnological studies.}, journal = {Current opinion in biotechnology}, volume = {74}, number = {}, pages = {61-65}, doi = {10.1016/j.copbio.2021.10.022}, pmid = {34800848}, issn = {1879-0429}, mesh = {Animals ; Biotechnology ; *Petrosia ; Phylogeny ; *Porifera ; Symbiosis ; }, }
@article {pmid34798282, year = {2022}, author = {Decroës, A and Li, JM and Richardson, L and Mutasa-Gottgens, E and Lima-Mendez, G and Mahillon, M and Bragard, C and Finn, RD and Legrève, A}, title = {Metagenomics approach for Polymyxa betae genome assembly enables comparative analysis towards deciphering the intracellular parasitic lifestyle of the plasmodiophorids.}, journal = {Genomics}, volume = {114}, number = {1}, pages = {9-22}, doi = {10.1016/j.ygeno.2021.11.018}, pmid = {34798282}, issn = {1089-8646}, mesh = {*Genome, Mitochondrial ; Genomics ; Metagenomics ; *Plasmodiophorida/genetics ; }, abstract = {Genomic knowledge of the tree of life is biased to specific groups of organisms. For example, only six full genomes are currently available in the rhizaria clade. Here, we have applied metagenomic techniques enabling the assembly of the genome of Polymyxa betae (Rhizaria, Plasmodiophorida) RES F41 isolate from unpurified zoospore holobiont and comparison with the A26-41 isolate. Furthermore, the first P. betae mitochondrial genome was assembled. The two P. betae nuclear genomes were highly similar, each with just ~10.2 k predicted protein coding genes, ~3% of which were unique to each isolate. Extending genomic comparisons revealed a greater overlap with Spongospora subterranea than with Plasmodiophora brassicae, including orthologs of the mammalian cation channel sperm-associated proteins, raising some intriguing questions about zoospore physiology. This work validates our metagenomics pipeline for eukaryote genome assembly from unpurified samples and enriches plasmodiophorid genomics; providing the first full annotation of the P. betae genome.}, }
@article {pmid34788073, year = {2022}, author = {Xiang, N and Hassenrück, C and Pogoreutz, C and Rädecker, N and Simancas-Giraldo, SM and Voolstra, CR and Wild, C and Gärdes, A}, title = {Contrasting Microbiome Dynamics of Putative Denitrifying Bacteria in Two Octocoral Species Exposed to Dissolved Organic Carbon (DOC) and Warming.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {2}, pages = {e0188621}, pmid = {34788073}, issn = {1098-5336}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Coral Reefs ; Dissolved Organic Matter ; *Microbiota ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms; however, little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. Although bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift toward Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava but decreased by 1 order of magnitude in X. umbellata under excess DOC, likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes based on N availability, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. IMPORTANCE Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a 6-week exposure to excess dissolved organic carbon under concomitant warming conditions. The specific responses of denitrifier communities of the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation based on N availability in the coral holobiont.}, }
@article {pmid34765156, year = {2021}, author = {Morrissey, KL and Iveša, L and Delva, S and D'Hondt, S and Willems, A and De Clerck, O}, title = {Impacts of environmental stress on resistance and resilience of algal-associated bacterial communities.}, journal = {Ecology and evolution}, volume = {11}, number = {21}, pages = {15004-15019}, pmid = {34765156}, issn = {2045-7758}, abstract = {Algal-associated bacteria are fundamental to the ecological success of marine green macroalgae such as Caulerpa. The resistance and resilience of algal-associated microbiota to environmental stress can promote algal health and genetic adaptation to changing environments. The composition of bacterial communities has been shown to be unique to algal morphological niches. Therefore, the level of response to various environmental perturbations may in fact be different for each niche-specific community. Factorial in situ experiments were set up to investigate the effect of nutrient enrichment and temperature stress on the bacterial communities associated with Caulerpa cylindracea. Bacteria were characterized using the 16S rRNA gene, and the community compositions were compared between different parts of the algal thallus (endo-, epi-, and rhizomicrobiome). Resistance and resilience were calculated to further understand the changes of microbial composition in response to perturbations. The results of this study provide evidence that nutrient enrichment has a significant influence on the taxonomic and functional structure of the epimicrobiota, with a low community resistance index observed for both. Temperature and nutrient stress had a significant effect on the rhizomicrobiota taxonomic composition, exhibiting the lowest overall resistance to change. The functional performance of the rhizomicrobiota had low resilience to the combination of stressors, indicating potential additive effects. Interestingly, the endomicrobiota had the highest overall resistance, yet the lowest overall resilience to environmental stress. This further contributes to our understanding of algal microbiome dynamics in response to environmental changes.}, }
@article {pmid34749049, year = {2022}, author = {Thatcher, C and Høj, L and Bourne, DG}, title = {Probiotics for coral aquaculture: challenges and considerations.}, journal = {Current opinion in biotechnology}, volume = {73}, number = {}, pages = {380-386}, doi = {10.1016/j.copbio.2021.09.009}, pmid = {34749049}, issn = {1879-0429}, mesh = {Animals ; *Anthozoa/microbiology ; Aquaculture ; Climate Change ; Coral Reefs ; *Probiotics ; }, abstract = {Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.}, }
@article {pmid34737272, year = {2021}, author = {Dubé, CE and Ziegler, M and Mercière, A and Boissin, E and Planes, S and Bourmaud, CA and Voolstra, CR}, title = {Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {6402}, pmid = {34737272}, issn = {2041-1723}, mesh = {Coral Reefs ; Ecosystem ; Genotype ; Microbiota/genetics/*physiology ; }, abstract = {Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.}, }
@article {pmid34721372, year = {2021}, author = {Wale, M and Daffonchio, D and Fusi, M and Marasco, R and Garuglieri, E and Diele, K}, title = {The Importance of Larval Stages for Considering Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {770245}, pmid = {34721372}, issn = {1664-302X}, }
@article {pmid34718260, year = {2021}, author = {Banić, M and Pleško, S and Urek, M and Babić, Ž and Kardum, D}, title = {Immunosenescence, Inflammaging and Resilience: An Evolutionary Perspective of Adaptation in the Light of COVID-19 Pandemic.}, journal = {Psychiatria Danubina}, volume = {33}, number = {Suppl 4}, pages = {427-431}, pmid = {34718260}, issn = {0353-5053}, mesh = {Aged ; Aging ; *COVID-19 ; Humans ; Immunity, Innate ; *Immunosenescence ; Inflammation ; Lymphocytes ; Pandemics ; SARS-CoV-2 ; }, abstract = {The evolution of immunology enabled the study of role of innate and adaptive immunity in systems biology network of immunosenescence and inflammaging. Due to global reduction in birth rates and reduced mortality, in year 2025 there will be about 1.2 billion of people over age of sixty, worldwide. The notion that the real age is not chronological, but the biological one led to the concept of "bioage", defining the biologic reactivity and resilience, including the immune competence of an individual. A competent immune network, systemic and mucosal is intrinsic to resilience and homeostasis of the human holobiont as the unit of evolution. In elderly, the immunosenescence could be associated with higher levels of proinflammatory mediators (such as IL-6), frialty and mortality. Proi-inflammatory state in elderly is denoted as inflammaging, characterized with low-grade (sterile) inflammation, as a physiologic response to life-long antigenic stimuli. When under control, inflammaging could be regarded as an efficient defense mechanism, oposed and regulated by anti-inflammatory pathways and molecules. Immunosensecence. The emerging concepts of "individual immunobiography" and "trained immunity" speak in favour that the immunological experience during the life would shape the ability of each individual to respond to various stimuli, strongly influencing the elements of innate and adaptive immunity, including macrophages and innate lymphoid cells. Older age is one of the main risk factors for the severe clinical picture and adverse outcome of COVID-19 infection, due to immunosenscence and chronic low-grade inflammation (inflammaging), both characterizing the immune reactioin in elderly. The senescent immune system, along with the advanced process of inflammaging is prone to react with uncontrolled activation of innate immune response that leads to cytokine release syndrome, tissue damage and adverse outcome of infection. Further research is aimed to nutritional and pharmacologic (immunomodulatory) interventions to influence the process of bioaging and immunosenscence, and to modulate the reaction of elderly to infection, including the COVID-19.}, }
@article {pmid34714176, year = {2021}, author = {Czernik, PJ and Golonka, RM and Chakraborty, S and Yeoh, BS and Abokor, AA and Saha, P and Yeo, JY and Mell, B and Cheng, X and Baroi, S and Tian, Y and Patterson, AD and Joe, B and Vijay-Kumar, M and Lecka-Czernik, B}, title = {Reconstitution of the host holobiont in germ-free born male rats acutely increases bone growth and affects marrow cellular content.}, journal = {Physiological genomics}, volume = {53}, number = {12}, pages = {518-533}, pmid = {34714176}, issn = {1531-2267}, support = {R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Adipocytes/metabolism ; Animals ; Bacteria/*genetics/*metabolism ; Bone Density/physiology ; Bone Development/*physiology ; Bone Marrow Cells/*metabolism ; Cell Proliferation/physiology ; Chondrocytes/metabolism ; Coprophagia ; Dysbiosis ; Fatty Acids, Volatile/analysis/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Germ-Free Life ; Host Microbial Interactions/*genetics ; Male ; Osteogenesis/*physiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; }, abstract = {Integration of microbiota in a host begins at birth and progresses during adolescence, forming a multidirectional system of physiological interactions. Here, we present an instantaneous effect of natural, bacterial gut colonization on the acceleration of longitudinal and radial bone growth in germ-free born, 7-wk-old male rats. Changes in bone mass and structure were analyzed after 10 days following the onset of colonization through cohousing with conventional rats and revealed unprecedented acceleration of bone accrual in cortical and trabecular compartments, increased bone tissue mineral density, improved proliferation and hypertrophy of growth plate chondrocytes, bone lengthening, and preferential deposition of periosteal bone in the tibia diaphysis. In addition, the number of small in size adipocytes increased, whereas the number of megakaryocytes decreased, in the bone marrow of conventionalized germ-free rats indicating that not only bone mass but also bone marrow environment is under control of gut microbiota signaling. The changes in bone status paralleled with a positive shift in microbiota composition toward short-chain fatty acids (SCFA)-producing microbes and a considerable increase in cecal SCFA concentrations, specifically butyrate. Furthermore, reconstitution of the host holobiont increased hepatic expression of IGF-1 and its circulating levels. Elevated serum levels of 25-hydroxy vitamin D and alkaline phosphatase pointed toward an active process of bone formation. The acute stimulatory effect on bone growth occurred independently of body mass increase. Overall, the presented model of conventionalized germ-free rats could be used to study microbiota-based therapeutics for combatting dysbiosis-related bone disorders.}, }
@article {pmid34713541, year = {2022}, author = {Iltis, C and Tougeron, K and Hance, T and Louâpre, P and Foray, V}, title = {A perspective on insect-microbe holobionts facing thermal fluctuations in a climate-change context.}, journal = {Environmental microbiology}, volume = {24}, number = {1}, pages = {18-29}, doi = {10.1111/1462-2920.15826}, pmid = {34713541}, issn = {1462-2920}, mesh = {Animals ; *Climate Change ; Heat-Shock Response ; *Insecta ; Symbiosis ; Temperature ; }, abstract = {Temperature influences the ecology and evolution of insects and their symbionts by impacting each partner independently and their interactions, considering the holobiont as a primary unit of selection. There are sound data about the responses of these partnerships to constant temperatures and sporadic thermal stress (mostly heat shock). However, the current understanding of the thermal ecology of insect-microbe holobionts remains patchy because the complex thermal fluctuations (at different spatial and temporal scales) experienced by these organisms in nature have often been overlooked experimentally. This may drastically constrain our ability to predict the fate of mutualistic interactions under climate change, which will alter both mean temperatures and thermal variability. Here, we tackle down these issues by focusing on the effects of temperature fluctuations on the evolutionary ecology of insect-microbe holobionts. We propose potentially worth-investigating research avenues to (i) evaluate the relevance of theoretical concepts used to predict the biological impacts of temperature fluctuations when applied to holobionts; (ii) acknowledge the plastic (behavioural thermoregulation, physiological acclimation) and genetic responses (evolution) expressed by holobionts in fluctuating thermal environments; and (iii) explore the potential impacts of previously unconsidered patterns of temperature fluctuations on the outcomes and the dynamic of these insect-microbe associations.}, }
@article {pmid34710723, year = {2022}, author = {Varasteh, T and Tschoeke, D and Silva-Lima, AW and Thompson, C and Thompson, F}, title = {Transcriptome of the coral Mussismilia braziliensis symbiont Sargassococcus simulans.}, journal = {Marine genomics}, volume = {61}, number = {}, pages = {100912}, doi = {10.1016/j.margen.2021.100912}, pmid = {34710723}, issn = {1876-7478}, mesh = {Animals ; *Anthozoa/genetics ; Biological Transport ; Brazil ; Transcriptome ; }, abstract = {A transcriptomic profile of Sargassococcus simulans 103B3, isolated from the coral Mussismilia braziliensis in Abrolhos, Brazil, is presented. A total of 631.3 Mbp transcriptomic sequences were obtained. The transcriptomic analysis disclosed transcripts coding for enzymes relevant for holobiont health including genes involved in I. Light harvesting complex (LHC), II. Organic matter utilization and III. Oxidative stress and microbial defense (Oxidoreductases) enzymes. The isolate exhibited transcripts for uptake and utilization of a variety of carbon sources, such as sugars, oligopeptides, and amino acids by ATP-binding cassette (ABC) and tripartite ATP-independent periplasmic (TRAP) type transporters. Collectively, these enzymes indicate a mixotrophic metabolism in S. simulans with metabolic capabilities for the degradation of an array of organic carbon compounds in the coral Mussismilia and light harvesting within the low-light environments of Abrolhos.}, }
@article {pmid34709051, year = {2021}, author = {Mead, OL and Hahn, EE and Adamska, MA}, title = {Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn.}, journal = {Microbiology resource announcements}, volume = {10}, number = {43}, pages = {e0085821}, pmid = {34709051}, issn = {2576-098X}, support = {//Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; //Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; //Centre of Excellence for Coral Reef Studies, Australian Research Council (ARC Centre of Excellence for Coral Reef Studies)/ ; }, abstract = {Sponges have complex relationships with bacteria, the roles of which include food, important components of the holobiont, pathogens, and accidentally accumulated elements of the environment. Consequently, sponges are reservoirs of microbial genomes and novel compounds. Therefore, we isolated and sequenced the whole genomes of bacterial species from the calcareous sponge Sycon capricorn.}, }
@article {pmid34697892, year = {2021}, author = {Merges, D and Dal Grande, F and Greve, C and Otte, J and Schmitt, I}, title = {Virus diversity in metagenomes of a lichen symbiosis (Umbilicaria phaea): complete viral genomes, putative hosts and elevational distributions.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6637-6650}, doi = {10.1111/1462-2920.15802}, pmid = {34697892}, issn = {1462-2920}, mesh = {*Ascomycota/genetics ; *Bacteriophages/genetics ; Genome, Viral/genetics ; *Lichens/genetics/microbiology ; Metagenome ; Phylogeny ; Symbiosis ; }, abstract = {Viruses can play critical roles in symbioses by initiating horizontal gene transfer, affecting host phenotypes, or expanding their host's ecological niche. However, knowledge of viral diversity and distribution in symbiotic organisms remains elusive. Here we use deep-sequenced metagenomic DNA (PacBio Sequel II; two individuals), paired with a population genomics approach (Pool-seq; 11 populations, 550 individuals) to understand viral distributions in the lichen Umbilicaria phaea. We assess (i) viral diversity in lichen thalli, (ii) putative viral hosts (fungi, algae, bacteria) and (iii) viral distributions along two replicated elevation gradients. We identified five novel viruses, showing 28%-40% amino acid identity to known viruses. They tentatively belong to the families Caulimoviridae, Myoviridae, Podoviridae and Siphoviridae. Our analysis suggests that the Caulimovirus is associated with green algal photobionts (Trebouxia) of the lichen, and the remaining viruses with bacterial hosts. We did not detect viral sequences in the mycobiont. Caulimovirus abundance decreased with increasing elevation, a pattern reflected by a specific algal lineage hosting this virus. Bacteriophages showed population-specific patterns. Our work provides the first comprehensive insights into viruses associated with a lichen holobiont and suggests an interplay of viral hosts and environment in structuring viral distributions.}, }
@article {pmid34685796, year = {2021}, author = {Alotaibi, F and Lee, SJ and St-Arnaud, M and Hijri, M}, title = {Salix purpurea and Eleocharis obtusa Rhizospheres Harbor a Diverse Rhizospheric Bacterial Community Characterized by Hydrocarbons Degradation Potentials and Plant Growth-Promoting Properties.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {10}, pages = {}, pmid = {34685796}, issn = {2223-7747}, support = {RGPIN-2018-04178//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Phytoremediation, a method of phytomanagement using the plant holobiont to clean up polluted soils, is particularly effective for degrading organic pollutants. However, the respective contributions of host plants and their associated microbiota within the holobiont to the efficiency of phytoremediation is poorly understood. The identification of plant-associated bacteria capable of efficiently utilizing these compounds as a carbon source while stimulating plant-growth is a keystone for phytomanagement engineering. In this study, we sampled the rhizosphere and the surrounding bulk soil of Salixpurpurea and Eleocharis obusta from the site of a former petrochemical plant in Varennes, QC, Canada. Our objectives were to: (i) isolate and identify indigenous bacteria inhabiting these biotopes; (ii) assess the ability of isolated bacteria to utilize alkanes and polycyclic aromatic hydrocarbons (PAHS) as the sole carbon source, and (iii) determine the plant growth-promoting (PGP) potential of the isolates using five key traits. A total of 438 morphologically different bacterial isolates were obtained, purified, preserved and identified through PCR and 16S rRNA gene sequencing. Identified isolates represent 62 genera. Approximately, 32% of bacterial isolates were able to utilize all five different hydrocarbons compounds. Additionally, 5% of tested isolates belonging to genera Pseudomonas, Acinetobacter, Serratia, Klebsiella, Microbacterium, Bacillus and Stenotrophomonas possessed all five of the tested PGP functional traits. This culture collection of diverse, petroleum-hydrocarbon degrading bacteria, with multiple PGP traits, represents a valuable resource for future use in environmental bio- and phyto-technology applications.}, }
@article {pmid34685638, year = {2021}, author = {Kriaa, A and Jablaoui, A and Rhimi, S and Soussou, S and Mkaouar, H and Mariaule, V and Gruba, N and Gargouri, A and Maguin, E and Lesner, A and Rhimi, M}, title = {SP-1, a Serine Protease from the Gut Microbiota, Influences Colitis and Drives Intestinal Dysbiosis in Mice.}, journal = {Cells}, volume = {10}, number = {10}, pages = {}, pmid = {34685638}, issn = {2073-4409}, mesh = {Amino Acid Sequence ; Animals ; Colitis/chemically induced/*enzymology/*microbiology ; Conserved Sequence ; Dextran Sulfate ; Dysbiosis/*enzymology/*microbiology ; Feces/enzymology ; *Gastrointestinal Microbiome ; Inflammation/pathology ; Intestinal Mucosa/pathology ; Intestines/*pathology ; Kinetics ; Lactobacillus/enzymology ; Male ; Mice, Inbred C57BL ; Phylogeny ; Serine Proteases/administration &amp; dosage/chemistry/isolation &amp; purification/*metabolism ; Substrate Specificity ; Subtilisin/chemistry ; }, abstract = {Increased protease activity has been linked to the pathogenesis of IBD. While most studies have been focusing on host proteases in gut inflammation, it remains unclear how to address the potential contribution of their bacterial counterparts. In the present study, we report a functional characterization of a newly identified serine protease, SP-1, from the human gut microbiota. The serine protease repertoire of gut Clostridium was first explored, and the specificity of SP-1 was analyzed using a combinatorial chemistry method. Combining in vitro analyses and a mouse model of colitis, we show that oral administration of recombinant bacteria secreting SP-1 (i) compromises the epithelial barrier, (ii) alters the microbial community, and (ii) exacerbates colitis. These findings suggest that gut microbial protease activity may constitute a valuable contributor to IBD and could, therefore, represent a promising target for the treatment of the disease.}, }
@article {pmid34678546, year = {2021}, author = {Zhu, W and Xia, J and Ren, Y and Xie, M and Yin, H and Liu, X and Huang, J and Zhu, M and Li, X}, title = {Coastal corals during heat stress and eutrophication: A case study in Northwest Hainan coastal areas.}, journal = {Marine pollution bulletin}, volume = {173}, number = {Pt B}, pages = {113048}, doi = {10.1016/j.marpolbul.2021.113048}, pmid = {34678546}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa ; Chlorophyll A ; *Dinoflagellida ; Eutrophication ; Heat-Shock Response ; Symbiosis ; }, abstract = {This study initially investigated the coral status during the unexpected bleaching event in three coastal areas in Northwest Hainan coastal areas and analyzed changes in coral holobionts of the healthy and bleached Galaxea fascicularis. Coral coverage had declined severely, and the bleaching rate was extremely high during heat stress. The bleached corals had lower maximum photosynthetic yield, actual photosynthetic yield, zooxanthellae density, and chlorophyll a content than the healthy G. fascicularis, but there was no significant difference in protein, carbohydrate and lipid in eutrophic waters. The diversity and community composition of Symbiodiniaceae and symbiotic bacteria between healthy and bleached G. fascicularis showed no difference. Function prediction of the symbiotic bacteria revealed that the metabolism process was the main pathway of annotation. Present findings suggested that energy reserve functioning and high stability of the holobiont structure and might provide opportunities to G. fascicularis to adapt to eutrophication and heat stress.}, }
@article {pmid34674103, year = {2021}, author = {Bonthond, G and Shalygin, S and Bayer, T and Weinberger, F}, title = {Draft genome and description of Waterburya agarophytonicola gen. nov. sp. nov. (Pleurocapsales, Cyanobacteria): a seaweed symbiont.}, journal = {Antonie van Leeuwenhoek}, volume = {114}, number = {12}, pages = {2189-2203}, pmid = {34674103}, issn = {1572-9699}, support = {WE2700/5-1//Deutsche Forschungsgemeinshaft/ ; BA5508/2-1//Deutsche Forschungsgemeinshaft/ ; }, mesh = {*Cyanobacteria/genetics ; DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S ; *Rhodophyta ; *Seaweed ; Sequence Analysis, DNA ; }, abstract = {This work introduces Waterburya agarophytonicola Bonthond and Shalygin gen. nov., sp. nov, a baeocyte producing cyanobacterium that was isolated from the rhodophyte Agarophyton vermiculophyllum (Ohmi) Gurgel et al., an invasive seaweed that has spread across the northern hemisphere. The new species genome reveals a diverse repertoire of chemotaxis and adhesion related genes, including genes coding for type IV pili assembly proteins and a high number of genes coding for filamentous hemagglutinin family (FHA) proteins. Among a genetic basis for the synthesis of siderophores, carotenoids and numerous vitamins, W. agarophytonicola is potentially capable of producing cobalamin (vitamin B12), for which A. vermiculophyllum is an auxotroph. With a taxonomic description of the genus and species and a draft genome, this study provides as a basis for future research, to uncover the nature of this geographically independent association between seaweed and cyanobiont.}, }
@article {pmid34659277, year = {2021}, author = {Bharadwaj, R and Noceda, C and Mohanapriya, G and Kumar, SR and Thiers, KLL and Costa, JH and Macedo, ES and Kumari, A and Gupta, KJ and Srivastava, S and Adholeya, A and Oliveira, M and Velada, I and Sircar, D and Sathishkumar, R and Arnholdt-Schmitt, B}, title = {Adaptive Reprogramming During Early Seed Germination Requires Temporarily Enhanced Fermentation-A Critical Role for Alternative Oxidase Regulation That Concerns Also Microbiota Effectiveness.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {686274}, pmid = {34659277}, issn = {1664-462X}, abstract = {Plants respond to environmental cues via adaptive cell reprogramming that can affect whole plant and ecosystem functionality. Microbiota constitutes part of the inner and outer environment of the plant. This Umwelt underlies steady dynamics, due to complex local and global biotic and abiotic changes. Hence, adaptive plant holobiont responses are crucial for continuous metabolic adjustment at the systems level. Plants require oxygen-dependent respiration for energy-dependent adaptive morphology, such as germination, root and shoot growth, and formation of adventitious, clonal, and reproductive organs, fruits, and seeds. Fermentative paths can help in acclimation and, to our view, the role of alternative oxidase (AOX) in coordinating complex metabolic and physiological adjustments is underestimated. Cellular levels of sucrose are an important sensor of environmental stress. We explored the role of exogenous sucrose and its interplay with AOX during early seed germination. We found that sucrose-dependent initiation of fermentation during the first 12 h after imbibition (HAI) was beneficial to germination. However, parallel upregulated AOX expression was essential to control negative effects by prolonged sucrose treatment. Early downregulated AOX activity until 12 HAI improved germination efficiency in the absence of sucrose but suppressed early germination in its presence. The results also suggest that seeds inoculated with arbuscular mycorrhizal fungi (AMF) can buffer sucrose stress during germination to restore normal respiration more efficiently. Following this approach, we propose a simple method to identify organic seeds and low-cost on-farm perspectives for early identifying disease tolerance, predicting plant holobiont behavior, and improving germination. Furthermore, the research strengthens the view that AOX can serve as a powerful functional marker source for seed hologenomes.}, }
@article {pmid34641951, year = {2021}, author = {Paix, B and Layglon, N and Le Poupon, C and D'Onofrio, S and Misson, B and Garnier, C and Culioli, G and Briand, JF}, title = {Integration of spatio-temporal variations of surface metabolomes and epibacterial communities highlights the importance of copper stress as a major factor shaping host-microbiota interactions within a Mediterranean seaweed holobiont.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {201}, pmid = {34641951}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Copper ; Metabolome ; *Microbiota/genetics ; *Seaweed ; }, abstract = {BACKGROUND: Although considered as holobionts, macroalgae and their surface microbiota share intimate interactions that are still poorly understood. Little is known on the effect of environmental parameters on the close relationships between the host and its surface-associated microbiota, and even more in a context of coastal pollutions. Therefore, the main objective of this study was to decipher the impact of local environmental parameters, especially trace metal concentrations, on an algal holobiont dynamics using the Phaeophyta Taonia atomaria as a model. Through a multidisciplinary multi-omics approach combining metabarcoding and untargeted LC-MS-based metabolomics, the epibacterial communities and the surface metabolome of T. atomaria were monitored along a spatio-temporal gradient in the bay of Toulon (Northwestern Mediterranean coast) and its surrounding. Indeed, this geographical area displays a well-described trace metal gradient particularly relevant to investigate the effect of such pollutants on marine organisms.<br><br>RESULTS: Epibacterial communities of T. atomaria exhibited a high specificity whatever the five environmentally contrasted collecting sites investigated on the NW Mediterranean coast. By integrating metabarcoding and metabolomics analyses, the holobiont dynamics varied as a whole. During the occurrence period of T. atomaria, epibacterial densities and α-diversity increased while the relative proportion of core communities decreased. Pioneer bacterial colonizers constituted a large part of the specific and core taxa, and their decrease might be linked to biofilm maturation through time. Then, the temporal increase of the Roseobacter was proposed to result from the higher temperature conditions, but also the increased production of dimethylsulfoniopropionate (DMSP) at the algal surface which could constitute of the source of carbon and sulfur for the catabolism pathways of these taxa. Finally, as a major result of this study, copper concentration constituted a key factor shaping the holobiont system. Thus, the higher expression of carotenoids suggested an oxidative stress which might result from an adaptation of the algal surface metabolome to high copper levels. In turn, this change in the surface metabolome composition could result in the selection of particular epibacterial taxa.<br><br>CONCLUSION: We showed that associated epibacterial communities were highly specific to the algal host and that the holobiont dynamics varied as a whole. While temperature increase was confirmed to be one of the main parameters associated to Taonia dynamics, the originality of this study was highlighting copper-stress as a major driver of seaweed-epibacterial interactions. In a context of global change, this study brought new insights on the dynamics of a Mediterranean algal holobiont submitted to heavy anthropic pressures. Video abstract.}, }
@article {pmid34641725, year = {2021}, author = {Muller, EM and Dungan, AM and Million, WC and Eaton, KR and Petrik, C and Bartels, E and Hall, ER and Kenkel, CD}, title = {Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1960}, pages = {20210923}, pmid = {34641725}, issn = {1471-2954}, mesh = {Animals ; *Anthozoa/genetics ; *Climate Change ; Coral Reefs ; Ecosystem ; Endangered Species ; }, abstract = {Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.}, }
@article {pmid34638430, year = {2021}, author = {Oldenburg, M and Rüchel, N and Janssen, S and Borkhardt, A and Gössling, KL}, title = {The Microbiome in Childhood Acute Lymphoblastic Leukemia.}, journal = {Cancers}, volume = {13}, number = {19}, pages = {}, pmid = {34638430}, issn = {2072-6694}, support = {428917761//Deutsche Forschungsgemeinschaft/ ; 2020-24//Research Committee of the Heinrich Heine University Duesseldorf/ ; }, abstract = {For almost 30 years, the term "holobiont" has referred to an ecological unit where a host (e.g., human) and all species living in or around it are considered together. The concept highlights the complex interactions between the host and the other species, which, if disturbed may lead to disease and premature aging. Specifically, the impact of microbiome alterations on the etiology of acute lymphoblastic leukemia (ALL) in children is not fully understood, but has been the focus of much research in recent years. In ALL patients, significant reductions in microbiome diversity are already observable at disease onset. It remains unclear whether such alterations at diagnosis are etiologically linked with leukemogenesis or simply due to immunological alteration preceding ALL onset. Regardless, all chemotherapeutic treatment regimens severely affect the microbiome, accompanied by severe side effects, including mucositis, systemic inflammation, and infection. In particular, dominance of Enterococcaceae is predictive of infections during chemotherapy. Long-term dysbiosis, like depletion of Faecalibacterium, has been observed in ALL survivors. Modulation of the microbiome (e.g., by fecal microbiota transplant, probiotics, or prebiotics) is currently being researched for potential protective effects. Herein, we review the latest microbiome studies in pediatric ALL patients.}, }
@article {pmid34612522, year = {2022}, author = {Kaniewska, P and Sampayo, EM}, title = {Macro- and micro-scale adaptations allow distinct Stylophora pistillata-symbiodiniaceae holobionts to optimize performance across a broad light habitat.}, journal = {Journal of phycology}, volume = {58}, number = {1}, pages = {55-70}, doi = {10.1111/jpy.13215}, pmid = {34612522}, issn = {1529-8817}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida/physiology ; Ecosystem ; Symbiosis/physiology ; }, abstract = {In sessile organisms, phenotypic plasticity represents an important strategy for dealing with environmental variability. Here we test if phenotypic plasticity enables the common coral Stylophora pistillata to occupy a broad niche. We find clear differences in the photo-physiology of four putative species of photosynthetic dinoflagellate symbionts associated with the coral S. pistillata, namely, Cladocopium 'C35a', 'C79', 'C78a' and 'C8a'. Coral phenotypic responses were also tightly linked to symbiont identity. Corals with Cladocopium 'C8a' have more "open" macro-morphology compared to colonies associating with depth-restricted Cladocopium 'C35a' or 'C78a' in the same shallow water habitat. Corals with Cladocopium 'C8a' had 40 to 60% lower symbiont cell densities compared to other holobionts but were more efficient at acclimating over a range of light levels, with clear mechanisms to dissipate excess light energy. This holobiont contains host-based green fluorescent pigments, increased concentrations of symbiont-based mycosporine amino acids, and xanthophyll cycling in high light habitats. Photosynthetic efficiency was also adjusted over the light habitat. In contrast, limited micro-scale responses were observed between three depth-restricted symbionts: Cladocopium 'C79', 'C35a', and 'C78a'. To optimize light levels reaching the photosynthetic unit, these colonies rely on a more closed macro-morphology under high light levels, which reduces incident light levels by up to 43%, and higher symbiont densities . Our results show that distinct macro- and micro-scale adaptations lead to functional differences between four distinct S. pistillata holobionts, allowing them to co-exist by filling specific niches on a small, but environmentally diverse, spatial scale. Key index words: Light, Symbiodiniaceae, coral, pigments, Stylophora pistillata, ITS2, phenotypic plasticity, niche diversification.}, }
@article {pmid34597574, year = {2022}, author = {Zhang, Y and Ip, JC and Xie, JY and Yeung, YH and Sun, Y and Qiu, JW}, title = {Host-symbiont transcriptomic changes during natural bleaching and recovery in the leaf coral Pavona decussata.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150656}, doi = {10.1016/j.scitotenv.2021.150656}, pmid = {34597574}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa/genetics ; Chlorophyll A ; Coral Reefs ; Plant Leaves ; Symbiosis ; Transcriptome ; }, abstract = {Coral bleaching has become a major threat to coral reefs worldwide, but for most coral species little is known about their resilience to environmental changes. We aimed to understand the gene expressional regulation underlying natural bleaching and recovery in Pavona decussata, a dominant species of scleractinian coral in the northern South China Sea. Analyzing samples collected in 2017 from the field revealed distinct zooxanthellae density, chlorophyll a concentration and transcriptomic signatures corresponding to changes in health conditions of the coral holobiont. In the host, normal-looking tissues of partially bleached colonies were frontloaded with stress responsive genes, as indicated by upregulation of immune defense, response to endoplasmic reticulum, and oxidative stress genes. Bleaching was characterized by upregulation of apoptosis-related genes which could cause a reduction in algal symbionts, and downregulation of genes involved in stress responses and metabolic processes. The transcription factors stat5b and irf1 played key roles in bleaching by regulating immune and apoptosis pathways. Recovery from bleaching was characterized by enrichment of pathways involved in mitosis, DNA replication, and recombination for tissue repairing, as well as restoration of energy and metabolism. In the symbionts, bleaching corresponded to imbalance in photosystems I and II activities which enhanced oxidative stress and limited energy production and nutrient assimilation. Overall, our study revealed distinct gene expressional profiles and regulation in the different phases of the bleaching and recovery process, and provided new insight into the molecular mechanisms underlying the holobiont's resilience that may determine the species' fate in response to global and regional environmental changes.}, }
@article {pmid34593802, year = {2021}, author = {Avila-Magaña, V and Kamel, B and DeSalvo, M and Gómez-Campo, K and Enríquez, S and Kitano, H and Rohlfs, RV and Iglesias-Prieto, R and Medina, M}, title = {Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {5731}, pmid = {34593802}, issn = {2041-1723}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/*microbiology/physiology ; Caribbean Region ; Coral Reefs ; Dinoflagellida/*genetics/metabolism ; Evolution, Molecular ; *Heat-Shock Response ; Metabolic Networks and Pathways/genetics ; Microbiota/*genetics ; Photosynthesis/genetics ; Phylogeny ; Symbiosis/genetics ; }, abstract = {As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.}, }
@article {pmid34582942, year = {2022}, author = {Ravindran, C and Raveendran, HP and Irudayarajan, L}, title = {Ciliated protozoan occurrence and association in the pathogenesis of coral disease.}, journal = {Microbial pathogenesis}, volume = {162}, number = {}, pages = {105211}, doi = {10.1016/j.micpath.2021.105211}, pmid = {34582942}, issn = {1096-1208}, mesh = {Animals ; *Anthozoa ; *Ciliophora ; }, abstract = {Various microbial infections have significantly contributed to disease progression leading to the mortality of corals. However, the holobiont and the external surfaces of coral, including the secreted mucus, provide a varied microenvironment that attracts ciliates based on their feeding preferences. Besides, some ciliates (e.g., Philasterine scuticociliate) may enter through the injuries or lesions on corals or through their indirect interactions with other types of microbes that influence coral health. Thus, ciliates occurrence and association are described with 12 different diseases worldwide. White syndrome disease lesions have diverse ciliate associations, and higher ciliate diversity was observed with diseased genera Acropora. Also, it was described, about sixteen ciliate species ingest coral Symbiodiniaceae and histophagous ciliates for coral tissue loss as secondary invaders. However, the ciliates nature of association with the coral disease remains unclear for primary or opportunistic secondary pathogenicity. Herein, we explore the urgent need to understand the complex interactions of ciliates in coral health.}, }
@article {pmid34582868, year = {2022}, author = {Kenigsberg, C and Titelboim, D and Ashckenazi-Polivoda, S and Herut, B and Kucera, M and Zukerman, Y and Hyams-Kaphzan, O and Almogi-Labin, A and Abramovich, S}, title = {The combined effects of rising temperature and salinity may halt the future proliferation of symbiont-bearing foraminifera as ecosystem engineers.}, journal = {The Science of the total environment}, volume = {806}, number = {Pt 2}, pages = {150581}, doi = {10.1016/j.scitotenv.2021.150581}, pmid = {34582868}, issn = {1879-1026}, mesh = {Cell Proliferation ; Ecosystem ; *Foraminifera ; Salinity ; Seawater ; Temperature ; }, abstract = {Rising sea surface temperatures and extreme heat waves are affecting symbiont-bearing tropical calcifiers such as corals and Large Benthic Foraminifera (LBF). In many ecosystems, parallel to warming, global change unleashes a host of additional changes to the marine environment, and the combined effect of such multiple stressors may be far greater than those of temperature alone. One such additional stressor, positively correlated to temperature in evaporation-dominated shallow-water settings is rising salinity. Here we used laboratory culture experiments to evaluate the combined thermohaline tolerance of one of the most common LBF species and carbonate producer, Amphistegina lobifera. The experiments were done under ambient (39 psu) and modified (30, 45, 50 psu) salinities and at optimum (25 °C) and warm temperatures (32 °C). Calcification of the A. lobifera holobiont was evaluated by measuring alkalinity loss in the culturing seawater, as an indication of carbonate ion uptake. The vitality of the symbionts was determined by monitoring pigment loss of the holobiont and their photosynthetic performances by measuring dissolved oxygen. We further evaluated the growth of Peneroplis (P. pertusus and P. planatus), a Rhodophyta bearing LBF, which is known to tolerate high temperatures, under elevated salinities. The results show that the A. lobifera holobiont exhibits optimal performance at 39 psu and 25 °C, and its growth is significantly reduced upon exposure to 30, 45, 50 psu and under all 32 °C treatments. Salinity and temperature exhibit a significant interaction, with synergic effects observed in most treatments. Our results confirm that Peneroplis has a higher tolerance to elevated temperature and salinity compared to A. lobifera, implying that a further increase of salinity and temperatures may result in a regime shift from Amphistegina- to Peneroplis-dominated assemblages.}, }
@article {pmid34576867, year = {2021}, author = {Liang, J and Deng, C and Yu, K and Ge, R and Xu, Y and Qin, Z and Chen, B and Wang, Y and Su, H and Huang, X and Huang, W and Wang, G and Gong, S}, title = {Cross-Linked Regulation of Coral-Associated Dinoflagellates and Bacteria in Pocillopora sp. during High-Temperature Stress and Recovery.}, journal = {Microorganisms}, volume = {9}, number = {9}, pages = {}, pmid = {34576867}, issn = {2076-2607}, support = {42090041, 41666005, 42030502 and 41866006//National Natural Science Foundation of China/ ; }, abstract = {As the problem of ocean warming worsens, the environmental adaptation potential of symbiotic Symbiodiniaceae and bacteria is directly related to the future and fate of corals. This study aimed to analyse the comprehensive community dynamics and physiology of these two groups of organisms in the coral Pocillopora sp. through indoor simulations of heat stress (which involved manually adjusting the temperature between both 26 °C and 34 °C). Heat treatment (≥30 °C) significantly reduced the abundance of Symbiodiniaceae and bacteria by more than 70%. After the temperature was returned to 26 °C for one month, the Symbiodiniaceae density was still low, while the absolute number of bacteria quickly recovered to 55% of that of the control. At this time point, the Fv/Fm value rose to 91% of the pretemperature value. The content of chlorophyll b associated with Cyanobacteria increased by 50% compared with that under the control conditions. Moreover, analysis of the Symbiodiniaceae subclade composition suggested that the relative abundance of C1c.C45, C1, and C1ca increased during heat treatment, indicating that they might constitute heat-resistant subgroups. We suggest that the increase in the absolute number of bacteria during the recovery period could be an important indicator of coral holobiont recovery after heat stress. This study provides insight into the cross-linked regulation of key symbiotic microbes in the coral Pocillopora sp. during high-temperature stress and recovery and provides a scientific basis for exploring the mechanism underlying coral adaptation to global warming.}, }
@article {pmid34572284, year = {2021}, author = {Dietert, RR}, title = {Microbiome First Medicine in Health and Safety.}, journal = {Biomedicines}, volume = {9}, number = {9}, pages = {}, pmid = {34572284}, issn = {2227-9059}, abstract = {Microbiome First Medicine is a suggested 21st century healthcare paradigm that prioritizes the entire human, the human superorganism, beginning with the microbiome. To date, much of medicine has protected and treated patients as if they were a single species. This has resulted in unintended damage to the microbiome and an epidemic of chronic disorders [e.g., noncommunicable diseases and conditions (NCDs)]. Along with NCDs came loss of colonization resistance, increased susceptibility to infectious diseases, and increasing multimorbidity and polypharmacy over the life course. To move toward sustainable healthcare, the human microbiome needs to be front and center. This paper presents microbiome-human physiology from the view of systems biology regulation. It also details the ongoing NCD epidemic including the role of existing drugs and other factors that damage the human microbiome. Examples are provided for two entryway NCDs, asthma and obesity, regarding their extensive network of comorbid NCDs. Finally, the challenges of ensuring safety for the microbiome are detailed. Under Microbiome-First Medicine and considering the importance of keystone bacteria and critical windows of development, changes in even a few microbiota-prioritized medical decisions could make a significant difference in health across the life course.}, }
@article {pmid34570392, year = {2021}, author = {Florez, JZ and Camus, C and Hengst, MB and Buschmann, AH}, title = {A mesocosm study on bacteria-kelp interactions: Importance of nitrogen availability and kelp genetics.}, journal = {Journal of phycology}, volume = {57}, number = {6}, pages = {1777-1791}, doi = {10.1111/jpy.13213}, pmid = {34570392}, issn = {1529-8817}, mesh = {Bacteria/genetics ; *Kelp ; *Macrocystis ; Nitrogen ; }, abstract = {Macroalgal holobiont studies involve understanding interactions between the host, its microbiota, and the environment. We analyzed the effect of bacteria-kelp interactions on phenotypic responses of two genetically distinct populations of giant kelp, Macrocystis pyrifera (north and south), exposed to different nitrogen (N) concentrations. In co-culture experiments with different N concentration treatments, we evaluated kelp growth responses and changes in three specific molecular markers associated with the N cycle, both in epiphytic bacteria (relative abundance of nrfA-gene: cytochrome c nitrite reductase) and macroalgae (expression of NR-gene: nitrate reductase; GluSyn-gene: glutamate synthase). Both kelp populations responded differently to N limitation, with M. pyrifera-south sporophytes having a lower specific growth rate (SGR) under N-limiting conditions than the northern population; M. pyrifera-north sporophytes showed no significant differences in SGR when exposed to low-N and high-N concentrations. This corresponded to a higher GluSyn-gene expression in the M. pyrifera-north sporophytes and the co-occurrence of specific nrfA bacterial taxa. These bacteria may increase ammonium availability under low-N concentrations, allowing M. pyrifera-north to optimize nutrient assimilation by increasing the expression of GluSyn. We conclude that bacteria-kelp interactions are important in enhancing kelp growth rates under low N availability, although this effect may be regulated by the genetic background of kelp populations.}, }
@article {pmid34569131, year = {2022}, author = {Oberemok, V and Laikova, K and Golovkin, I and Kryukov, L and Kamenetsky-Goldstein, R}, title = {Biotechnology of virus eradication and plant vaccination in phytobiome context.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {24}, number = {1}, pages = {3-8}, doi = {10.1111/plb.13338}, pmid = {34569131}, issn = {1438-8677}, support = {2019-220-07-5322//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Biotechnology ; Crops, Agricultural ; Plant Diseases ; *Plant Viruses ; Vaccination ; }, abstract = {A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.}, }
@article {pmid34561754, year = {2021}, author = {Varasteh, T and Salazar, V and Tschoeke, D and Francini-Filho, RB and Swings, J and Garcia, G and Thompson, CC and Thompson, FL}, title = {Breviolum and Cladocopium Are Dominant Among Symbiodiniaceae of the Coral Holobiont Madracis decactis.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, pmid = {34561754}, issn = {1432-184X}, abstract = {The scleractinian reef building coral Madracis decactis is a cosmopolitan species. Understanding host-symbiont associations is critical for assessing coral's habitat requirements and its response to environmental changes. In this study, we performed a fine grained phylogenetic analyses of Symbiodiniaceae associated with Madracis in two locations in the Southwest Atlantic Ocean (Abrolhos Bank and St. Peter and St. Paul Archipelago). Previous studies have argued that Madracis is a specialist coral, with colonies harboring a single symbiont from the genus Breviolum (formerly clade B). However, these previous studies have not precisely addressed if Madracis is colonized by several types of Symbiodiniaceae simultaneously or whether this coral is a specialist. The hypothesis that Madracis is a generalist coral host was evaluated in the present study. A total of 1.9 million reads of ITS2 nuclear ribosomal DNA were obtained by Illumina MiSeq sequencing. While Symbiodiniaceae ITS2 sequences between two sampling depths were almost entirely (62%) from the genus Breviolum (formerly clade B), shallow (10-15 m) populations in Abrolhos had a greater diversity of ITS2 sequences in comparison to deeper (25-35 m) populations of St. Peter and St. Paul Archipelago. Cladocopium (formerly clade C) and Symbiodinium (formerly clade A) were also found in Abrolhos. A single Madracis colony can host different symbiont types with > 30 Symbiodiniaceae ITS2-type profiles. Abrolhos corals presented a higher photosynthetic potential as a possible result of co-occurrence of multiple Symbiodiniaceae in a single coral colony. Multiple genera/clades of Symbiodiniaceae possibly confer coral hosts with broader environmental tolerance and ability to occupy diverse or changing habitats.}, }
@article {pmid34519538, year = {2021}, author = {Waterworth, SC and Parker-Nance, S and Kwan, JC and Dorrington, RA}, title = {Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.}, journal = {mBio}, volume = {12}, number = {5}, pages = {e0157721}, pmid = {34519538}, issn = {2150-7511}, mesh = {Animals ; Bacteria/classification/*genetics ; *Genomics ; *Host Specificity ; Microbiota ; Phylogeny ; Porifera/*microbiology ; RNA, Ribosomal, 16S ; Seawater/microbiology ; *Symbiosis ; }, abstract = {The fossil record indicates that the earliest evidence of extant marine sponges (phylum Porifera) existed during the Cambrian explosion and that their symbiosis with microbes may have begun in their extinct ancestors during the Precambrian period. Many symbionts have adapted to their sponge host, where they perform specific, specialized functions. There are also widely distributed bacterial taxa such as Poribacteria, SAUL, and Tethybacterales that are found in a broad range of invertebrate hosts. Here, we added 11 new genomes to the Tethybacterales order, identified a novel family, and show that functional potential differs between the three Tethybacterales families. We compare the Tethybacterales with the well-characterized Entoporibacteria and show that these symbionts appear to preferentially associate with low-microbial abundance (LMA) and high-microbial abundance (HMA) sponges, respectively. Within these sponges, we show that these symbionts likely perform distinct functions and may have undergone multiple association events, rather than a single association event followed by coevolution. IMPORTANCE Marine sponges often form symbiotic relationships with bacteria that fulfil a specific need within the sponge holobiont, and these symbionts are often conserved within a narrow range of related taxa. To date, there exist only three known bacterial taxa (Entoporibacteria, SAUL, and Tethybacterales) that are globally distributed and found in a broad range of sponge hosts, and little is known about the latter two. We show that the functional potential of broad-host range symbionts is conserved at a family level and that these symbionts have been acquired several times over evolutionary history. Finally, it appears that the Entoporibacteria are associated primarily with high-microbial abundance sponges, while the Tethybacterales associate with low-microbial abundance sponges.}, }
@article {pmid34504670, year = {2021}, author = {Fernández-González, AJ and Ramírez-Tejero, JA and Nevado-Berzosa, MP and Luque, F and Fernández-López, M and Mercado-Blanco, J}, title = {Coupling the endophytic microbiome with the host transcriptome in olive roots.}, journal = {Computational and structural biotechnology journal}, volume = {19}, number = {}, pages = {4777-4789}, pmid = {34504670}, issn = {2001-0370}, abstract = {The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.}, }
@article {pmid34495983, year = {2021}, author = {Nobre, T}, title = {Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: Two new symbiont haplotypes in the Mediterranean basin.}, journal = {PloS one}, volume = {16}, number = {9}, pages = {e0256284}, pmid = {34495983}, issn = {1932-6203}, mesh = {Animals ; DNA, Bacterial/genetics ; DNA, Mitochondrial/genetics ; Erwinia/*physiology ; Haplotypes ; Mediterranean Region ; Phylogeny ; Symbiosis ; Tephritidae/*microbiology/physiology ; }, abstract = {The olive fruit fly, specialized to become monophagous during several life stages, remains the most important olive tree pest with high direct production losses, but also affecting the quality, composition, and inherent properties of the olives. Thought to have originated in Africa is nowadays present wherever olive groves are grown. The olive fruit fly evolved to harbor a vertically transmitted and obligate bacterial symbiont -Candidatus Erwinia dacicola- leading thus to a tight evolutionary history between olive tree, fruit fly and obligate, vertical transmitted symbiotic bacterium. Considering this linkage, the genetic diversity (at a 16S fragment) of this obligate symbiont was added in the understanding of the distribution pattern of the holobiont at nine locations throughout four countries in the Mediterranean Basin. This was complemented with mitochondrial (four mtDNA fragments) and nuclear (ten microsatellites) data of the host. We focused on the previously established Iberian cluster for the B. oleae structure and hypothesised that the Tunisian samples would fall into a differentiated cluster. From the host point of view, we were unable to confirm this hypothesis. Looking at the symbiont, however, two new 16S haplotypes were found exclusively in the populations from Tunisia. This finding is discussed in the frame of host-symbiont specificity and transmission mode. To understand olive fruit fly population diversity and dispersion, the dynamics of the symbiont also needs to be taken into consideration, as it enables the fly to, so efficiently and uniquely, exploit the olive fruit resource.}, }
@article {pmid34490980, year = {2021}, author = {Paix, B and Potin, P and Schires, G and Le Poupon, C and Misson, B and Leblanc, C and Culioli, G and Briand, JF}, title = {Synergistic effects of temperature and light affect the relationship between Taonia atomaria and its epibacterial community: a controlled conditions study.}, journal = {Environmental microbiology}, volume = {23}, number = {11}, pages = {6777-6797}, doi = {10.1111/1462-2920.15758}, pmid = {34490980}, issn = {1462-2920}, mesh = {Bacteria/genetics ; *Microbiota ; *Phaeophyta ; *Seaweed/microbiology ; Temperature ; }, abstract = {In the context of global warming, this study aimed to assess the effect of temperature and irradiance on the macroalgal Taonia atomaria holobiont dynamics. We developed an experimental set-up using aquaria supplied by natural seawater with three temperatures combined with three irradiances. The holobiont response was monitored over 14 days using a multi-omics approach coupling algal surface metabolomics and metabarcoding. Both temperature and irradiance appeared to shape the microbiota and the surface metabolome, but with a distinct temporality. Epibacterial community first changed according to temperature, and later in relation to irradiance, while the opposite occurred for the surface metabolome. An increased temperature revealed a decreasing richness of the epiphytic community together with an increase of several bacterial taxa. Irradiance changes appeared to quickly impact surface metabolites production linked with the algal host photosynthesis (e.g. mannitol, fucoxanthin, dimethylsulfoniopropionate), which was hypothesized to explain modifications of the structure of the epiphytic community. Algal host may also directly adapt its surface metabolome to changing temperature with time (e.g. lipids content) and also in response to changing microbiota (e.g. chemical defences). Finally, this study brought new insights highlighting complex direct and indirect responses of seaweeds and their associated microbiota under changing environments.}, }
@article {pmid34490977, year = {2021}, author = {Marasco, R and Fusi, M and Rolli, E and Ettoumi, B and Tambone, F and Borin, S and Ouzari, HI and Boudabous, A and Sorlini, C and Cherif, A and Adani, F and Daffonchio, D}, title = {Aridity modulates belowground bacterial community dynamics in olive tree.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {6275-6291}, doi = {10.1111/1462-2920.15764}, pmid = {34490977}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Desert Climate ; *Ecosystem ; *Olea ; Soil ; Soil Microbiology ; }, abstract = {Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.}, }
@article {pmid34481401, year = {2022}, author = {Ahmed, T and Noman, M and Rizwan, M and Ali, S and Ijaz, U and Nazir, MM and ALHaithloul, HAS and Alghanem, SM and Abdulmajeed, AM and Bin Li, }, title = {Green molybdenum nanoparticles-mediated bio-stimulation of Bacillus sp. strain ZH16 improved the wheat growth by managing in planta nutrients supply, ionic homeostasis and arsenic accumulation.}, journal = {Journal of hazardous materials}, volume = {423}, number = {Pt A}, pages = {127024}, doi = {10.1016/j.jhazmat.2021.127024}, pmid = {34481401}, issn = {1873-3336}, mesh = {*Arsenic/toxicity ; *Bacillus ; Homeostasis ; Molybdenum ; *Nanoparticles ; Nutrients ; Plant Roots ; Soil Microbiology ; Triticum ; }, abstract = {The present work mechanistically addressed the problem of arsenic (As) contamination in agricultural soils by using locally isolated Bacillus sp. strain ZH16 and biogenic molybdenum nanoparticles (MoNPs) simultaneously for the first time. The interactions of MoNPs with strain ZH16 and ZH16-inoculated wheat plants were examined under As non-spiked and spiked conditions. The biogenic MoNPs showed efficient biocompatibility with strain ZH16 by promoting indole-3-acetic acid synthesis, phosphate solubilization and ACC deaminase activity without and with As stress. The results from greenhouse experiment revealed that co-application of biogenic MoNPs and bacterial strain ZH16 significantly promoted the morphological parameters, nutrients content and ionic balance of wheat plants under normal and As spiked conditions. Furthermore, combining the bacterial strain ZH16 with biogenic MoNPs dramatically reduced As translocation in plants (30.3%) as compared to ZH16-inoculated wheat plants. Conclusively, our results elucidate the importance of synergistic application of plant growth promoting rhizobacteria (PGPR) and biogenic MoNPs to counteract global food safety issues in a sustainable manner. The biogenic NPs could serve as stabilizing agent for PGPR by facilitating their colonization in plant holobiont regardless of environmental conditions. These novel advancements will provide new insights into nano-oriented PGPR research in the agricultural sector.}, }
@article {pmid34479653, year = {2021}, author = {Filek, K and Trotta, A and Gračan, R and Di Bello, A and Corrente, M and Bosak, S}, title = {Characterization of oral and cloacal microbial communities of wild and rehabilitated loggerhead sea turtles (Caretta caretta).}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {59}, pmid = {34479653}, issn = {2524-4671}, support = {UIP-2017-05-5635//Hrvatska Zaklada za Znanost/ ; }, abstract = {BACKGROUND: Microbial communities of wild animals are being increasingly investigated to provide information about the hosts' biology and promote conservation. Loggerhead sea turtles (Caretta caretta) are a keystone species in marine ecosystems and are considered vulnerable in the IUCN Red List, which led to growing efforts in sea turtle conservation by rescue centers around the world. Understanding the microbial communities of sea turtles in the wild and how affected they are by captivity, is one of the stepping stones in improving the conservation efforts. Describing oral and cloacal microbiota of wild animals could shed light on the previously unknown aspects of sea turtle holobiont biology, ecology, and contribute to best practices for husbandry conditions.<br><br>RESULTS: We describe the oral and cloacal microbiota of Mediterranean loggerhead sea turtles by 16S rRNA gene sequencing to compare the microbial communities of wild versus turtles in, or after, rehabilitation at the Adriatic Sea rescue centers and clinics. Our results show that the oral microbiota is more sensitive to environmental shifts than the cloacal microbiota, and that it does retain a portion of microbial taxa regardless of the shift from the wild and into rehabilitation. Additionally, Proteobacteria and Bacteroidetes dominated oral and cloacal microbiota, while Kiritimatiellaeota were abundant in cloacal samples. Unclassified reads were abundant in the aforementioned groups, which indicates high incidence of yet undiscovered bacteria of the marine reptile microbial communities.<br><br>CONCLUSIONS: We provide the first insights into the oral microbial communities of wild and rehabilitated loggerhead sea turtles, and establish a framework for quick and non-invasive sampling of oral and cloacal microbial communities, useful for the expansion of the sample collection in wild loggerhead sea turtles. Finally, our investigation of effects of captivity on the gut-associated microbial community provides a baseline for studying the impact of husbandry conditions on turtles' health and survival upon their return to the wild.}, }
@article {pmid34473860, year = {2021}, author = {Meunier, V and Geissler, L and Bonnet, S and Rädecker, N and Perna, G and Grosso, O and Lambert, C and Rodolfo-Metalpa, R and Voolstra, CR and Houlbrèque, F}, title = {Microbes support enhanced nitrogen requirements of coral holobionts in a high CO2 environment.}, journal = {Molecular ecology}, volume = {30}, number = {22}, pages = {5888-5899}, doi = {10.1111/mec.16163}, pmid = {34473860}, issn = {1365-294X}, support = {ANR15CE02-0006-01//French National Research Agency (ANR/ ; 1598//Fonds Pacifique/ ; }, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Coral Reefs ; Hydrogen-Ion Concentration ; Nitrogen ; Seawater ; }, abstract = {Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2 seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2 site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.}, }
@article {pmid34469576, year = {2021}, author = {Kapun, M and Nunez, JCB and Bogaerts-Márquez, M and Murga-Moreno, J and Paris, M and Outten, J and Coronado-Zamora, M and Tern, C and Rota-Stabelli, O and Guerreiro, MPG and Casillas, S and Orengo, DJ and Puerma, E and Kankare, M and Ometto, L and Loeschcke, V and Onder, BS and Abbott, JK and Schaeffer, SW and Rajpurohit, S and Behrman, EL and Schou, MF and Merritt, TJS and Lazzaro, BP and Glaser-Schmitt, A and Argyridou, E and Staubach, F and Wang, Y and Tauber, E and Serga, SV and Fabian, DK and Dyer, KA and Wheat, CW and Parsch, J and Grath, S and Veselinovic, MS and Stamenkovic-Radak, M and Jelic, M and Buendía-Ruíz, AJ and Gómez-Julián, MJ and Espinosa-Jimenez, ML and Gallardo-Jiménez, FD and Patenkovic, A and Eric, K and Tanaskovic, M and Ullastres, A and Guio, L and Merenciano, M and Guirao-Rico, S and Horváth, V and Obbard, DJ and Pasyukova, E and Alatortsev, VE and Vieira, CP and Vieira, J and Torres, JR and Kozeretska, I and Maistrenko, OM and Montchamp-Moreau, C and Mukha, DV and Machado, HE and Lamb, K and Paulo, T and Yusuf, L and Barbadilla, A and Petrov, D and Schmidt, P and Gonzalez, J and Flatt, T and Bergland, AO}, title = {Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.}, journal = {Molecular biology and evolution}, volume = {38}, number = {12}, pages = {5782-5805}, pmid = {34469576}, issn = {1537-1719}, support = {R01 GM100366/GM/NIGMS NIH HHS/United States ; R01 GM137430/GM/NIGMS NIH HHS/United States ; R35 GM118165/GM/NIGMS NIH HHS/United States ; R35 GM119686/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Drosophila melanogaster/genetics ; Gene Frequency ; Genetics, Population ; Genomics ; *Metagenomics ; }, abstract = {Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome data sets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate data sets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in >20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This data set, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental metadata. A web-based genome browser and web portal provide easy access to the SNP data set. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan data set. Our resource will enable population geneticists to analyze spatiotemporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.}, }
@article {pmid34459547, year = {2021}, author = {Wahdan, SFM and Tanunchai, B and Wu, YT and Sansupa, C and Schädler, M and Dawoud, TM and Buscot, F and Purahong, W}, title = {Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes.}, journal = {MicrobiologyOpen}, volume = {10}, number = {4}, pages = {e1217}, pmid = {34459547}, issn = {2045-8827}, mesh = {Acclimatization/*genetics ; Bacteria/classification/*genetics ; *Climate Change ; Fungi/classification/*genetics ; Germany ; Indoleacetic Acids/metabolism ; Microbiota/genetics ; Mycobiome/genetics ; Nitrogen Fixation/physiology ; Phosphorus/metabolism ; Plant Roots/microbiology ; Rhizosphere ; Siderophores/biosynthesis ; Soil Microbiology ; Trifolium/*growth &amp; development/*microbiology ; }, abstract = {The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.}, }
@article {pmid34442809, year = {2021}, author = {Rumbou, A and Vainio, EJ and Büttner, C}, title = {Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442809}, issn = {2076-2607}, abstract = {Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus-virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.}, }
@article {pmid34442634, year = {2021}, author = {Malassigné, S and Minard, G and Vallon, L and Martin, E and Valiente Moro, C and Luis, P}, title = {Diversity and Functions of Yeast Communities Associated with Insects.}, journal = {Microorganisms}, volume = {9}, number = {8}, pages = {}, pmid = {34442634}, issn = {2076-2607}, abstract = {Following the concept of the holobiont, insect-microbiota interactions play an important role in insect biology. Many examples of host-associated microorganisms have been reported to drastically influence insect biological processes such as development, physiology, nutrition, survival, immunity, or even vector competence. While a huge number of studies on insect-associated microbiota have focused on bacteria, other microbial partners including fungi have been comparatively neglected. Yeasts, which establish mostly commensal or symbiotic relationships with their host, can dominate the mycobiota of certain insects. This review presents key advances and progress in the research field highlighting the diversity of yeast communities associated with insects, as well as their impact on insect life-history traits, immunity, and behavior.}, }
@article {pmid34432867, year = {2021}, author = {Astolfi, A and Masetti, R and Indio, V and Bertuccio, SN and Messelodi, D and Rampelli, S and Leardini, D and Carella, M and Serravalle, S and Libri, V and Bandini, J and Volinia, S and Candela, M and Pession, A}, title = {Torque teno mini virus as a cause of childhood acute promyelocytic leukemia lacking PML/RARA fusion.}, journal = {Blood}, volume = {138}, number = {18}, pages = {1773-1777}, doi = {10.1182/blood.2021011677}, pmid = {34432867}, issn = {1528-0020}, mesh = {Anelloviridae/pathogenicity/physiology ; Antineoplastic Agents/therapeutic use ; Child ; Female ; Humans ; Karyotype ; Leukemia, Promyelocytic, Acute/*genetics/pathology/therapy ; Oncogene Proteins, Fusion/*genetics ; Oncogenic Viruses/pathogenicity/*physiology ; *Retinoic Acid Receptor alpha ; Torque teno virus/pathogenicity/*physiology ; Tretinoin/therapeutic use ; }, }
@article {pmid34427504, year = {2021}, author = {Motaung, TE and Steenkamp, ET}, title = {Extracellular Vesicles in Teasing Apart Complex Plant-Microbiota Links: Implications for Microbiome-Based Biotechnology.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0073421}, pmid = {34427504}, issn = {2379-5077}, support = {129580//National Research Foundation (NRF)/ ; }, abstract = {Extracellular vesicles (EVs) are subcellular carriers of bioactive compounds with a complex array of functional effects on target cells. In mammals, circulating bodily fluid microbiota EVs (mbEVs) deliver cargo from source cells and adversely or favorably alter the physiology of the same source, neighboring, and distant recipient cells in an autocrine, paracrine, or endocrine fashion, respectively. Plant mbEVs may similarly mediate these interactive effects within the holobiont framework. However, the majority of plant EV research has focused on a small number of individual microbes, thus failing to reflect the importance of EVs in a community and consequently leaving a wide gap in scientific knowledge. Addressing this gap should entail a systems-level approach that combines vesicle characterization with microbiome analyses. This would certainly usher in a new age in microbial biotechnology entailing EVs as a microbiome manipulation strategy, a biomarker for stable microbiomes, and a diagnostic tool for plant infectious diseases.}, }
@article {pmid34427502, year = {2021}, author = {Garg, N}, title = {Metabolomics in Functional Interrogation of Individual Holobiont Members.}, journal = {mSystems}, volume = {6}, number = {4}, pages = {e0084121}, pmid = {34427502}, issn = {2379-5077}, support = {2047235//National Science Foundation (NSF)/ ; }, abstract = {Eukaryotes and their environments serve as petri dishes, hosting an abundant and a rich prokaryotic microbiome. The assemblage of a eukaryotic host and its microbiome is referred to as a holobiont. The holobiont's microbiome interacts within itself, with the environment, and with the host at the chemical level through production of specialized metabolites resulting in homeostasis or dysbiosis. These interactions are triggered by a multitude of factors, such as community composition, age, presence of nutrients, xenobiotics, and change in physical conditions, such as temperature and oxygen. Understanding how holobionts respond and adapt to diverse triggers is necessary to uncover mechanisms of resilience or susceptibility to dysbiosis and to modulate the collective functioning of microbiome in health and disease. This article highlights the challenges associated with uncovering chemical contributions of individual holobiont members and the applicability of metabolomics-based approaches to uncover chemical signatures of microbial processes in the natural environment.}, }
@article {pmid34426366, year = {2021}, author = {Leite, MFA and Dimitrov, MR and Freitas-Iório, RP and de Hollander, M and Cipriano, MAP and Andrade, SAL and da Silveira, APD and Kuramae, EE}, title = {Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input.}, journal = {The Science of the total environment}, volume = {800}, number = {}, pages = {149493}, doi = {10.1016/j.scitotenv.2021.149493}, pmid = {34426366}, issn = {1879-1026}, mesh = {Bacteria ; Burkholderiaceae ; Enterobacteriaceae ; Herbaspirillum ; Nitrogen ; Plant Roots ; Rhizosphere ; *Saccharum ; Soil Microbiology ; }, abstract = {The development and productivity of plants are governed by their genetic background, nutrient input, and the microbial communities they host, i.e. the holobiont. Accordingly, engineering beneficial root microbiomes has emerged as a novel and sustainable approach to crop production with reduced nutrient input. Here, we tested the effects of six bacterial strains isolated from sugarcane stalks on sugarcane growth and physiology as well as the dynamics of prokaryote community assembly in the rhizosphere and root endosphere under two N fertilization regimes. All six strains, Paraburkholderia caribensis IAC/BECa 88, Kosakonia oryzae IAC/BECa 90, Kosakonia radicincitans IAC/BECa 95, Paraburkholderia tropica IAC/BECa 135, Pseudomonas fluorescens IAC/BECa 141 and Herbaspirillum frisingense IAC/BECa 152, increased in shoot and root dry mass, and influenced the concentration and accumulation of important macro- and micronutrients. However, N input reduced the impact of inoculation by shifting the sugarcane microbiome (rhizosphere and root endosphere) and weakening the co-dependence between soil microbes and sugarcane biomass and nutrients. The results show that these beneficial microbes improved plant nutrient uptake conditioned to a reduced N nutrient input. Therefore, reduced fertilization is not only desirable consequence of bacterial inoculation but essential for higher impact of these beneficial bacteria on the sugarcane microbiome.}, }
@article {pmid34408733, year = {2021}, author = {Schapheer, C and Pellens, R and Scherson, R}, title = {Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {702763}, pmid = {34408733}, issn = {1664-302X}, abstract = {Recent reports indicate that the health of our planet is getting worse and that genuine transformative changes are pressing. So far, efforts to ameliorate Earth's ecosystem crises have been insufficient, as these often depart from current knowledge of the underlying ecological processes. Nowadays, biodiversity loss and the alterations in biogeochemical cycles are reaching thresholds that put the survival of our species at risk. Biological interactions are fundamental for achieving biological conservation and restoration of ecological processes, especially those that contribute to nutrient cycles. Microorganism are recognized as key players in ecological interactions and nutrient cycling, both free-living and in symbiotic associations with multicellular organisms. This latter assemblage work as a functional ecological unit called "holobiont." Here, we review the emergent ecosystem properties derived from holobionts, with special emphasis on detritivorous terrestrial arthropods and their symbiotic microorganisms. We revisit their relevance in the cycling of recalcitrant organic compounds (e.g., lignin and cellulose). Finally, based on the interconnection between biodiversity and nutrient cycling, we propose that a multicellular organism and its associates constitute an Ecosystem Holobiont (EH). This EH is the functional unit characterized by carrying out key ecosystem processes. We emphasize that in order to meet the challenge to restore the health of our planet it is critical to reduce anthropic pressures that may threaten not only individual entities (known as "bionts") but also the stability of the associations that give rise to EH and their ecological functions.}, }
@article {pmid34394058, year = {2021}, author = {Kostygov, AY and Alves, JMP and Yurchenko, V}, title = {Editorial: Symbioses Between Protists and Bacteria/Archaea.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {709184}, pmid = {34394058}, issn = {1664-302X}, }
@article {pmid34371395, year = {2021}, author = {Ferreira, V and Pavlaki, MD and Martins, R and Monteiro, MS and Maia, F and Tedim, J and Soares, AMVM and Calado, R and Loureiro, S}, title = {Effects of nanostructure antifouling biocides towards a coral species in the context of global changes.}, journal = {The Science of the total environment}, volume = {799}, number = {}, pages = {149324}, doi = {10.1016/j.scitotenv.2021.149324}, pmid = {34371395}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; *Biofouling/prevention &amp; control ; Coral Reefs ; *Disinfectants/toxicity ; Ecosystem ; *Nanostructures/toxicity ; Thiazoles ; }, abstract = {Biofouling prevention is one of the biggest challenges faced by the maritime industry, but antifouling agents commonly impact marine ecosystems. Advances in antifouling technology include the use of nanomaterials. Herein we test an antifouling nano-additive based on the encapsulation of the biocide 4,5-dichloro-2-octyl-4-isothiazolin-3-one (DCOIT) in engineered silica nanocontainers (SiNC). The work aims to assess the biochemical and physiological effects on the symbiotic coral Sarcophyton cf. glaucum caused by (1) thermal stress and (2) DCOIT exposure (free or nanoencapsulated forms), in a climate change scenario. Accordingly, the following hypotheses were addressed: (H1) ocean warming can cause toxicity on S. cf. glaucum; (H2) the nanoencapsulation process decreases DCOIT toxicity towards this species; (H3) the biocide toxicity, free or encapsulated forms, can be affected by ocean warming. Coral fragments were exposed for seven days to DCOIT in both free and encapsulated forms, SiNC and negative controls, under two water temperature regimes (26 °C and 30.5 °C). Coral polyp behavior and photosynthetic efficiency were determined in the holobiont, while biochemical markers were assessed individually in the endosymbiont and coral host. Results showed transient coral polyp retraction and diminished photosynthetic efficiency in the presence of heat stress or free DCOIT, with effects being magnified in the presence of both stressors. The activity of catalase and glutathione-S-transferase were modulated by temperature in each partner of the symbiosis. The shifts in enzymatic activity were more pronounced in the presence of free DCOIT, but to a lower extent for encapsulated DCOIT. Increased levels of oxidative damage were detected under heat conditions. The findings highlight the physiological constrains elicited by the increase of seawater temperature to symbiotic corals and demonstrate that DCOIT toxicity can be minimized through encapsulation in SiNC. The presence of both stressors magnifies toxicity and confirm that ocean warming enhances the vulnerability of tropical photosynthetic corals to local stressors.}, }
@article {pmid34370107, year = {2021}, author = {Schneider, T}, title = {The holobiont self: understanding immunity in context.}, journal = {History and philosophy of the life sciences}, volume = {43}, number = {3}, pages = {99}, pmid = {34370107}, issn = {1742-6316}, mesh = {Host Microbial Interactions/immunology/*physiology ; Immune System/*physiology ; Immunity/*physiology ; }, abstract = {Both concepts of the holobiont and the immune system are at the heart of an ongoing scientific and philosophical examination concerning questions of the organism's individuality and identity as well as the relations between organisms and their environment. Examining the holobiont, the question of boundaries and individuality is challenging because it is both an assemblage of organisms with physiological cohesive aspects. I discuss the concept of immunity and the immune system function from the holobiont perspective. Because of the host-microbial close relations of codependence and interdependence, the holobiont is more often than not confused with the host, as the host is the domain in which this entity exists. I discuss the holobiont unique ecological characteristics of microbial assemblages connected to a host in a network of interactions in which the host is one of the organisms in the community but also its landscape. Therefore, I suggest viewing the holobiont as a host-ecosystem and discuss the implication of such a view on the concept of immunity and the meaning of protection. Furthermore, I show that viewing the holobiont as a host ecosystem opens the possibility of using the same ecological definition of boundaries and immunity dealing with an ecological system. Thus, the holobiont's boundaries and immunity are defined by the persistence of its complex system of interactions integrating existing and new interactions. This way of thinking presents a notion of immunity that materializes as the result of the complex interdependence relations between the different organisms composing the holobiont similar to that of an ecosystem. Taking this view further, I discuss the notion of immunogenicity that is ontologically heterogeneous with various causal explanations of the processes of tolerance and targeted immune response. Finally, I discuss the possible conceptualization of already existing and new biomedical practices.}, }
@article {pmid34367078, year = {2021}, author = {Legüe, M and Aguila, B and Calixto, A}, title = {Interspecies RNA Interactome of Pathogen and Host in a Heritable Defensive Strategy.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {649858}, pmid = {34367078}, issn = {1664-302X}, abstract = {Communication with bacteria deeply impacts the life history traits of their hosts. Through specific molecules and metabolites, bacteria can promote short- and long-term phenotypic and behavioral changes in the nematode Caenorhabditis elegans. The chronic exposure of C. elegans to pathogens promotes the adaptive behavior in the host's progeny called pathogen-induced diapause formation (PIDF). PIDF is a pathogen avoidance strategy induced in the second generation of animals infected and can be recalled transgenerationally. This behavior requires the RNA interference machinery and specific nematode and bacteria small RNAs (sRNAs). In this work, we assume that RNAs from both species co-exist and can interact with each other. Under this principle, we explore the potential interspecies RNA interactions during PIDF-triggering conditions, using transcriptomic data from the holobiont. We study two transcriptomics datasets: first, the dual sRNA expression of Pseudomonas aeruginosa PAO1 and C. elegans in a transgenerational paradigm for six generations and second, the simultaneous expression of sRNAs and mRNA in intergenerational PIDF. We focus on those bacterial sRNAs that are systematically overexpressed in the intestines of animals compared with sRNAs expressed in host-naïve bacteria. We selected diverse in silico methods that represent putative mechanisms of RNA-mediated interspecies interaction. These interactions are as follows: heterologous perfect and incomplete pairing between bacterial RNA and host mRNA; sRNAs of similar sequence expressed in both species that could mimic each other; and known or predicted eukaryotic motifs present in bacterial transcripts. We conclude that a broad spectrum of tools can be applied for the identification of potential sRNA and mRNA targets of the interspecies RNA interaction that can be subsequently tested experimentally.}, }
@article {pmid34361898, year = {2021}, author = {Barra Caracciolo, A and Terenzi, V}, title = {Rhizosphere Microbial Communities and Heavy Metals.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34361898}, issn = {2076-2607}, abstract = {The rhizosphere is a microhabitat where there is an intense chemical dialogue between plants and microorganisms. The two coexist and develop synergistic actions, which can promote plants' functions and productivity, but also their capacity to respond to stress conditions, including heavy metal (HM) contamination. If HMs are present in soils used for agriculture, there is a risk of metal uptake by edible plants with subsequent bioaccumulation in humans and animals and detrimental consequences for their health. Plant productivity can also be negatively affected. Many bacteria have defensive mechanisms for resisting heavy metals and, through various complex processes, can improve plant response to HM stress. Bacteria-plant synergic interactions in the rhizosphere, as a homeostatic ecosystem response to HM disturbance, are common in soil. However, this is hard to achieve in agroecosystems managed with traditional practices, because concentrating on maximizing crop yield does not make it possible to establish rhizosphere interactions. Improving knowledge of the complex interactions mediated by plant exudates and secondary metabolites can lead to nature-based solutions for plant health in HM contaminated soils. This paper reports the main ecotoxicological effects of HMs and the various compounds (including several secondary metabolites) produced by plant-microorganism holobionts for removing, immobilizing and containing toxic elements.}, }
@article {pmid34349734, year = {2021}, author = {Herrera, M and Liew, YJ and Venn, A and Tambutté, E and Zoccola, D and Tambutté, S and Cui, G and Aranda, M}, title = {New Insights From Transcriptomic Data Reveal Differential Effects of CO2 Acidification Stress on Photosynthesis of an Endosymbiotic Dinoflagellate in hospite.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {666510}, pmid = {34349734}, issn = {1664-302X}, abstract = {Ocean acidification (OA) has both detrimental as well as beneficial effects on marine life; it negatively affects calcifiers while enhancing the productivity of photosynthetic organisms. To date, many studies have focused on the impacts of OA on calcification in reef-building corals, a process particularly susceptible to acidification. However, little is known about the effects of OA on their photosynthetic algal partners, with some studies suggesting potential benefits for symbiont productivity. Here, we investigated the transcriptomic response of the endosymbiont Symbiodinium microadriaticum (CCMP2467) in the Red Sea coral Stylophora pistillata subjected to different long-term (2 years) OA treatments (pH 8.0, 7.8, 7.4, 7.2). Transcriptomic analyses revealed that symbionts from corals under lower pH treatments responded to acidification by increasing the expression of genes related to photosynthesis and carbon-concentrating mechanisms. These processes were mostly up-regulated and associated metabolic pathways were significantly enriched, suggesting an overall positive effect of OA on the expression of photosynthesis-related genes. To test this conclusion on a physiological level, we analyzed the symbiont's photochemical performance across treatments. However, in contrast to the beneficial effects suggested by the observed gene expression changes, we found significant impairment of photosynthesis with increasing pCO2. Collectively, our data suggest that over-expression of photosynthesis-related genes is not a beneficial effect of OA but rather an acclimation response of the holobiont to different water chemistries. Our study highlights the complex effects of ocean acidification on these symbiotic organisms and the role of the host in determining symbiont productivity and performance.}, }
@article {pmid34342082, year = {2021}, author = {Voolstra, CR and Valenzuela, JJ and Turkarslan, S and Cárdenas, A and Hume, BCC and Perna, G and Buitrago-López, C and Rowe, K and Orellana, MV and Baliga, NS and Paranjape, S and Banc-Prandi, G and Bellworthy, J and Fine, M and Frias-Torres, S and Barshis, DJ}, title = {Contrasting heat stress response patterns of coral holobionts across the Red Sea suggest distinct mechanisms of thermal tolerance.}, journal = {Molecular ecology}, volume = {30}, number = {18}, pages = {4466-4480}, doi = {10.1111/mec.16064}, pmid = {34342082}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; Heat-Shock Response ; Indian Ocean ; Symbiosis/genetics ; }, abstract = {Corals from the northern Red Sea, in particular the Gulf of Aqaba (GoA), have exceptionally high bleaching thresholds approaching >5℃ above their maximum monthly mean (MMM) temperatures. These elevated thresholds are thought to be due to historical selection, as corals passed through the warmer Southern Red Sea during recolonization from the Arabian Sea. To test this hypothesis, we determined thermal tolerance thresholds of GoA versus central Red Sea (CRS) Stylophora pistillata corals using multi-temperature acute thermal stress assays to determine thermal thresholds. Relative thermal thresholds of GoA and CRS corals were indeed similar and exceptionally high (~7℃ above MMM). However, absolute thermal thresholds of CRS corals were on average 3℃ above those of GoA corals. To explore the molecular underpinnings, we determined gene expression and microbiome response of the coral holobiont. Transcriptomic responses differed markedly, with a strong response to the thermal stress in GoA corals and their symbiotic algae versus a remarkably muted response in CRS colonies. Concomitant to this, coral and algal genes showed temperature-induced expression in GoA corals, while exhibiting fixed high expression (front-loading) in CRS corals. Bacterial community composition of GoA corals changed dramatically under heat stress, whereas CRS corals displayed stable assemblages. We interpret the response of GoA corals as that of a resilient population approaching a tipping point in contrast to a pattern of consistently elevated thermal resistance in CRS corals that cannot further attune. Such response differences suggest distinct thermal tolerance mechanisms that may affect the response of coral populations to ocean warming.}, }
@article {pmid34331071, year = {2022}, author = {Haydon, TD and Suggett, DJ and Siboni, N and Kahlke, T and Camp, EF and Seymour, JR}, title = {Temporal Variation in the Microbiome of Tropical and Temperate Octocorals.}, journal = {Microbial ecology}, volume = {83}, number = {4}, pages = {1073-1087}, pmid = {34331071}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Bacteria/genetics ; Biodiversity ; Coral Reefs ; *Gammaproteobacteria/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacterial members of the coral holobiont play an important role in determining coral fitness. However, most knowledge of the coral microbiome has come from reef-building scleractinian corals, with far less known about the nature and importance of the microbiome of octocorals (subclass Octocorallia), which contribute significantly to reef biodiversity and functional complexity. We examined the diversity and structure of the bacterial component of octocoral microbiomes over summer and winter, with a focus on two temperate (Erythropodium hicksoni, Capnella gaboensis; Sydney Harbour) and two tropical (Sinularia sp., Sarcophyton sp.; Heron Island) species common to reefs in eastern Australia. Bacterial communities associated with these octocorals were also compared to common temperate (Plesiastrea versipora) and tropical (Acropora aspera) hard corals from the same reefs. Using 16S rRNA amplicon sequencing, bacterial diversity was found to be heterogeneous among octocorals, but we observed changes in composition between summer and winter for some species (C. gaboensis and Sinularia sp.), but not for others (E. hicksoni and Sarcophyton sp.). Bacterial community structure differed significantly between all octocoral species within both the temperate and tropical environments. However, on a seasonal basis, those differences were less pronounced. The microbiomes of C. gaboensis and Sinularia sp. were dominated by bacteria belonging to the genus Endozoicomonas, which were a key conserved feature of their core microbiomes. In contrast to previous studies, our analysis revealed that Endozoicomonas phylotypes are shared across different octocoral species, inhabiting different environments. Together, our data demonstrates that octocorals harbour a broad diversity of bacterial partners, some of which comprise 'core microbiomes' that potentially impart important functional roles to their hosts.}, }
@article {pmid34326856, year = {2021}, author = {Gaete, A and Pulgar, R and Hodar, C and Maldonado, J and Pavez, L and Zamorano, D and Pastenes, C and González, M and Franck, N and Mandakovic, D}, title = {Tomato Cultivars With Variable Tolerances to Water Deficit Differentially Modulate the Composition and Interaction Patterns of Their Rhizosphere Microbial Communities.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {688533}, pmid = {34326856}, issn = {1664-462X}, abstract = {Since drought is the leading environmental factor limiting crop productivity, and plants have a significant impact in defining the assembly of plant-specific microbial communities associated with roots, we aimed to determine the effect of thoroughly selected water deficit tolerant and susceptible Solanum lycopersicum cultivars on their rhizosphere microbiome and compared their response with plant-free soil microbial communities. We identified a total of 4,248 bacterial and 276 fungal different operational taxonomic units (OTUs) in soils by massive sequencing. We observed that tomato cultivars significantly affected the alpha and beta diversity of their bacterial rhizosphere communities but not their fungal communities compared with bulk soils (BSs), showing a plant effect exclusively on the bacterial soil community. Also, an increase in alpha diversity in response to water deficit of both bacteria and fungi was observed in the susceptible rhizosphere (SRz) but not in the tolerant rhizosphere (TRz) cultivar, implying a buffering effect of the tolerant cultivar on its rhizosphere microbial communities. Even though water deficit did not affect the microbial diversity of the tolerant cultivar, the interaction network analysis revealed that the TRz microbiota displayed the smallest and least complex soil network in response to water deficit with the least number of connected components, nodes, and edges. This reduction of the TRz network also correlated with a more efficient community, reflected in increased cooperation within kingdoms. Furthermore, we identified some specific bacteria and fungi in the TRz in response to water deficit, which, given that they belong to taxa with known beneficial characteristics for plants, could be contributing to the tolerant phenotype, highlighting the metabolic bidirectionality of the holobiont system. Future assays involving characterization of root exudates and exchange of rhizospheres between drought-tolerant and susceptible cultivars could determine the effect of specific metabolites on the microbiome community and may elucidate their functional contribution to the tolerance of plants to water deficit.}, }
@article {pmid34249034, year = {2021}, author = {Kaur, J and Sharma, J}, title = {Orchid Root Associated Bacteria: Linchpins or Accessories?.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {661966}, pmid = {34249034}, issn = {1664-462X}, abstract = {Besides the plant-fungus symbiosis in arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) plants, many endorhizal and rhizosphere bacteria (Root Associated Bacteria, or RAB) also enhance plant fitness, diversity, and coexistence among plants via bi- or tripartite interactions with plant hosts and mycorrhizal fungi. Assuming that bacterial associations are just as important for the obligate mycorrhizal plant family Orchidaceae, surprisingly little is known about the RAB associated with orchids. Herein, we first present the current, underwhelming state of RAB research including their interactions with fungi and the influence of holobionts on plant fitness. We then delineate the need for novel investigations specifically in orchid RAB ecology, and sketch out questions and hypotheses which, when addressed, will advance plant-microbial ecology. We specifically discuss the potential effects of beneficial RAB on orchids as: (1) Plant Growth Promoting Rhizobacteria (PGPR), (2) Mycorrhization Helper Bacteria (MHB), and (3) constituents of an orchid holobiont. We further posit that a hologenomic view should be considered as a framework for addressing co-evolution of the plant host, their obligate Orchid Mycorrhizal Fungi (OMF), and orchid RAB. We conclude by discussing implications of the suggested research for conservation of orchids, their microbial partners, and their collective habitats.}, }
@article {pmid34248863, year = {2021}, author = {Bednarz, VN and van de Water, JAJM and Grover, R and Maguer, JF and Fine, M and Ferrier-Pagès, C}, title = {Unravelling the Importance of Diazotrophy in Corals - Combined Assessment of Nitrogen Assimilation, Diazotrophic Community and Natural Stable Isotope Signatures.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {631244}, pmid = {34248863}, issn = {1664-302X}, abstract = {There is an increasing interest in understanding the structure and function of the microbiota associated with marine and terrestrial organisms, because it can play a major role in host nutrition and resistance to environmental stress. Reef-building corals live in association with diazotrophs, which are microbes able to fix dinitrogen. Corals are known to assimilate diazotrophically-derived nitrogen (DDN), but it is still not clear whether this nitrogen source is derived from coral-associated diazotrophs and whether it substantially contributes to the coral's nitrogen budget. In this study, we aimed to provide a better understanding of the importance of DDN for corals using a holistic approach by simultaneously assessing DDN assimilation rates (using 15N2 tracer technique), the diazotrophic bacterial community (using nifH gene amplicon sequencing) and the natural δ15N signature in Stylophora pistillata corals from the Northern Red Sea along a depth gradient in winter and summer. Overall, our results show a discrepancy between the three parameters. DDN was assimilated by the coral holobiont during winter only, with an increased assimilation with depth. Assimilation rates were, however, not linked to the presence of coral-associated diazotrophs, suggesting that the presence of nifH genes does not necessarily imply functionality. It also suggests that DDN assimilation was independent from coral-associated diazotrophs and may instead result from nitrogen derived from planktonic diazotrophs. In addition, the δ15N signature presented negative values in almost all coral samples in both seasons, suggesting that nitrogen sources other than DDN contribute to the nitrogen budget of corals from this region. This study yields novel insight into the origin and importance of diazotrophy for scleractinian corals from the Northern Red Sea using multiple proxies.}, }
@article {pmid34237996, year = {2021}, author = {Paglia, L}, title = {From native core micriobiome to milk-oriented microbiome.}, journal = {European journal of paediatric dentistry}, volume = {22}, number = {2}, pages = {89}, doi = {10.23804/ejpd.2021.22.02.1}, pmid = {34237996}, issn = {2035-648X}, mesh = {Breast Feeding ; Child ; Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Milk, Human ; Mothers ; Pregnancy ; }, abstract = {The human microbiome is the full set of microorganisms (microbiota) present on and in our body. Its importance is such that the human being has been defined as a holobiont, that is, a superorganism made up of human eukaryotic cells and microbial cells. A balanced microbiota (eubiosis) is a prerequisite for health and well-being; on the contrary, an altered microbiota (dysbiosis) is the cause of pathological conditions. This concept is the cornerstone of the "microbiota revolution": Currently there is no disease that cannot be re- interpreted as a function of microbiome. While all human beings have similar DNA, it is the microbiome that make every person genetically unique; therefore the microbiome is the variable component of the genome which characterises each one of us. About one third of the microbiome is common to all individuals, while two thirds are specific to each subject and constitute a sort of fingerprint that forms and stabilises in the first 2-3 years of life. This timeframe is extremely important since it has been shown that the structure of the microbiome is already acquired in the embryonic-fetal period, it is completed within 3 years and lasts a lifetime. The native core microbiome is the first microbiota and characterises individuals for their whole life. It is affected by four main variables: The quality of family and social life of the mother-to-be, the intake of drugs during pregnancy, as well as the type of birth and breastfeeding. It is renowned that breast milk is a complex, unique and essential food for the growth of the child, but one of its functions - which is still under investigation today - is to feed and guide the formation of the microbiome of the newborn even after the introduction of solid foods, during the first 3 years of life. This function is carried out by the over one hundred different types of oligosaccharides that are present in breast milk, which is why these days we talk about the so-called MOM (milk-oriented microbiome). The correct formation of the microbiome affects the entire life of an individual. This is a more than valid reason to promote breastfeeding even after eruption of baby teeth and throughout the weaning period. The role of pediatric dentists, together with hygienists and pediatricians, is to spread and stress out the importance of oral hygiene so that breastfeeding can only bring benefits and not carious lesions!}, }
@article {pmid34237402, year = {2021}, author = {Thompson, HF and Gutierrez, T}, title = {Detection of hydrocarbon-degrading bacteria on deepwater corals of the northeast Atlantic using CARD-FISH.}, journal = {Journal of microbiological methods}, volume = {187}, number = {}, pages = {106277}, doi = {10.1016/j.mimet.2021.106277}, pmid = {34237402}, issn = {1872-8359}, mesh = {Animals ; Anthozoa/*microbiology ; Atlantic Ocean ; Biodegradation, Environmental ; Catalysis ; *Coral Reefs ; Hydrocarbons/*metabolism ; In Situ Hybridization, Fluorescence ; Marinobacter/*isolation &amp; purification/*metabolism ; Symbiosis ; }, abstract = {Recently, studies have begun to identify oil-degrading bacteria and host-taxon specific bacterial assemblages associated with the coral holobiont, including deep-sea cold-water corals, which are thought to provide metabolic functions and additional carbon sources to their coral hosts. Here, we describe the identification of Marinobacter on the soft tissue of Lophelia pertusa coral polyps by Catalyzed Reporter Deposition Fluorescence in situ Hybridization (CARD-FISH). L. pertusa samples from three reef sites in the northeast Atlantic (Logachev, Mingulay and Pisces) were collected at depth by vacuum seal to eliminate contamination issues. After decalcification, histological processing and sagittal sectioning of the soft coral polyp tissues, the 16S rRNA-targeted oligonucleotide HRP-labelled probe Mrb-0625-a, and Cyanine 3 (Cy3)-labelled tyramides, were used to identify members of the hydrocarbon-degrading genus Marinobacter. Mrb-0625-a-hybridized bacterial cell signals were detected in different anatomical sites of all polyps collected from each of the three reef sites, suggesting a close, possibly intimate, association between them, but the purpose of which remains unknown. We posit that Marinobacter, and possibly other hydrocarbon-degrading bacteria associated with Lophelia, may confer the coral with the ability to cope with toxic levels of hydrocarbons in regions of natural oil seepage and where there is an active oil and gas industry presence.}, }
@article {pmid34226659, year = {2022}, author = {Glaze, TD and Erler, DV and Siljanen, HMP}, title = {Microbially facilitated nitrogen cycling in tropical corals.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {68-77}, pmid = {34226659}, issn = {1751-7370}, mesh = {*Ammonium Compounds ; Animals ; *Anthozoa ; Denitrification ; Nitrates ; Nitrification ; Nitrogen ; }, abstract = {Tropical scleractinian corals support a diverse assemblage of microbial symbionts. This 'microbiome' possesses the requisite functional diversity to conduct a range of nitrogen (N) transformations including denitrification, nitrification, nitrogen fixation and dissimilatory nitrate reduction to ammonium (DNRA). Very little direct evidence has been presented to date verifying that these processes are active within tropical corals. Here we use a combination of stable isotope techniques, nutrient uptake calculations and captured metagenomics to quantify rates of nitrogen cycling processes in a selection of tropical scleractinian corals. Denitrification activity was detected in all species, albeit with very low rates, signifying limited importance in holobiont N removal. Relatively greater nitrogen fixation activity confirms that corals are net N importers to reef systems. Low net nitrification activity suggests limited N regeneration capacity; however substantial gross nitrification activity may be concealed through nitrate consumption. Based on nrfA gene abundance and measured inorganic N fluxes, we calculated significant DNRA activity in the studied corals, which has important implications for coral reef N cycling and warrants more targeted investigation. Through the quantification and characterisation of all relevant N-cycling processes, this study provides clarity on the subject of tropical coral-associated biogeochemical N-cycling.}, }
@article {pmid34220847, year = {2021}, author = {Schmittmann, L and Franzenburg, S and Pita, L}, title = {Individuality in the Immune Repertoire and Induced Response of the Sponge Halichondria panicea.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {689051}, pmid = {34220847}, issn = {1664-3224}, mesh = {Animals ; Gene Expression Regulation/drug effects ; Lipopolysaccharides/*pharmacology ; Porifera/*drug effects/genetics/immunology ; RNA-Seq ; Receptors, Pattern Recognition/*genetics ; }, abstract = {The animal immune system mediates host-microbe interactions from the host perspective. Pattern recognition receptors (PRRs) and the downstream signaling cascades they induce are a central part of animal innate immunity. These molecular immune mechanisms are still not fully understood, particularly in terms of baseline immunity vs induced specific responses regulated upon microbial signals. Early-divergent phyla like sponges (Porifera) can help to identify the evolutionarily conserved mechanisms of immune signaling. We characterized both the expressed immune gene repertoire and the induced response to lipopolysaccharides (LPS) in Halichondria panicea, a promising model for sponge symbioses. We exposed sponges under controlled experimental conditions to bacterial LPS and performed RNA-seq on samples taken 1h and 6h after exposure. H. panicea possesses a diverse array of putative PRRs. While part of those PRRs was constitutively expressed in all analyzed sponges, the majority was expressed individual-specific and regardless of LPS treatment or timepoint. The induced immune response by LPS involved differential regulation of genes related to signaling and recognition, more specifically GTPases and post-translational regulation mechanisms like ubiquitination and phosphorylation. We have discovered individuality in both the immune receptor repertoire and the response to LPS, which may translate into holobiont fitness and susceptibility to stress. The three different layers of immune gene control observed in this study, - namely constitutive expression, individual-specific expression, and induced genes -, draw a complex picture of the innate immune gene regulation in H. panicea. Most likely this reflects synergistic interactions among the different components of immunity in their role to control and respond to a stable microbiome, seawater bacteria, and potential pathogens.}, }
@article {pmid34218251, year = {2022}, author = {Posadas, N and Baquiran, JIP and Nada, MAL and Kelly, M and Conaco, C}, title = {Microbiome diversity and host immune functions influence survivorship of sponge holobionts under future ocean conditions.}, journal = {The ISME journal}, volume = {16}, number = {1}, pages = {58-67}, pmid = {34218251}, issn = {1751-7370}, mesh = {Animals ; Bacteria ; Immunity ; *Microbiota/genetics ; Oceans and Seas ; *Porifera/immunology/microbiology ; }, abstract = {The sponge-associated microbial community contributes to the overall health and adaptive capacity of the sponge holobiont. This community is regulated by the environment and the immune system of the host. However, little is known about the effect of environmental stress on the regulation of host immune functions and how this may, in turn, affect sponge-microbe interactions. In this study, we compared the bacterial diversity and immune repertoire of the demosponge, Neopetrosia compacta, and the calcareous sponge, Leucetta chagosensis, under varying levels of acidification and warming stress based on climate scenarios predicted for 2100. Neopetrosia compacta harbors a diverse microbial community and possesses a rich repertoire of scavenger receptors while L. chagosensis has a less diverse microbiome and an expanded range of pattern recognition receptors and immune response-related genes. Upon exposure to RCP 8.5 conditions, the microbiome composition and host transcriptome of N. compacta remained stable, which correlated with high survival (75%). In contrast, tissue necrosis and low survival (25%) of L. chagosensis was accompanied by microbial community shifts and downregulation of host immune-related pathways. Meta-analysis of microbiome diversity and immunological repertoire across poriferan classes further highlights the importance of host-microbe interactions in predicting the fate of sponges under future ocean conditions.}, }
@article {pmid34207399, year = {2021}, author = {Van Gerrewey, T and El-Nakhel, C and De Pascale, S and De Paepe, J and Clauwaert, P and Kerckhof, FM and Boon, N and Geelen, D}, title = {Root-Associated Bacterial Community Shifts in Hydroponic Lettuce Cultured with Urine-Derived Fertilizer.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34207399}, issn = {2076-2607}, support = {Not applicable//MELiSSA/ ; }, abstract = {Recovery of nutrients from source-separated urine can truncate our dependency on synthetic fertilizers, contributing to more sustainable food production. Urine-derived fertilizers have been successfully applied in soilless cultures. However, little is known about the adaptation of the plant to the nutrient environment. This study investigated the impact of urine-derived fertilizers on plant performance and the root-associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Shoot biomass, chlorophyll, phenolic, antioxidant, and mineral content were associated with shifts in the root-associated bacterial community structures. K-struvite, a high-performing urine-derived fertilizer, supported root-associated bacterial communities that overlapped most strongly with control NPK fertilizer. Contrarily, lettuce performed poorly with electrodialysis (ED) concentrate and hydrolyzed urine and hosted distinct root-associated bacterial communities. Comparing the identified operational taxonomic units (OTU) across the fertilizer conditions revealed strong correlations between specific bacterial genera and the plant physiological characteristics, salinity, and NO3-/NH4+ ratio. The root-associated bacterial community networks of K-struvite and NPK control fertilized plants displayed fewer nodes and node edges, suggesting that good plant growth performance does not require highly complex ecological interactions in hydroponic growth conditions.}, }
@article {pmid34201731, year = {2021}, author = {Bona, E and Massa, N and Toumatia, O and Novello, G and Cesaro, P and Todeschini, V and Boatti, L and Mignone, F and Titouah, H and Zitouni, A and Lingua, G and Vuolo, F and Gamalero, E}, title = {Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria.}, journal = {Microorganisms}, volume = {9}, number = {7}, pages = {}, pmid = {34201731}, issn = {2076-2607}, abstract = {Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a "holobiont". In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.}, }
@article {pmid34201354, year = {2021}, author = {Fetsiukh, A and Conrad, J and Bergquist, J and Timmusk, S}, title = {Silica Particles Trigger the Exopolysaccharide Production of Harsh Environment Isolates of Growth-Promoting Rhizobacteria and Increase Their Ability to Enhance Wheat Biomass in Drought-Stressed Soils.}, journal = {International journal of molecular sciences}, volume = {22}, number = {12}, pages = {}, pmid = {34201354}, issn = {1422-0067}, support = {222-2014-1326//FORMAS/ ; 2017-5224//Swedish Research Council/ ; }, mesh = {Bacteria/classification/*isolation &amp; purification/metabolism ; *Droughts ; Polysaccharides, Bacterial/*metabolism ; Rhizosphere ; Silicon Dioxide/*pharmacology ; Soil/*chemistry ; *Soil Microbiology ; Triticum/drug effects/*growth &amp; development/metabolism ; }, abstract = {In coming decades, drought is expected to expand globally owing to increased evaporation and reduced rainfall. Understanding, predicting, and controlling crop plants' rhizosphere has the potential to manipulate its responses to environmental stress. Our plant growth-promoting rhizobacteria (PGPR) are isolated from a natural laboratory, 'The Evolution Canyon', Israel, (EC), from the wild progenitors of cereals, where they have been co-habituating with their hosts for long periods of time. The study revealed that commercial TM50 silica particles (SN) triggered the PGPR production of exopolysaccharides (EPS) containing D-glucuronate (D-GA). The increased EPS content increased the PGPR water-holding capacity (WHC) and osmotic pressure of the biofilm matrix, which led to enhanced plant biomass in drought-stressed growth environments. Light- and cryo-electron- microscopic studies showed that, in the presence of silica (SN) particles, bacterial morphology is changed, indicating that SNs are associated with significant reprogramming in bacteria. The findings encourage the development of large-scale methods for isolate formulation with natural silicas that ensure higher WHC and hyperosmolarity under field conditions. Osmotic pressure involvement of holobiont cohabitation is also discussed.}, }
@article {pmid34200095, year = {2021}, author = {Mkaouar, H and Mariaule, V and Rhimi, S and Hernandez, J and Kriaa, A and Jablaoui, A and Akermi, N and Maguin, E and Lesner, A and Korkmaz, B and Rhimi, M}, title = {Gut Serpinome: Emerging Evidence in IBD.}, journal = {International journal of molecular sciences}, volume = {22}, number = {11}, pages = {}, pmid = {34200095}, issn = {1422-0067}, support = {ANR-18-CE18-0019-03//Agence Nationale de la Recherche/ ; ANR-CE16-0018-01//Agence Nationale de la Recherche/ ; 41786NC//Campus France/ ; MICAfrica 952583//Horizon 2020/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*physiopathology ; Serine Proteases/*chemistry ; Serpins/*metabolism ; }, abstract = {Inflammatory bowel diseases (IBD) are incurable disorders whose prevalence and global socioeconomic impact are increasing. While the role of host genetics and immunity is well documented, that of gut microbiota dysbiosis is increasingly being studied. However, the molecular basis of the dialogue between the gut microbiota and the host remains poorly understood. Increased activity of serine proteases is demonstrated in IBD patients and may contribute to the onset and the maintenance of the disease. The intestinal proteolytic balance is the result of an equilibrium between the proteases and their corresponding inhibitors. Interestingly, the serine protease inhibitors (serpins) encoded by the host are well reported; in contrast, those from the gut microbiota remain poorly studied. In this review, we provide a concise analysis of the roles of serine protease in IBD physiopathology and we focus on the serpins from the gut microbiota (gut serpinome) and their relevance as a promising therapeutic approach.}, }
@article {pmid34192342, year = {2021}, author = {Salsbery, ME and DeLong, JP}, title = {Thermal adaptation in a holobiont accompanied by phenotypic changes in an endosymbiont.}, journal = {Evolution; international journal of organic evolution}, volume = {75}, number = {8}, pages = {2074-2084}, doi = {10.1111/evo.14301}, pmid = {34192342}, issn = {1558-5646}, mesh = {Acclimatization ; Adaptation, Physiological ; *Ciliophora ; *Paramecium ; Symbiosis ; Temperature ; }, abstract = {How and if organisms can adapt to changing temperatures has drastic consequences for the natural world. Thermal adaptation involves finding a match between temperatures permitting growth and the expected temperature distribution of the environment. However, if and how this match is achieved, and how tightly linked species change together, is poorly understood. Paramecium bursaria is a ciliate that has a tight physiological interaction with endosymbiotic green algae (zoochlorellae). We subjected a wild population of P. bursaria to a cold and warm climate (20 and 32℃) for ∼300 generations. We then measured the thermal performance curve (TPC) for intrinsic rate of growth (rmax) for these evolved lines across temperatures. We also evaluated number and size of the zoochlorellae populations within paramecia cells. TPCs for warm-adapted populations were shallower and broader than TPCs of cold-adapted populations, indicating that the warm populations adapted by moving along a thermal generalist/specialist trade off rather than right-shifting the TPC. Zoochlorellae populations within cold-adapted paramecia had fewer and larger zoochlorellae than hot-adapted paramecia, indicating phenotypic shifts in the endosymbiont accompany thermal adaptation in the host. Our results provide new and novel insight into how species involved in complex interactions will be affected by continuing increasing global temperatures.}, }
@article {pmid34183060, year = {2021}, author = {Ingham, AC and Kielsen, K and Mordhorst, H and Ifversen, M and Aarestrup, FM and Müller, KG and Pamp, SJ}, title = {Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {148}, pmid = {34183060}, issn = {2049-2618}, support = {643476//Horizon2020/ ; }, mesh = {Bacteria/genetics ; Child ; *Gastrointestinal Microbiome ; *Graft vs Host Disease ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; *Microbiota ; }, abstract = {BACKGROUND: Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients' microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT.<br><br>RESULTS: The bacterial diversity decreased in the gut, nose, and mouth during the first month and reconstituted again 1-3 months after allo-HSCT. The microbial community composition traversed three phases over 1 year. Distinct taxa discriminated the microbiota temporally at all three body sides, including Enterococcus spp., Lactobacillus spp., and Blautia spp. in the gut. Of note, certain microbial taxa appeared already changed in the patients prior to allo-HSCT as compared with healthy children. Acute GvHD occurring after allo-HSCT could be predicted from the microbiota composition at all three body sites prior to HSCT. The reconstitution of CD4+ T cells, TH17, and B cells was associated with distinct taxa of the gut, oral, and nasal microbiota.<br><br>CONCLUSIONS: This study reveals for the first time bacteria in the mouth and nose that may predict aGvHD. Monitoring of the microbiota at different body sites in HSCT patients and particularly through involvement of samples prior to transplantation may be of prognostic value and could assist in guiding personalized treatment strategies. The identification of distinct bacteria that have a potential to predict post-transplant aGvHD might provide opportunities for an improved preventive clinical management, including a modulation of microbiomes. The host-microbiota associations shared between several body sites might also support an implementation of more feasible oral and nasal swab sampling-based analyses. Altogether, the findings suggest that the microbiota and host factors together could provide actionable information to guiding precision medicine. Video Abstract.}, }
@article {pmid34176151, year = {2021}, author = {Capistrant-Fossa, KA and Morrison, HG and Engelen, AH and Quigley, CTC and Morozov, A and Serrão, EA and Brodie, J and Gachon, CMM and Badis, Y and Johnson, LE and Hoarau, G and Abreu, MH and Tester, PA and Stearns, LA and Brawley, SH}, title = {The microbiome of the habitat-forming brown alga Fucus vesiculosus (Phaeophyceae) has similar cross-Atlantic structure that reflects past and present drivers1.}, journal = {Journal of phycology}, volume = {57}, number = {6}, pages = {1681-1698}, doi = {10.1111/jpy.13194}, pmid = {34176151}, issn = {1529-8817}, mesh = {*Fucus ; *Microbiota ; North Carolina ; Phylogeny ; Phylogeography ; }, abstract = {Latitudinal diversity gradients have provided many insights into species differentiation and community processes. In the well-studied intertidal zone, however, little is known about latitudinal diversity in microbiomes associated with habitat-forming hosts. We investigated microbiomes of Fucus vesiculosus because of deep understanding of this model system and its latitudinally large, cross-Atlantic range. Given multiple effects of photoperiod, we predicted that cross-Atlantic microbiomes of the Fucus microbiome would be similar at similar latitudes and correlate with environmental factors. We found that community structure and individual amplicon sequencing variants (ASVs) showed distinctive latitudinal distributions, but alpha diversity did not. Latitudinal differentiation was mostly driven by ASVs that were more abundant in cold temperate to subarctic (e.g., Granulosicoccus_t3260, Burkholderia/Caballeronia/Paraburkholderia_t8371) or warm temperate (Pleurocapsa_t10392) latitudes. Their latitudinal distributions correlated with different humidity, tidal heights, and air/sea temperatures, but rarely with irradiance or photoperiod. Many ASVs in potentially symbiotic genera displayed novel phylogenetic biodiversity with differential distributions among tissues and regions, including closely related ASVs with differing north-south distributions that correlated with Fucus phylogeography. An apparent southern range contraction of F. vesiculosus in the NW Atlantic on the North Carolina coast mimics that recently observed in the NE Atlantic. We suggest cross-Atlantic microbial structure of F. vesiculosus is related to a combination of past (glacial-cycle) and contemporary environmental drivers.}, }
@article {pmid34163371, year = {2021}, author = {Dellisanti, W and Chung, JTH and Chow, CFY and Wu, J and Wells, ML and Chan, LL}, title = {Experimental Techniques to Assess Coral Physiology in situ Under Global and Local Stressors: Current Approaches and Novel Insights.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {656562}, pmid = {34163371}, issn = {1664-042X}, abstract = {Coral reefs are declining worldwide due to global changes in the marine environment. The increasing frequency of massive bleaching events in the tropics is highlighting the need to better understand the stages of coral physiological responses to extreme conditions. Moreover, like many other coastal regions, coral reef ecosystems are facing additional localized anthropogenic stressors such as nutrient loading, increased turbidity, and coastal development. Different strategies have been developed to measure the health status of a damaged reef, ranging from the resolution of individual polyps to the entire coral community, but techniques for measuring coral physiology in situ are not yet widely implemented. For instance, while there are many studies of the coral holobiont response in single or limited-number multiple stressor experiments, they provide only partial insights into metabolic performance under more complex and temporally and spatially variable natural conditions. Here, we discuss the current status of coral reefs and their global and local stressors in the context of experimental techniques that measure core processes in coral metabolism (respiration, photosynthesis, and biocalcification) in situ, and their role in indicating the health status of colonies and communities. We highlight the need to improve the capability of in situ studies in order to better understand the resilience and stress response of corals under multiple global and local scale stressors.}, }
@article {pmid34159693, year = {2021}, author = {Campana, S and Busch, K and Hentschel, U and Muyzer, G and de Goeij, JM}, title = {DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM).}, journal = {Environmental microbiology}, volume = {23}, number = {8}, pages = {4489-4504}, pmid = {34159693}, issn = {1462-2920}, mesh = {Animals ; Bacteria/genetics ; DNA ; Isotopes ; *Microbiota ; *Porifera ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sponges possess exceptionally diverse associated microbial communities and play a major role in (re)cycling of dissolved organic matter (DOM) in marine ecosystems. Linking sponge-associated community structure with DOM utilization is essential to understand host-microbe interactions in the uptake, processing, and exchange of resources. We coupled, for the first time, DNA-stable isotope probing (DNA-SIP) with 16S rRNA amplicon sequencing in a sponge holobiont to identify which symbiotic bacterial taxa are metabolically active in DOM uptake. Parallel incubation experiments with the sponge Plakortis angulospiculatus were amended with equimolar quantities of unlabelled (12 C) and labelled (13 C) DOM. Seven bacterial amplicon sequence variants (ASVs), belonging to the phyla PAUC34f, Proteobacteria, Poribacteria, Nitrospirae, and Chloroflexi, were identified as the first active consumers of DOM. Our results support the predictions that PAUC34f, Poribacteria, and Chloroflexi are capable of organic matter degradation through heterotrophic carbon metabolism, while Nitrospirae may have a potential mixotrophic metabolism. We present a new analytical application of DNA-SIP to detect substrate incorporation into a marine holobiont with a complex associated bacterial community and provide new experimental evidence that links the identity of diverse sponge-associated bacteria to the consumption of DOM.}, }
@article {pmid34156291, year = {2021}, author = {Sweet, M and Villela, H and Keller-Costa, T and Costa, R and Romano, S and Bourne, DG and Cárdenas, A and Huggett, MJ and Kerwin, AH and Kuek, F and Medina, M and Meyer, JL and Müller, M and Pollock, FJ and Rappé, MS and Sere, M and Sharp, KH and Voolstra, CR and Zaccardi, N and Ziegler, M and Peixoto, R}, title = {Insights into the Cultured Bacterial Fraction of Corals.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {e0124920}, pmid = {34156291}, issn = {2379-5077}, support = {P20 GM103430/GM/NIGMS NIH HHS/United States ; UIDB/04565/2020//UNL | Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa (FCT/UNL)/ ; P20GM103430//Delaware IDeA Network of Biomedical Research Excellence (Delaware INBRE)/ ; Out of the Blue Box Reef Innovation Challenge People's Choice Award//Great Barrier Reef Foundation (GBRF)/ ; ANP 21005-4//Shell Brasil (Shell Brasil Ltda)/ ; }, abstract = {Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Despite their putative importance, the work dedicated to culturing coral-associated bacteria has received little attention. Combining published and unpublished data, here we report a comprehensive overview of the diversity and function of culturable bacteria isolated from corals originating from tropical, temperate, and cold-water habitats. A total of 3,055 isolates from 52 studies were considered by our metasurvey. Of these, 1,045 had full-length 16S rRNA gene sequences, spanning 138 formally described and 12 putatively novel bacterial genera across the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. We performed comparative genomic analysis using the available genomes of 74 strains and identified potential signatures of beneficial bacterium-coral symbioses among the strains. Our analysis revealed >400 biosynthetic gene clusters that underlie the biosynthesis of antioxidant, antimicrobial, cytotoxic, and other secondary metabolites. Moreover, we uncovered genomic features-not previously described for coral-bacterium symbioses-potentially involved in host colonization and host-symbiont recognition, antiviral defense mechanisms, and/or integrated metabolic interactions, which we suggest as novel targets for the screening of coral probiotics. Our results highlight the importance of bacterial cultures to elucidate coral holobiont functioning and guide the selection of probiotic candidates to promote coral resilience and improve holistic and customized reef restoration and rehabilitation efforts. IMPORTANCE Our paper is the first study to synthesize currently available but decentralized data of cultured microbes associated with corals. We were able to collate 3,055 isolates across a number of published studies and unpublished collections from various laboratories and researchers around the world. This equated to 1,045 individual isolates which had full-length 16S rRNA gene sequences, after filtering of the original 3,055. We also explored which of these had genomes available. Originally, only 36 were available, and as part of this study, we added a further 38-equating to 74 in total. From this, we investigated potential genetic signatures that may facilitate a host-associated lifestyle. Further, such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and potentially applied as a novel strategy in reef restoration and rehabilitation efforts. In the spirit of open access, we have ensured this collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope many scientists across the globe will ask for access to these cultures for future studies.}, }
@article {pmid34153755, year = {2021}, author = {Yu, X and Yu, K and Liao, Z and Chen, B and Deng, C and Yu, J and Yao, Q and Qin, Z and Liang, J}, title = {Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea.}, journal = {The Science of the total environment}, volume = {792}, number = {}, pages = {148438}, doi = {10.1016/j.scitotenv.2021.148438}, pmid = {34153755}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.}, }
@article {pmid34152600, year = {2021}, author = {Nguyen, KU and Zhang, R and Taniguchi, M and Lindsey, JS}, title = {Fluorescence Assay for Tolyporphins Amidst Abundant Chlorophyll in Crude Cyanobacterial Extracts.}, journal = {Photochemistry and photobiology}, volume = {97}, number = {6}, pages = {1507-1515}, doi = {10.1111/php.13474}, pmid = {34152600}, issn = {1751-1097}, mesh = {*Chlorophyll/chemistry ; Chlorophyll A ; *Cyanobacteria/chemistry ; Fluorescence ; Spectrometry, Fluorescence ; }, abstract = {Tolyporphins are distinctive tetrapyrrole natural products found singularly in a filamentous cyanobacterial-microbial holobiont (termed HT-58-2) from Micronesia. The absorption and fluorescence features of tolyporphins resemble those of chlorophyll a, complicating direct analysis of culture samples. Treatment of the crude (unfractionated) organic extract (CH2 Cl2 /2-propanol, 1:1) of HT-58-2 cultures with NaBH4 in methanol causes reduction of the peripheral ketone auxochromes, whereupon tolyporphins (predominantly 7,17-dioxobacteriochlorins) exhibit a bathochromic shift (λabs ˜ 676 → ˜ 700 nm) and chlorophyll a (a 131 -oxochlorin) exhibits a hypsochromic shift (λabs 665 → 634 nm). Fluorescence excitation spectroscopy (at 368 and 491 nm with λem 710 nm) enabled detection of reduced tolyporphins amidst abundant reduced chlorophyll a (1:19 ratio), a detection sensitivity >5 times that without reduction. The resulting assay combines simple sample preparation from non-axenic cultures at microscale quantities (2 mL, 2 μm), absence of any fractionation procedures, and fluorescence detection. Tolyporphins were readily detected in cultures of HT-58-2 at reasonable growth periods in the absence of environmental stressors, which was not possible previously.}, }
@article {pmid34150209, year = {2021}, author = {Brahmi, C and Chapron, L and Le Moullac, G and Soyez, C and Beliaeff, B and Lazareth, CE and Gaertner-Mazouni, N and Vidal-Dupiol, J}, title = {Effects of elevated temperature and pCO2 on the respiration, biomineralization and photophysiology of the giant clam Tridacna maxima.}, journal = {Conservation physiology}, volume = {9}, number = {1}, pages = {coab041}, pmid = {34150209}, issn = {2051-1434}, abstract = {Many reef organisms, such as the giant clams, are confronted with global change effects. Abnormally high seawater temperatures can lead to mass bleaching events and subsequent mortality, while ocean acidification may impact biomineralization processes. Despite its strong ecological and socio-economic importance, its responses to these threats still need to be explored. We investigated physiological responses of 4-year-old Tridacna maxima to realistic levels of temperature (+1.5°C) and partial pressure of carbon dioxide (pCO2) (+800 μatm of CO2) predicted for 2100 in French Polynesian lagoons during the warmer season. During a 65-day crossed-factorial experiment, individuals were exposed to two temperatures (29.2°C, 30.7°C) and two pCO2 (430 μatm, 1212 μatm) conditions. The impact of each environmental parameter and their potential synergetic effect were evaluated based on respiration, biomineralization and photophysiology. Kinetics of thermal and/or acidification stress were evaluated by performing measurements at different times of exposure (29, 41, 53, 65 days). At 30.7°C, the holobiont O2 production, symbiont photosynthetic yield and density were negatively impacted. High pCO2 had a significant negative effect on shell growth rate, symbiont photosynthetic yield and density. No significant differences of the shell microstructure were observed between control and experimental conditions in the first 29 days; however, modifications (i.e. less-cohesive lamellae) appeared from 41 days in all temperature and pCO2 conditions. No significant synergetic effect was found. Present thermal conditions (29.2°C) appeared to be sufficiently stressful to induce a host acclimatization response. All these observations indicate that temperature and pCO2 are both forcing variables affecting T. maxima's physiology and jeopardize its survival under environmental conditions predicted for the end of this century.}, }
@article {pmid34149752, year = {2021}, author = {Marín, O and González, B and Poupin, MJ}, title = {From Microbial Dynamics to Functionality in the Rhizosphere: A Systematic Review of the Opportunities With Synthetic Microbial Communities.}, journal = {Frontiers in plant science}, volume = {12}, number = {}, pages = {650609}, pmid = {34149752}, issn = {1664-462X}, abstract = {Synthetic microbial communities (SynComs) are a useful tool for a more realistic understanding of the outcomes of multiple biotic interactions where microbes, plants, and the environment are players in time and space of a multidimensional and complex system. Toward a more in-depth overview of the knowledge that has been achieved using SynComs in the rhizosphere, a systematic review of the literature on SynComs was performed to identify the overall rationale, design criteria, experimental procedures, and outcomes of in vitro or in planta tests using this strategy. After an extensive bibliography search and a specific selection process, a total of 30 articles were chosen for further analysis, grouping them by their reported SynCom size. The reported SynComs were constituted with a highly variable number of members, ranging from 3 to 190 strains, with a total of 1,393 bacterial isolates, where the three most represented phyla were Proteobacteria, Actinobacteria, and Firmicutes. Only four articles did not reference experiments with SynCom on plants, as they considered only microbial in vitro studies, whereas the others chose different plant models and plant-growth systems; some of them are described and reviewed in this article. Besides, a discussion on different approaches (bottom-up and top-down) to study the microbiome role in the rhizosphere is provided, highlighting how SynComs are an effective system to connect and fill some knowledge gaps and to have a better understanding of the mechanisms governing these multiple interactions. Although the SynCom approach is already helpful and has a promising future, more systematic and standardized studies are needed to harness its full potential.}, }
@article {pmid34142885, year = {2021}, author = {Silva, CBP and Elias-Oliveira, J and McCarthy, CG and Wenceslau, CF and Carlos, D and Tostes, RC}, title = {Ethanol: striking the cardiovascular system by harming the gut microbiota.}, journal = {American journal of physiology. Heart and circulatory physiology}, volume = {321}, number = {2}, pages = {H275-H291}, pmid = {34142885}, issn = {1522-1539}, support = {K99 HL151889/HL/NHLBI NIH HHS/United States ; R00GM118885//Foundation for the National Institutes of Health (FNIH)/ ; R01 HL149762/HL/NHLBI NIH HHS/United States ; R01HL149762//Foundation for the National Institutes of Health (FNIH)/ ; R00 GM118885/GM/NIGMS NIH HHS/United States ; }, mesh = {Alcohol Drinking/immunology/*physiopathology ; Anti-Bacterial Agents/therapeutic use ; Anti-Infective Agents, Local ; Cardiovascular Diseases/immunology/*physiopathology/therapy ; Dysbiosis/immunology/*physiopathology/therapy ; Ethanol ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Prebiotics ; Probiotics/therapeutic use ; }, abstract = {Ethanol consumption represents a significant public health problem, and excessive ethanol intake is a risk factor for cardiovascular disease (CVD), one of the leading causes of death and disability worldwide. The mechanisms underlying the effects of ethanol on the cardiovascular system are complex and not fully comprehended. The gut microbiota and their metabolites are indispensable symbionts essential for health and homeostasis and therefore, have emerged as potential contributors to ethanol-induced cardiovascular system dysfunction. By mechanisms that are not completely understood, the gut microbiota modulates the immune system and activates several signaling pathways that stimulate inflammatory responses, which in turn, contribute to the development and progression of CVD. This review summarizes preclinical and clinical evidence on the effects of ethanol in the gut microbiota and discusses the mechanisms by which ethanol-induced gut dysbiosis leads to the activation of the immune system and cardiovascular dysfunction. The cross talk between ethanol consumption and the gut microbiota and its implications are detailed. In summary, an imbalance in the symbiotic relationship between the host and the commensal microbiota in a holobiont, as seen with ethanol consumption, may contribute to CVD. Therefore, manipulating the gut microbiota, by using antibiotics, probiotics, prebiotics, and fecal microbiota transplantation might prove a valuable opportunity to prevent/mitigate the deleterious effects of ethanol and improve cardiovascular health and risk prevention.}, }
@article {pmid34139059, year = {2021}, author = {Rolli, E and Vergani, L and Ghitti, E and Patania, G and Mapelli, F and Borin, S}, title = {'Cry-for-help' in contaminated soil: a dialogue among plants and soil microbiome to survive in hostile conditions.}, journal = {Environmental microbiology}, volume = {23}, number = {10}, pages = {5690-5703}, pmid = {34139059}, issn = {1462-2920}, mesh = {Biodegradation, Environmental ; Environmental Pollution ; *Microbiota ; *Polychlorinated Biphenyls/analysis/metabolism ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {An open question in environmental ecology regards the mechanisms triggered by root chemistry to drive the assembly and functionality of a beneficial microbiome to rapidly adapt to stress conditions. This phenomenon, originally described in plant defence against pathogens and predators, is encompassed in the 'cry-for-help' hypothesis. Evidence suggests that this mechanism may be part of the adaptation strategy to ensure the holobiont fitness in polluted environments. Polychlorinated biphenyls (PCBs) were considered as model pollutants due to their toxicity, recalcitrance and poor phyto-extraction potential, which lead to a plethora of phytotoxic effects and rise environmental safety concerns. Plants have inefficient detoxification processes to catabolize PCBs, even leading to by-products with a higher toxicity. We propose that the 'cry-for-help' mechanism could drive the exudation-mediated recruitment and sustainment of the microbial services for PCBs removal, exerted by an array of anaerobic and aerobic microbial degrading populations working in a complex metabolic network. Through this synergistic interaction, the holobiont copes with the soil contamination, releasing the plant from the pollutant stress by the ecological services provided by the boosted metabolism of PCBs microbial degraders. Improving knowledge of root chemistry under PCBs stress is, therefore, advocated to design rhizoremediation strategies based on plant microbiome engineering.}, }
@article {pmid34136011, year = {2021}, author = {Vallet, M and Kaftan, F and Grabe, V and Ghaderiardakani, F and Fenizia, S and Svatoš, A and Pohnert, G and Wichard, T}, title = {A new glance at the chemosphere of macroalgal-bacterial interactions: In situ profiling of metabolites in symbiosis by mass spectrometry.}, journal = {Beilstein journal of organic chemistry}, volume = {17}, number = {}, pages = {1313-1322}, pmid = {34136011}, issn = {1860-5397}, abstract = {Symbiosis is a dominant form of life that has been observed numerous times in marine ecosystems. For example, macroalgae coexist with bacteria that produce factors that promote algal growth and morphogenesis. The green macroalga Ulva mutabilis (Chlorophyta) develops into a callus-like phenotype in the absence of its essential bacterial symbionts Roseovarius sp. MS2 and Maribacter sp. MS6. Spatially resolved studies are required to understand symbiont interactions at the microscale level. Therefore, we used mass spectrometry profiling and imaging techniques with high spatial resolution and sensitivity to gain a new perspective on the mutualistic interactions between bacteria and macroalgae. Using atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionisation high-resolution mass spectrometry (AP-SMALDI-HRMS), low-molecular-weight polar compounds were identified by comparative metabolomics in the chemosphere of Ulva. Choline (2-hydroxy-N,N,N-trimethylethan-1-aminium) was only determined in the alga grown under axenic conditions, whereas ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidinecarboxylic acid) was found in bacterial presence. Ectoine was used as a metabolic marker for localisation studies of Roseovarius sp. within the tripartite community because it was produced exclusively by these bacteria. By combining confocal laser scanning microscopy (cLSM) and AP-SMALDI-HRMS, we proved that Roseovarius sp. MS2 settled mainly in the rhizoidal zone (holdfast) of U. mutabilis. Our findings provide the fundament to decipher bacterial symbioses with multicellular hosts in aquatic ecosystems in an ecologically relevant context. As a versatile tool for microbiome research, the combined AP-SMALDI and cLSM imaging analysis with a resolution to level of a single bacterial cell can be easily applied to other microbial consortia and their hosts. The novelty of this contribution is the use of an in situ setup designed to avoid all types of external contamination and interferences while resolving spatial distributions of metabolites and identifying specific symbiotic bacteria.}, }
@article {pmid34113972, year = {2021}, author = {Sugiyama, A}, title = {Flavonoids and saponins in plant rhizospheres: roles, dynamics, and the potential for agriculture.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {85}, number = {9}, pages = {1919-1931}, doi = {10.1093/bbb/zbab106}, pmid = {34113972}, issn = {1347-6947}, support = {JPMJCR17O2//JST/ ; //CREST/ ; 18H02313//JSPS/ ; //Kyoto University/ ; }, mesh = {*Agriculture ; Flavonoids/*analysis ; Microbiota ; Plant Roots/*chemistry ; *Rhizosphere ; Saponins/*analysis ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Plants are in constant interaction with a myriad of soil microorganisms in the rhizosphere, an area of soil in close contact with plant roots. Recent research has highlighted the importance of plant-specialized metabolites (PSMs) in shaping and modulating the rhizosphere microbiota; however, the molecular mechanisms underlying the establishment and function of the microbiota mostly remain unaddressed. Flavonoids and saponins are a group of PSMs whose biosynthetic pathways have largely been revealed. Although these PSMs are abundantly secreted into the rhizosphere and exert various functions, the secretion mechanisms have not been clarified. This review summarizes the roles of flavonoids and saponins in the rhizosphere with a special focus on interactions between plants and the rhizosphere microbiota. Furthermore, this review introduces recent advancements in the dynamics of these metabolites in the rhizosphere and indicates potential applications of PSMs for crop production and discusses perspectives in this emerging research field.}, }
@article {pmid34109033, year = {2021}, author = {Tilstra, A and Roth, F and El-Khaled, YC and Pogoreutz, C and Rädecker, N and Voolstra, CR and Wild, C}, title = {Relative abundance of nitrogen cycling microbes in coral holobionts reflects environmental nitrate availability.}, journal = {Royal Society open science}, volume = {8}, number = {6}, pages = {201835}, pmid = {34109033}, issn = {2054-5703}, abstract = {Recent research suggests that nitrogen (N) cycling microbes are important for coral holobiont functioning. In particular, coral holobionts may acquire bioavailable N via prokaryotic dinitrogen (N2) fixation or remove excess N via denitrification activity. However, our understanding of environmental drivers on these processes in hospite remains limited. Employing the strong seasonality of the central Red Sea, this study assessed the effects of environmental parameters on the proportional abundances of N cycling microbes associated with the hard corals Acropora hemprichii and Stylophora pistillata. Specifically, we quantified changes in the relative ratio between nirS and nifH gene copy numbers, as a proxy for seasonal shifts in denitrification and N2 fixation potential in corals, respectively. In addition, we assessed coral tissue-associated Symbiodiniaceae cell densities and monitored environmental parameters to provide a holobiont and environmental context, respectively. While ratios of nirS to nifH gene copy numbers varied between seasons, they revealed similar seasonal patterns in both coral species, with ratios closely following patterns in environmental nitrate availability. Symbiodiniaceae cell densities aligned with environmental nitrate availability, suggesting that the seasonal shifts in nirS to nifH gene abundance ratios were probably driven by nitrate availability in the coral holobiont. Thereby, our results suggest that N cycling in coral holobionts probably adjusts to environmental conditions by increasing and/or decreasing denitrification and N2 fixation potential according to environmental nitrate availability. Microbial N cycling may, thus, extenuate the effects of changes in environmental nitrate availability on coral holobionts to support the maintenance of the coral-Symbiodiniaceae symbiosis.}, }
@article {pmid34089786, year = {2021}, author = {Pootakham, W and Mhuantong, W and Yoocha, T and Sangsrakru, D and Kongkachana, W and Sonthirod, C and Naktang, C and Jomchai, N and U-Thoomporn, S and Yeemin, T and Pengsakun, S and Sutthacheep, M and Tangphatsornruang, S}, title = {Taxonomic profiling of Symbiodiniaceae and bacterial communities associated with Indo-Pacific corals in the Gulf of Thailand using PacBio sequencing of full-length ITS and 16S rRNA genes.}, journal = {Genomics}, volume = {113}, number = {4}, pages = {2717-2729}, doi = {10.1016/j.ygeno.2021.06.001}, pmid = {34089786}, issn = {1089-8646}, mesh = {Animals ; *Anthozoa/genetics ; Bacteria/genetics ; *Dinoflagellida/genetics ; Genes, rRNA ; RNA, Ribosomal, 16S/genetics ; Thailand ; }, abstract = {Corals live with complex assemblages of microbes including bacteria, the dinoflagellate Symbiodiniaceae, fungi and viruses in a coral holobiont. These coral-associated microorganisms play an important role in their host fitness and survival. Here, we investigated the structure and diversity of algal and bacterial communities associated with five Indo-Pacific coral species, using full-length 16S rRNA and internal transcribed spacer sequences. While the dinoflagellate communities associated with Poriteslutea were dominated with Symbiodiniaceae genus Cladocopium, the other four coral hosts were associated mainly with members of the Durusdinium genus, suggesting that host species was one of the underlying factors influencing the structure and composition of dinoflagellate communities associated with corals in the Gulf of Thailand. Alphaproteobacteria dominated the microbiomes of Pocillopora spp. while Pavonafrondifera and P. lutea were associated primarily with Gammaproteobacteria. Finally, we demonstrated a superior performance of full-length 16S rRNA sequences in achieving species-resolution taxonomic classification of coral-associated microbiota.}, }
@article {pmid34078452, year = {2021}, author = {Röthig, T and Puntin, G and Wong, JCY and Burian, A and McLeod, W and Baker, DM}, title = {Holobiont nitrogen control and its potential for eutrophication resistance in an obligate photosymbiotic jellyfish.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {127}, pmid = {34078452}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; *Cnidaria ; *Dinoflagellida ; Eutrophication ; Nitrogen ; Phylogeny ; Symbiosis ; }, abstract = {BACKGROUND: Marine holobionts depend on microbial members for health and nutrient cycling. This is particularly evident in cnidarian-algae symbioses that facilitate energy and nutrient acquisition. However, this partnership is highly sensitive to environmental change-including eutrophication-that causes dysbiosis and contributes to global coral reef decline. Yet, some holobionts exhibit resistance to dysbiosis in eutrophic environments, including the obligate photosymbiotic scyphomedusa Cassiopea xamachana.<br><br>METHODS: Our aim was to assess the mechanisms in C. xamachana that stabilize symbiotic relationships. We combined labelled bicarbonate (13C) and nitrate (15N) with metabarcoding approaches to evaluate nutrient cycling and microbial community composition in symbiotic and aposymbiotic medusae.<br><br>RESULTS: C-fixation and cycling by algal Symbiodiniaceae was essential for C. xamachana as even at high heterotrophic feeding rates aposymbiotic medusae continuously lost weight. Heterotrophically acquired C and N were readily shared among host and algae. This was in sharp contrast to nitrate assimilation by Symbiodiniaceae, which appeared to be strongly restricted. Instead, the bacterial microbiome seemed to play a major role in the holobiont's DIN assimilation as uptake rates showed a significant positive relationship with phylogenetic diversity of medusa-associated bacteria. This is corroborated by inferred functional capacity that links the dominant bacterial taxa (~90 %) to nitrogen cycling. Observed bacterial community structure differed between apo- and symbiotic C. xamachana putatively highlighting enrichment of ammonium oxidizers and nitrite reducers and depletion of nitrogen-fixers in symbiotic medusae.<br><br>CONCLUSION: Host, algal symbionts, and bacterial associates contribute to regulated nutrient assimilation and cycling in C. xamachana. We found that the bacterial microbiome of symbiotic medusae was seemingly structured to increase DIN removal and enforce algal N-limitation-a mechanism that would help to stabilize the host-algae relationship even under eutrophic conditions. Video abstract.}, }
@article {pmid34078289, year = {2021}, author = {Moitinho-Silva, L and Wegener, M and May, S and Schrinner, F and Akhtar, A and Boysen, TJ and Schaeffer, E and Hansen, C and Schmidt, T and Rühlemann, MC and Hübenthal, M and Rausch, P and Kondakci, MT and Maetzler, W and Weidinger, S and Laudes, M and Süß, P and Schulte, D and Junker, R and Sommer, F and Weisser, B and Bang, C and Franke, A}, title = {Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {162}, pmid = {34078289}, issn = {1471-2180}, support = {EXC2167//Deutsche Forschungsgemeinschaft/ ; FOR5042//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Diet ; *Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {BACKGROUND: Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements.<br><br>RESULTS: Different biometric responses between endurance and strength activities were identified, such as a significant increase of lymphocytes and decrease of mean corpuscular haemoglobin concentration (MCHC) only within the strength intervention group. In the endurance group, we observed a significant reduction in hip circumference and an increase in physical working capacity (PWC). Though a large variation of microbiota changes were observed between individuals of the same group, we did not find specific collective alterations in the endurance nor the strength groups, arguing for microbiome variations specific to individuals, and therefore, were not captured in our analysis.<br><br>CONCLUSIONS: We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology.<br><br>TRIAL REGISTRATION: DRKS, DRKS00015873 . Registered 12 December 2018; Retrospectively registered.}, }
@article {pmid34072177, year = {2021}, author = {Liu, Y and Palaniveloo, K and Alias, SA and Sathiya Seelan, JS}, title = {Species Diversity and Secondary Metabolites of Sarcophyton-Associated Marine Fungi.}, journal = {Molecules (Basel, Switzerland)}, volume = {26}, number = {11}, pages = {}, pmid = {34072177}, issn = {1420-3049}, mesh = {Alkaloids/*chemistry ; Alternaria ; Amino Acids/chemistry ; Animals ; Anthozoa/metabolism/*microbiology ; Anthraquinones/metabolism ; Biodiversity ; Biological Assay ; Biological Products/chemistry/*metabolism ; Fungi/*metabolism ; Inhibitory Concentration 50 ; Ketones/metabolism ; Microbiota ; Symbiosis ; }, abstract = {Soft corals are widely distributed across the globe, especially in the Indo-Pacific region, with Sarcophyton being one of the most abundant genera. To date, there have been 50 species of identified Sarcophyton. These soft corals host a diverse range of marine fungi, which produce chemically diverse, bioactive secondary metabolites as part of their symbiotic nature with the soft coral hosts. The most prolific groups of compounds are terpenoids and indole alkaloids. Annually, there are more bio-active compounds being isolated and characterised. Thus, the importance of the metabolite compilation is very much important for future reference. This paper compiles the diversity of Sarcophyton species and metabolites produced by their associated marine fungi, as well as the bioactivity of these identified compounds. A total of 88 metabolites of structural diversity are highlighted, indicating the huge potential these symbiotic relationships hold for future research.}, }
@article {pmid34067328, year = {2021}, author = {Bourgin, M and Kriaa, A and Mkaouar, H and Mariaule, V and Jablaoui, A and Maguin, E and Rhimi, M}, title = {Bile Salt Hydrolases: At the Crossroads of Microbiota and Human Health.}, journal = {Microorganisms}, volume = {9}, number = {6}, pages = {}, pmid = {34067328}, issn = {2076-2607}, support = {PhD fellowship-BM//MICA Department - INRAE/ ; PhD fellowship-BM//ONIRIS/ ; MICAfrica - 952583//Horizon 2020/ ; }, abstract = {The gut microbiota has been increasingly linked to metabolic health and disease over the last few decades. Several factors have been suggested to be involved in lipid metabolism and metabolic responses. One mediator that has gained great interest as a clinically important enzyme is bile salt hydrolase (BSH). BSH enzymes are widely distributed in human gastrointestinal microbial communities and are believed to play key roles in both microbial and host physiology. In this review, we discuss the current evidence related to the role of BSHs in health and provide useful insights that may pave the way for new therapeutic targets in human diseases.}, }
@article {pmid34066959, year = {2021}, author = {Miller, WB and Enguita, FJ and Leitão, AL}, title = {Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution.}, journal = {Cells}, volume = {10}, number = {5}, pages = {}, pmid = {34066959}, issn = {2073-4409}, mesh = {Animals ; *Biological Evolution ; *Cell Engineering ; Cognition/*physiology ; *Gene Editing ; *Homeostasis ; Humans ; *Selection, Genetic ; }, abstract = {Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.}, }
@article {pmid34065848, year = {2021}, author = {Lyu, D and Msimbira, LA and Nazari, M and Antar, M and Pagé, A and Shah, A and Monjezi, N and Zajonc, J and Tanney, CAS and Backer, R and Smith, DL}, title = {The Coevolution of Plants and Microbes Underpins Sustainable Agriculture.}, journal = {Microorganisms}, volume = {9}, number = {5}, pages = {}, pmid = {34065848}, issn = {2076-2607}, support = {RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Terrestrial plants evolution occurred in the presence of microbes, the phytomicrobiome. The rhizosphere microbial community is the most abundant and diverse subset of the phytomicrobiome and can include both beneficial and parasitic/pathogenic microbes. Prokaryotes of the phytomicrobiome have evolved relationships with plants that range from non-dependent interactions to dependent endosymbionts. The most extreme endosymbiotic examples are the chloroplasts and mitochondria, which have become organelles and integral parts of the plant, leading to some similarity in DNA sequence between plant tissues and cyanobacteria, the prokaryotic symbiont of ancestral plants. Microbes were associated with the precursors of land plants, green algae, and helped algae transition from aquatic to terrestrial environments. In the terrestrial setting the phytomicrobiome contributes to plant growth and development by (1) establishing symbiotic relationships between plant growth-promoting microbes, including rhizobacteria and mycorrhizal fungi, (2) conferring biotic stress resistance by producing antibiotic compounds, and (3) secreting microbe-to-plant signal compounds, such as phytohormones or their analogues, that regulate aspects of plant physiology, including stress resistance. As plants have evolved, they recruited microbes to assist in the adaptation to available growing environments. Microbes serve themselves by promoting plant growth, which in turn provides microbes with nutrition (root exudates, a source of reduced carbon) and a desirable habitat (the rhizosphere or within plant tissues). The outcome of this coevolution is the diverse and metabolically rich microbial community that now exists in the rhizosphere of terrestrial plants. The holobiont, the unit made up of the phytomicrobiome and the plant host, results from this wide range of coevolved relationships. We are just beginning to appreciate the many ways in which this complex and subtle coevolution acts in agricultural systems.}, }
@article {pmid34058984, year = {2021}, author = {Medina Munoz, M and Brenner, C and Richmond, D and Spencer, N and Rio, RVM}, title = {The holobiont transcriptome of teneral tsetse fly species of varying vector competence.}, journal = {BMC genomics}, volume = {22}, number = {1}, pages = {400}, pmid = {34058984}, issn = {1471-2164}, support = {R01 AI118789/AI/NIAID NIH HHS/United States ; R01AI118789//National Institute of Allergy and Infectious Diseases/ ; }, mesh = {Animals ; Enterobacteriaceae/genetics ; Humans ; Transcriptome ; *Tsetse Flies/genetics ; Wigglesworthia/genetics ; }, abstract = {BACKGROUND: Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment and development, yet our understanding of why remains fragmentary. The tsetse gut microbiome is dominated by two Gammaproteobacteria, an essential and ancient mutualist Wigglesworthia glossinidia and a commensal Sodalis glossinidius. Here, we characterize and compare the metatranscriptome of teneral Glossina morsitans to that of G. brevipalpis and describe unique immunological, physiological, and metabolic landscapes that may impact vector competence differences between these two species.<br><br>RESULTS: An active expression profile was observed for Wigglesworthia immediately following host adult metamorphosis. Specifically, 'translation, ribosomal structure and biogenesis' followed by 'coenzyme transport and metabolism' were the most enriched clusters of orthologous genes (COGs), highlighting the importance of nutrient transport and metabolism even following host species diversification. Despite the significantly smaller Wigglesworthia genome more differentially expressed genes (DEGs) were identified between interspecific isolates (n = 326, ~ 55% of protein coding genes) than between the corresponding Sodalis isolates (n = 235, ~ 5% of protein coding genes) likely reflecting distinctions in host co-evolution and adaptation. DEGs between Sodalis isolates included genes involved in chitin degradation that may contribute towards trypanosome susceptibility by compromising the immunological protection provided by the peritrophic matrix. Lastly, G. brevipalpis tenerals demonstrate a more immunologically robust background with significant upregulation of IMD and melanization pathways.<br><br>CONCLUSIONS: These transcriptomic differences may collectively contribute to vector competence differences between tsetse species and offers translational relevance towards the design of novel vector control strategies.}, }
@article {pmid34048702, year = {2021}, author = {Traylor-Knowles, N}, title = {Unlocking the single-cell mysteries of a reef-building coral.}, journal = {Cell}, volume = {184}, number = {11}, pages = {2802-2804}, doi = {10.1016/j.cell.2021.05.007}, pmid = {34048702}, issn = {1097-4172}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; Ecosystem ; }, abstract = {Coral reefs are one of the most important ecosystems in the world but least understood from a cellular level. In this issue of Cell, Levy et al. unravel the single-cell gene expression of the coral holobiont and open the doors to better understand the novel diversity of cell types.}, }
@article {pmid34025595, year = {2021}, author = {Manriquez, B and Muller, D and Prigent-Combaret, C}, title = {Experimental Evolution in Plant-Microbe Systems: A Tool for Deciphering the Functioning and Evolution of Plant-Associated Microbial Communities.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {619122}, pmid = {34025595}, issn = {1664-302X}, abstract = {In natural environments, microbial communities must constantly adapt to stressful environmental conditions. The genetic and phenotypic mechanisms underlying the adaptive response of microbial communities to new (and often complex) environments can be tackled with a combination of experimental evolution and next generation sequencing. This combination allows to analyse the real-time evolution of microbial populations in response to imposed environmental factors or during the interaction with a host, by screening for phenotypic and genotypic changes over a multitude of identical experimental cycles. Experimental evolution (EE) coupled with comparative genomics has indeed facilitated the monitoring of bacterial genetic evolution and the understanding of adaptive evolution processes. Basically, EE studies had long been done on single strains, allowing to reveal the dynamics and genetic targets of natural selection and to uncover the correlation between genetic and phenotypic adaptive changes. However, species are always evolving in relation with other species and have to adapt not only to the environment itself but also to the biotic environment dynamically shaped by the other species. Nowadays, there is a growing interest to apply EE on microbial communities evolving under natural environments. In this paper, we provide a non-exhaustive review of microbial EE studies done with systems of increasing complexity (from single species, to synthetic communities and natural communities) and with a particular focus on studies between plants and plant-associated microorganisms. We highlight some of the mechanisms controlling the functioning of microbial species and their adaptive responses to environment changes and emphasize the importance of considering bacterial communities and complex environments in EE studies.}, }
@article {pmid34020587, year = {2021}, author = {Maire, J and Blackall, LL and van Oppen, MJH}, title = {Microbiome characterization of defensive tissues in the model anemone Exaiptasia diaphana.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {152}, pmid = {34020587}, issn = {1471-2180}, mesh = {Animal Structures/microbiology ; Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Coral Reefs ; DNA, Bacterial/genetics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sea Anemones/*microbiology/physiology ; Symbiosis ; }, abstract = {BACKGROUND: Coral reefs are among the most diverse and productive ecosystems on Earth. This success relies on the coral's association with a wide range of microorganisms, including dinoflagellates of the family Symbiodiniaceae that provide coral hosts with most of their organic carbon requirements. While bacterial associates have long been overlooked, research on these microorganisms is gaining traction, and deciphering bacterial identity and function is greatly enhancing our understanding of cnidarian biology. Here, we investigated bacterial communities in defensive tissues (acontia) of the coral model, the sea anemone Exaiptasia diaphana. Acontia are internal filaments that are ejected upon detection of an external threat and release toxins to repel predators.<br><br>RESULTS: Using culturing techniques and 16S rRNA gene metabarcoding we identified bacterial communities associated with acontia of four Great Barrier Reef-sourced E. diaphana genotypes. We show that bacterial communities are similar across genotypes, and dominated by Alteromonadaceae, Vibrionaceae, Rhodobacteraceae, and Saprospiraceae. By analyzing abundant amplicon sequence variants (ASVs) from metabarcoding data from acontia and comparing these to data from whole anemones, we identified five potentially important bacterial genera of the acontia microbiome: Vibrio, Sulfitobacter, Marivita, Alteromonas, and Lewinella. The role of these bacteria within the acontia remains uninvestigated but could entail assistance in defense processes such as toxin production.<br><br>CONCLUSIONS: This study provides insight into potential bacterial involvement in cnidarian defense tissues and highlights the need to study bacterial communities in individual compartments within a holobiont.}, }
@article {pmid34011286, year = {2021}, author = {Zhang, Y and Yang, Q and Ling, J and Long, L and Huang, H and Yin, J and Wu, M and Tang, X and Lin, X and Zhang, Y and Dong, J}, title = {Correction to: Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {150}, pmid = {34011286}, issn = {1471-2180}, }
@article {pmid33991262, year = {2021}, author = {Zhang, Y and Yang, Q and Zhang, Y and Ahmad, M and Ling, J and Dong, J and Wang, Y}, title = {The diversity and metabolic potential of the microbial functional gene associated with Porites pukoensis.}, journal = {Ecotoxicology (London, England)}, volume = {30}, number = {5}, pages = {986-995}, pmid = {33991262}, issn = {1573-3017}, support = {41676107//National Natural Science Foundation of China/ ; XDA13020300//Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Archaea ; Biodiversity ; Coral Reefs ; Fungi ; }, abstract = {Coral reef ecosystems usually distribute in oligotrophic tropical and subtropical marine environments, but they possess great biodiversity and high productivity. It may attribute to its efficient internal nutrient cycle system. However, the knowledge of functional microbial community structure is still limited. In this study, both functional gene array (Geochip 5.0) and nifH Illumina sequencing were used to profile the overall functional genes and diazotrophic communities associated with coral Porites pukoensis. More than 7500 microbial functional genes were detected from archaea, bacteria, and fungi. Most of these genes are related to the transformation of carbon, nitrogen, sulfur, and phosphorus, providing evidence that microbes in the coral holobiont play important roles in the biogeochemical cycle of coral reef ecosystems. Our results indicated a high diversity of diazotrophs associated with corals. The dominant diazotrophic groups were related to phyla Alphaproteobacteria, Deltaproteobacteria, Cyanobacteria, and Gammaproteobacteria. And the dominant diazotrophic communities were divided into four clusters. They were affiliated with nifH sequences from genera Zymomonas, Halorhodospira, Leptolyngbya, Trichormus, and Desulfovibrio, indicating these groups may play a more important role in the nitrogen-fixing process in the coral holobiont. This study revealed functional gene diversity and suggested the roles they played in the biogeochemical cycling of the coral holobiont.}, }
@article {pmid33990868, year = {2021}, author = {Aguirre-von-Wobeser, E}, title = {Type II Photosynthetic Reaction Center Genes of Avocado (Persea americana Mill.) Bark Microbial Communities are Dominated by Aerobic Anoxygenic Alphaproteobacteria.}, journal = {Current microbiology}, volume = {78}, number = {7}, pages = {2623-2630}, pmid = {33990868}, issn = {1432-0991}, support = {CB-2014-01-242956//SEP/CONACyT/ ; }, mesh = {*Alphaproteobacteria ; *Microbiota ; *Persea ; Photosynthesis ; *Photosynthetic Reaction Center Complex Proteins ; Plant Bark ; }, abstract = {The tree bark environment is an important microbial habitat distributed worldwide on thrillions of trees. However, the microbial communities of tree bark are largely unknown, with most studies on plant aerial surfaces focused on the leaves. Recently, we presented a metagenomic study of bark microbial communities from avocado. In these communities, oxygenic and anoxygenic photosynthesis genes were very abundant, especially when compared to rhizospheric soil from the same trees. In this work, Evolutionary Placement Algorithm analysis was performed on metagenomic reads orthologous to the PufLM gene cluster, encoding for the bacterial type II photosynthetic reaction center. These photosynthetic genes were found affiliated to different groups of bacteria, mostly aerobic anoxygenic photosynthetic Alphaproteobacteria, including Sphingomonas, Methylobacterium and several Rhodospirillales. These results suggest that anoxygenic photosynthesis in avocado bark microbial communities functions primarily as additional energy source for heterotrophic growth. Together with our previous results, showing a large abundance of cyanobacteria in these communities, a picture emerges of the tree holobiont, where light penetrating the tree canopies and reaching the inner stems, including the trunk, is probably utilized by cyanobacteria for oxygenic photosynthesis, and the far-red light aids the growth of aerobic anoxygenic photosynthetic bacteria.}, }
@article {pmid33990786, year = {2021}, author = {Nagpal, J and Cryan, JF}, title = {Host genetics, the microbiome &amp; behaviour-a 'Holobiont' perspective.}, journal = {Cell research}, volume = {31}, number = {8}, pages = {832-833}, pmid = {33990786}, issn = {1748-7838}, support = {SFI/12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; GOIPD/2019/714//Irish Research Council (An Chomhairle um Thaighde in Éirinn)/ ; }, mesh = {*Microbiota/genetics ; Symbiosis/genetics ; }, }
@article {pmid33957989, year = {2021}, author = {Doering, T and Wall, M and Putchim, L and Rattanawongwan, T and Schroeder, R and Hentschel, U and Roik, A}, title = {Towards enhancing coral heat tolerance: a "microbiome transplantation" treatment using inoculations of homogenized coral tissues.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {102}, pmid = {33957989}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; *Thermotolerance ; }, abstract = {BACKGROUND: Microbiome manipulation could enhance heat tolerance and help corals survive the pressures of ocean warming. We conducted coral microbiome transplantation (CMT) experiments using the reef-building corals, Pocillopora and Porites, and investigated whether this technique can benefit coral heat resistance while modifying the bacterial microbiome. Initially, heat-tolerant donors were identified in the wild. We then used fresh homogenates made from coral donor tissues to inoculate conspecific, heat-susceptible recipients and documented their bleaching responses and microbiomes by 16S rRNA gene metabarcoding.<br><br>RESULTS: Recipients of both coral species bleached at lower rates compared to the control group when exposed to short-term heat stress (34 °C). One hundred twelve (Pocillopora sp.) and sixteen (Porites sp.) donor-specific bacterial species were identified in the microbiomes of recipients indicating transmission of bacteria. The amplicon sequence variants of the majority of these transmitted bacteria belonged to known, putatively symbiotic bacterial taxa of corals and were linked to the observed beneficial effect on the coral stress response. Microbiome dynamics in our experiments support the notion that microbiome community evenness and dominance of one or few bacterial species, rather than host-species identity, were drivers for microbiome stability in a holobiont context.<br><br>CONCLUSIONS: Our results suggest that coral recipients likely favor the uptake of putative bacterial symbionts, recommending to include these taxonomic groups in future coral probiotics screening efforts. Our study suggests a scenario where these donor-specific bacterial symbionts might have been more efficient in supporting the recipients to resist heat stress compared to the native symbionts present in the control group. These findings urgently call for further experimental investigation of the mechanisms of action underlying the beneficial effect of CMT and for field-based long-term studies testing the persistence of the effect. Video abstract.}, }
@article {pmid33957417, year = {2021}, author = {Rinkevich, B}, title = {Augmenting coral adaptation to climate change via coral gardening (the nursery phase).}, journal = {Journal of environmental management}, volume = {291}, number = {}, pages = {112727}, doi = {10.1016/j.jenvman.2021.112727}, pmid = {33957417}, issn = {1095-8630}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa ; Climate Change ; Conservation of Natural Resources ; Coral Reefs ; Ecosystem ; Gardening ; }, abstract = {Unceasing climate change and anthropogenic impacts on coral reefs worldwide lead the needs for augmenting adaptive potential of corals. Currently, the most successful approach for restoring degraded reefs is 'coral gardening', where corals are farmed in underwater nurseries, then outplanted to damaged reefs. Dealing with enhanced coral adaptation, the 'coral gardening' approach is conceptually structured here within a hierarchical list of five encircling tiers that include all restoration activities, focusing on the nursery phase. Each tier encompasses all the activities performed in the levels below it hierarchically. The first is the 'coral mariculture' tier, followed by the 'ecological engineering' tier. The third is the adaptation-based reef restoration (ABRR) tier, preceding the fourth ('ecosystem seascape') and the fifth ('ecosystem services') tiers. The ABRR tier is further conceptualized and its constituent five classes (phenotypic plasticity, assisted migration, epigenetics, coral chimerism, holobiont modification) are detailed. It is concluded that the nursery phase of the 'gardening' tenet may further serve as a platform to enhance the adaptation capacities of corals to climate change through the five ABBR classes. Employing the 'gardening' tiers in reef restoration without considering ABRR will scarcely be able to meet global targets for healthy reef ecosystems in the future.}, }
@article {pmid33947806, year = {2021}, author = {Swain, TD and Lax, S and Gilbert, J and Backman, V and Marcelino, LA}, title = {A Phylogeny-Informed Analysis of the Global Coral-Symbiodiniaceae Interaction Network Reveals that Traits Correlated with Thermal Bleaching Are Specific to Symbiont Transmission Mode.}, journal = {mSystems}, volume = {6}, number = {3}, pages = {}, pmid = {33947806}, issn = {2379-5077}, abstract = {The complex network of associations between corals and their dinoflagellates (family Symbiodiniaceae) are the basis of coral reef ecosystems but are sensitive to increasing global temperatures. Coral-symbiont interactions are restricted by ecological and evolutionary determinants that constrain partner choice and influence holobiont response to environmental stress; however, little is known about how these processes shape thermal resilience of the holobiont. Here, we built a network of global coral-Symbiodiniaceae associations, mapped species traits (e.g., symbiont transmission mode and biogeography) and phylogenetic relationships of both partners onto the network, and assigned thermotolerance to both host and symbiont nodes. Using network analysis and phylogenetic comparative methods, we determined the contribution of species traits to thermal resilience of the holobiont, while accounting for evolutionary patterns among species. We found that the network shows nonrandom interactions among species, which are shaped by evolutionary history, symbiont transmission mode (horizontally transmitted [HT] or vertically transmitted [VT] corals) and biogeography. Coral phylogeny, but not Symbiodiniaceae phylogeny, symbiont transmission mode, or biogeography, was a good predictor of thermal resilience. Closely related corals have similar Symbiodiniaceae interaction patterns and bleaching susceptibilities. Nevertheless, the association patterns that explain increased host thermal resilience are not generalizable across the entire network but are instead unique to HT and VT corals. Under nonstress conditions, thermally resilient VT coral species associate with thermotolerant phylotypes and limit their number of unique symbionts and overall symbiont thermotolerance diversity, while thermally resilient HT coral species associate with a few host-specific symbiont phylotypes.IMPORTANCE Recent advances have revealed a complex network of interactions between coral and Symbiodiniaceae. Specifically, nonrandom association patterns, which are determined in part by restrictions imposed by symbiont transmission mode, increase the sensitivity of the overall network to thermal stress. However, little is known about the extent to which coral-Symbiodiniaceae network resistance to thermal stress is shaped by host and symbiont species phylogenetic relationships and host and symbiont species traits, such as symbiont transmission mode. We built a frequency-weighted global coral-Symbiodiniaceae network and used network analysis and phylogenetic comparative methods to show that evolutionary relatedness, but not transmission mode, predicts thermal resilience of the coral-Symbiodiniaceae holobiont. Consequently, thermal stress events could result in nonrandom pruning of susceptible lineages and loss of taxonomic diversity with catastrophic effects on community resilience to future events. Our results show that inclusion of the contribution of evolutionary and ecological processes will further our understanding of the fate of coral assemblages under climate change.}, }
@article {pmid33946450, year = {2021}, author = {Embacher, J and Neuhauser, S and Zeilinger, S and Kirchmair, M}, title = {Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {7}, number = {5}, pages = {}, pmid = {33946450}, issn = {2309-608X}, support = {//doctoral program 'Biointeractions from basics to application' (BioApp) at the University of Innsbruck./ ; }, abstract = {The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.}, }
@article {pmid33941698, year = {2021}, author = {Savary, R and Barshis, DJ and Voolstra, CR and Cárdenas, A and Evensen, NR and Banc-Prandi, G and Fine, M and Meibom, A}, title = {Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {19}, pages = {}, pmid = {33941698}, issn = {1091-6490}, mesh = {Acclimatization/*genetics ; Animals ; Anthozoa/classification/*genetics/microbiology ; Bacteria/classification/genetics ; *Coral Reefs ; Heat-Shock Response/*genetics ; Hot Temperature ; Indian Ocean ; Microbiota/*genetics/physiology ; RNA, Ribosomal, 16S/genetics ; RNA-Seq/methods ; Symbiosis/genetics ; Time Factors ; Transcriptome/*genetics ; }, abstract = {Corals from the northern Red Sea and Gulf of Aqaba exhibit extreme thermal tolerance. To examine the underlying gene expression dynamics, we exposed Stylophora pistillata from the Gulf of Aqaba to short-term (hours) and long-term (weeks) heat stress with peak seawater temperatures ranging from their maximum monthly mean of 27 °C (baseline) to 29.5 °C, 32 °C, and 34.5 °C. Corals were sampled at the end of the heat stress as well as after a recovery period at baseline temperature. Changes in coral host and symbiotic algal gene expression were determined via RNA-sequencing (RNA-Seq). Shifts in coral microbiome composition were detected by complementary DNA (cDNA)-based 16S ribosomal RNA (rRNA) gene sequencing. In all experiments up to 32 °C, RNA-Seq revealed fast and pervasive changes in gene expression, primarily in the coral host, followed by a return to baseline gene expression for the majority of coral (>94%) and algal (>71%) genes during recovery. At 34.5 °C, large differences in gene expression were observed with minimal recovery, high coral mortality, and a microbiome dominated by opportunistic bacteria (including Vibrio species), indicating that a lethal temperature threshold had been crossed. Our results show that the S. pistillata holobiont can mount a rapid and pervasive gene expression response contingent on the amplitude and duration of the thermal stress. We propose that the transcriptomic resilience and transcriptomic acclimation observed are key to the extraordinary thermal tolerance of this holobiont and, by inference, of other northern Red Sea coral holobionts, up to seawater temperatures of at least 32 °C, that is, 5 °C above their current maximum monthly mean.}, }
@article {pmid33930136, year = {2021}, author = {Zilber-Rosenberg, I and Rosenberg, E}, title = {Microbial-driven genetic variation in holobionts.}, journal = {FEMS microbiology reviews}, volume = {45}, number = {6}, pages = {}, doi = {10.1093/femsre/fuab022}, pmid = {33930136}, issn = {1574-6976}, mesh = {Animals ; Biological Evolution ; Gene Transfer, Horizontal ; Genetic Variation/genetics ; Humans ; *Microbiota/genetics ; *Symbiosis/genetics ; }, abstract = {Genetic variation in holobionts (host and microbiome), occurring in both host and microbiome genomes, can be observed from two perspectives: observable variations and processes that bring about the variation. Observable includes the enormous genetic diversity of prokaryotes, which gave rise to eukaryotes. Holobionts then evolved a rich microbiome with a stable core containing essential genes, less so common taxa and a more diverse non-core, enabling considerable genetic variation. Thus, the human gut microbiome, for example, contains 1000 times more unique genes than are present in the human genome. Microbial-driven genetic variation processes in holobionts include: (1) acquisition of novel microbes from the environment, (2) amplification/reduction of certain microbes in the microbiome, (3) horizontal gene transfer between microbes and between microbes and host and (4) mutation, which plays a role in optimizing interactions between microbiota and between microbiota and host. We suggest that invertebrates and plants, where microbes can live intracellularly, have a greater chance of genetic exchange between microbiota and host, a greater chance of vertical transmission and a greater effect of microbiome on evolution than vertebrates. However, even in vertebrates the microbiome can aid in environmental fluctuations by amplification/reduction and by acquisition of novel microorganisms.}, }
@article {pmid33914388, year = {2021}, author = {Wong, KH and Goodbody-Gringley, G and de Putron, SJ and Becker, DM and Chequer, A and Putnam, HM}, title = {Brooded coral offspring physiology depends on the combined effects of parental press and pulse thermal history.}, journal = {Global change biology}, volume = {27}, number = {13}, pages = {3179-3195}, doi = {10.1111/gcb.15629}, pmid = {33914388}, issn = {1365-2486}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Chlorophyll A ; Coral Reefs ; Hot Temperature ; }, abstract = {Reef-building corals respond to the temporal integration of both pulse events (i.e., heat waves) and press thermal history (i.e., local environment) via physiological changes, with ecological consequences. We used a "press-pulse-press" experimental framework to expose the brooding coral Porites astreoides to various thermal histories to understand the physiological response of temporal dynamics within and across generations. We collected adult colonies from two reefs (outer Rim reef and inner Patch reef) in Bermuda with naturally contrasting thermal regimes as our initial "press" scenario, followed by a 21-day ex situ "pulse" thermal stress of 30.4°C during larval brooding, and a "press" year-long adult reciprocal transplant between the original sites. Higher endosymbiont density and holobiont protein was found in corals originating from the lower thermal variability site (Rim) compared to the higher thermal variability site (Patch). The thermal pulse event drove significant declines in photosynthesis, endosymbiont density, and chlorophyll a, with bleaching phenotype convergence for adults from both histories. Following the reciprocal transplant, photosynthesis was higher in previously heated corals, indicating recovery from the thermal pulse. The effect of origin (initial press) modulated the response to transplant site for endosymbiont density and chlorophyll a, suggesting contrasting acclimation strategies. Higher respiration and photosynthetic rates were found in corals originating from the Rim site, indicating greater energy available for reproduction, supported by larger larvae released from Rim corals post-transplantation. Notably, parental exposure to the pulse thermal event resulted in increased offspring plasticity when parents were transplanted to foreign sites, highlighting the legacy of the pulse event and the importance of the environment during recovery in contributing to cross-generational or developmental plasticity. Together, these findings provide novel insight into the role of historical disturbance events in driving differential outcomes within and across generations, which is of critical importance in forecasting reef futures.}, }
@article {pmid33912198, year = {2020}, author = {Harman, G and Khadka, R and Doni, F and Uphoff, N}, title = {Benefits to Plant Health and Productivity From Enhancing Plant Microbial Symbionts.}, journal = {Frontiers in plant science}, volume = {11}, number = {}, pages = {610065}, pmid = {33912198}, issn = {1664-462X}, abstract = {Plants exist in close association with uncountable numbers of microorganisms around, on, and within them. Some of these endophytically colonize plant roots. The colonization of roots by certain symbiotic strains of plant-associated bacteria and fungi results in these plants performing better than plants whose roots are colonized by only the wild populations of microbes. We consider here crop plants whose roots are inhabited by introduced organisms, referring to them as Enhanced Plant Holobionts (EPHs). EPHs frequently exhibit resistance to specific plant diseases and pests (biotic stresses); resistance to abiotic stresses such as drought, cold, salinity, and flooding; enhanced nutrient acquisition and nutrient use efficiency; increased photosynthetic capability; and enhanced ability to maintain efficient internal cellular functioning. The microbes described here generate effects in part through their production of Symbiont-Associated Molecular Patterns (SAMPs) that interact with receptors in plant cell membranes. Such interaction results in the transduction of systemic signals that cause plant-wide changes in the plants' gene expression and physiology. EPH effects arise not only from plant-microbe interactions, but also from microbe-microbe interactions like competition, mycoparasitism, and antibiotic production. When root and shoot growth are enhanced as a consequence of these root endophytes, this increases the yield from EPH plants. An additional benefit from growing larger root systems and having greater photosynthetic capability is greater sequestration of atmospheric CO2. This is transferred to roots where sequestered C, through exudation or root decomposition, becomes part of the total soil carbon, which reduces global warming potential in the atmosphere. Forming EPHs requires selection and introduction of appropriate strains of microorganisms, with EPH performance affected also by the delivery and management practices.}, }
@article {pmid33910503, year = {2021}, author = {Zhang, Y and Yang, Q and Ling, J and Long, L and Huang, H and Yin, J and Wu, M and Tang, X and Lin, X and Zhang, Y and Dong, J}, title = {Shifting the microbiome of a coral holobiont and improving host physiology by inoculation with a potentially beneficial bacterial consortium.}, journal = {BMC microbiology}, volume = {21}, number = {1}, pages = {130}, pmid = {33910503}, issn = {1471-2180}, mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions/*physiology ; Microbiota/*physiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The coral microbiome plays a key role in host health by being involved in energy metabolism, nutrient cycling, and immune system formation. Inoculating coral with beneficial bacterial consortia may enhance the ability of this host to cope with complex and changing marine environments. In this study, the coral Pocillopora damicornis was inoculated with a beneficial microorganisms for corals (BMC) consortium to investigate how the coral host and its associated microbial community would respond.<br><br>RESULTS: High-throughput 16S rRNA gene sequencing revealed no significant differences in bacterial community α-diversity. However, the bacterial community structure differed significantly between the BMC and placebo groups at the end of the experiment. Addition of the BMC consortium significantly increased the relative abundance of potentially beneficial bacteria, including the genera Mameliella and Endozoicomonas. Energy reserves and calcification rates of the coral host were also improved by the addition of the BMC consortium. Co-occurrence network analysis indicated that inoculation of coral with the exogenous BMC consortium improved the physiological status of the host by shifting the coral-associated microbial community structure.<br><br>CONCLUSIONS: Manipulating the coral-associated microbial community may enhance the physiology of coral in normal aquarium conditions (no stress applied), which may hypothetically contribute to resilience and resistance in this host.}, }
@article {pmid33905604, year = {2021}, author = {Mayer, T and Mari, A and Almario, J and Murillo-Roos, M and Syed M Abdullah, H and Dombrowski, N and Hacquard, S and Kemen, EM and Agler, MT}, title = {Obtaining deeper insights into microbiome diversity using a simple method to block host and nontargets in amplicon sequencing.}, journal = {Molecular ecology resources}, volume = {21}, number = {6}, pages = {1952-1965}, doi = {10.1111/1755-0998.13408}, pmid = {33905604}, issn = {1755-0998}, support = {//Deutsche Forschungsgemeinschaft/ ; 390713860//Germany's Excellence Strategy/ ; //International Leibniz Research School/ ; //Max-Planck Gesellschaft/ ; //University of Tübingen/ ; //European Research Council (ERC)/ ; ERC-2018-COG 820124//DeCoCt research progra/ ; }, mesh = {Bacteria/classification ; Fungi/classification ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Oomycetes/classification ; Plants/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Profiling diverse microbiomes is revolutionizing our understanding of biological mechanisms and ecologically relevant problems, including metaorganism (host + microbiome) assembly, functions and adaptation. Amplicon sequencing of multiple conserved, phylogenetically informative loci has therefore become an instrumental tool for many researchers. Investigations in many systems are hindered, however, since essential sequencing depth can be lost by amplification of nontarget DNA from hosts or overabundant microorganisms. Here, we introduce "blocking oligos", a low-cost and flexible method using standard oligonucleotides to block amplification of diverse nontargets and software to aid their design. We apply them primarily in leaves, where exceptional challenges with host amplification prevail. A. thaliana-specific blocking oligos applied in eight different target loci reduce undesirable host amplification by up to 90%. To expand applicability, we designed universal 16S and 18S rRNA gene plant blocking oligos for targets that are conserved in diverse plant species and demonstrate that they efficiently block five plant species from five orders spanning monocots and dicots (Bromus erectus, Plantago lanceolata, Lotus corniculatus, Amaranth sp., Arabidopsis thaliana). These can increase alpha diversity discovery without biasing beta diversity patterns and do not compromise microbial load information inherent to plant-derived 16S rRNA gene amplicon sequencing data. Finally, we designed and tested blocking oligos to avoid amplification of 18S rRNA genes of a sporulating oomycete pathogen, demonstrating their effectiveness in applications well beyond plants. Using these tools, we generated a survey of the A. thaliana leaf microbiome based on eight loci targeting bacterial, fungal, oomycete and other eukaryotic microorganisms and discuss complementarity of commonly used amplicon sequencing regions for describing leaf microbiota. This approach has potential to make questions in a variety of study systems more tractable by making amplicon sequencing more targeted, leading to deeper, systems-based insights into microbial discovery. For fast and easy design for blocking oligos for any nontarget DNA in other study systems, we developed a publicly available R package.}, }
@article {pmid33898524, year = {2021}, author = {Mach, N and Moroldo, M and Rau, A and Lecardonnel, J and Le Moyec, L and Robert, C and Barrey, E}, title = {Understanding the Holobiont: Crosstalk Between Gut Microbiota and Mitochondria During Long Exercise in Horse.}, journal = {Frontiers in molecular biosciences}, volume = {8}, number = {}, pages = {656204}, pmid = {33898524}, issn = {2296-889X}, abstract = {Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPARγ, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.}, }
@article {pmid33897663, year = {2021}, author = {Berg, G and Kusstatscher, P and Abdelfattah, A and Cernava, T and Smalla, K}, title = {Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {650610}, pmid = {33897663}, issn = {1664-302X}, abstract = {Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.}, }
@article {pmid33897642, year = {2021}, author = {Costa, RM and Cárdenas, A and Loussert-Fonta, C and Toullec, G and Meibom, A and Voolstra, CR}, title = {Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {637834}, pmid = {33897642}, issn = {1664-302X}, abstract = {Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide important foundation data to extend Aiptasia as a coral model for bacterial functional studies.}, }
@article {pmid33896632, year = {2021}, author = {Saborío-Montero, A and López-García, A and Gutiérrez-Rivas, M and Atxaerandio, R and Goiri, I and García-Rodriguez, A and Jiménez-Montero, JA and González, C and Tamames, J and Puente-Sánchez, F and Varona, L and Serrano, M and Ovilo, C and González-Recio, O}, title = {A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding.}, journal = {Journal of dairy science}, volume = {104}, number = {7}, pages = {8135-8151}, doi = {10.3168/jds.2020-20005}, pmid = {33896632}, issn = {1525-3198}, mesh = {Animals ; Cattle/genetics ; Female ; Fermentation ; *Methane/metabolism ; *Microbiota/genetics ; Rumen/metabolism ; Selective Breeding ; Spain ; }, abstract = {The rumen is a complex microbial system of substantial importance in terms of greenhouse gas emissions and feed efficiency. This study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome toward reduced methane emissions. We analyzed nanopore long reads from the rumen metagenome of 437 Holstein cows from 14 commercial herds in 4 northern regions in Spain. After filtering, data were treated as compositional. The large complexity of the rumen microbiota was aggregated, through principal component analysis (PCA), into few principal components (PC) that were used as proxies of the core metagenome. The PCA allowed us to condense the huge and fuzzy taxonomical and functional information from the metagenome into a few PC. Bivariate animal models were applied using these PC and methane production as phenotypes. The variability condensed in these PC is controlled by the cow genome, with heritability estimates for the first PC of ~0.30 at all taxonomic levels, with a large probability (>83%) of the posterior distribution being >0.20 and with the 95% highest posterior density interval (95%HPD) not containing zero. Most genetic correlation estimates between PC1 and methane were large (≥0.70), with most of the posterior distribution (>82%) being >0.50 and with its 95%HPD not containing zero. Enteric methane production was positively associated with relative abundance of eukaryotes (protozoa and fungi) through the first component of the PCA at phylum, class, order, family, and genus. Nanopore long reads allowed the characterization of the core rumen metagenome using whole-metagenome sequencing, and the purposed aggregated variables could be used in animal breeding programs to reduce methane emissions in future generations.}, }
@article {pmid33845886, year = {2021}, author = {Cambon-Bonavita, MA and Aubé, J and Cueff-Gauchard, V and Reveillaud, J}, title = {Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {87}, pmid = {33845886}, issn = {2049-2618}, mesh = {Animals ; *Decapoda ; *Hydrothermal Vents ; Phylogeny ; Proteobacteria ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {BACKGROUND: Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations.<br><br>RESULTS: Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences.<br><br>CONCLUSION: These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.}, }
@article {pmid33841191, year = {2021}, author = {Aldana, M and Robeva, R}, title = {New Challenges in Systems Biology: Understanding the Holobiont.}, journal = {Frontiers in physiology}, volume = {12}, number = {}, pages = {662878}, pmid = {33841191}, issn = {1664-042X}, }
@article {pmid33833260, year = {2021}, author = {Li, S and Roger, LM and Kumar, L and Lewinski, NA and Klein-Seetharaman, J and Gagnon, A and Putnam, HM and Yang, J}, title = {Digital image processing to detect subtle motion in stony coral.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {7722}, pmid = {33833260}, issn = {2045-2322}, abstract = {Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community.}, }
@article {pmid33829521, year = {2021}, author = {Catania, F and Baedke, J and Fábregas-Tejeda, A and Nieves Delgado, A and Vitali, V and Long, LAN}, title = {Global climate change, diet, and the complex relationship between human host and microbiome: Towards an integrated picture.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {43}, number = {6}, pages = {e2100049}, doi = {10.1002/bies.202100049}, pmid = {33829521}, issn = {1521-1878}, mesh = {Climate Change ; Diet ; Dysbiosis ; Humans ; *Life History Traits ; *Microbiota ; }, abstract = {Dietary changes can alter the human microbiome with potential detrimental consequences for health. Given that environment, health, and evolution are interconnected, we ask: Could diet-driven microbiome perturbations have consequences that extend beyond their immediate impact on human health? We address this question in the context of the urgent health challenges posed by global climate change. Drawing on recent studies, we propose that not only can diet-driven microbiome changes lead to dysbiosis, they can also shape life-history traits and fuel human evolution. We posit that dietary shifts prompt mismatched microbiome-host genetics configurations that modulate human longevity and reproductive success. These mismatches can also induce a heritable intra-holobiont stress response, which encourages the holobiont to re-establish equilibrium within the changed nutritional environment. Thus, while mismatches between climate change-related genetic and epigenetic configurations within the holobiont increase the risk and severity of diseases, they may also affect life-history traits and facilitate adaptive responses. These propositions form a framework that can help systematize and address climate-related dietary challenges for policy and health interventions.}, }
@article {pmid33824199, year = {2021}, author = {Cross, KL and Leigh, BA and Hatmaker, EA and Mikaelyan, A and Miller, AK and Bordenstein, SR}, title = {Genomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown.}, journal = {mSystems}, volume = {6}, number = {2}, pages = {}, pmid = {33824199}, issn = {2379-5077}, abstract = {Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species? Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species. Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown.IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.}, }
@article {pmid33805166, year = {2021}, author = {Lyu, D and Zajonc, J and Pagé, A and Tanney, CAS and Shah, A and Monjezi, N and Msimbira, LA and Antar, M and Nazari, M and Backer, R and Smith, DL}, title = {Plant Holobiont Theory: The Phytomicrobiome Plays a Central Role in Evolution and Success.}, journal = {Microorganisms}, volume = {9}, number = {4}, pages = {}, pmid = {33805166}, issn = {2076-2607}, support = {G250030 AAFC BioFuelNet//Agriculture and Agri-Food Canada/ ; RGPIN 2020-07047.//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Under natural conditions, plants are always associated with a well-orchestrated community of microbes-the phytomicrobiome. The nature and degree of microbial effect on the plant host can be positive, neutral, or negative, and depends largely on the environment. The phytomicrobiome is integral for plant growth and function; microbes play a key role in plant nutrient acquisition, biotic and abiotic stress management, physiology regulation through microbe-to-plant signals, and growth regulation via the production of phytohormones. Relationships between the plant and phytomicrobiome members vary in intimacy, ranging from casual associations between roots and the rhizosphere microbial community, to endophytes that live between plant cells, to the endosymbiosis of microbes by the plant cell resulting in mitochondria and chloroplasts. If we consider these key organelles to also be members of the phytomicrobiome, how do we distinguish between the two? If we accept the mitochondria and chloroplasts as both members of the phytomicrobiome and the plant (entrained microbes), the influence of microbes on the evolution of plants becomes so profound that without microbes, the concept of the "plant" is not viable. This paper argues that the holobiont concept should take greater precedence in the plant sciences when referring to a host and its associated microbial community. The inclusivity of this concept accounts for the ambiguous nature of the entrained microbes and the wide range of functions played by the phytomicrobiome in plant holobiont homeostasis.}, }
@article {pmid33803291, year = {2021}, author = {Cuffaro, B and Assohoun, ALW and Boutillier, D and Peucelle, V and Desramaut, J and Boudebbouze, S and Croyal, M and Waligora-Dupriet, AJ and Rhimi, M and Grangette, C and Maguin, E}, title = {Identification of New Potential Biotherapeutics from Human Gut Microbiota-Derived Bacteria.}, journal = {Microorganisms}, volume = {9}, number = {3}, pages = {}, pmid = {33803291}, issn = {2076-2607}, abstract = {The role of the gut microbiota in health and disease is well recognized and the microbiota dysbiosis observed in many chronic diseases became a new therapeutic target. The challenge is to get a better insight into the functionality of commensal bacteria and to use this knowledge to select live biotherapeutics as new preventive or therapeutic products. In this study, we set up a screening approach to evaluate the functional capacities of a set of 21 strains isolated from the gut microbiota of neonates and adults. For this purpose, we selected key biological processes involved in the microbiome-host symbiosis and known to impact the host physiology i.e., the production of short-chain fatty acids and the ability to strengthen an epithelial barrier (Caco-2), to induce the release of the anti-inflammatory IL-10 cytokine after co-culture with human immune cells (PBMC) or to increase GLP-1 production from STC-1 endocrine cell line. This strategy highlighted fifteen strains exhibiting beneficial activities among which seven strains combined several of them. Interestingly, this work revealed for the first time a high prevalence of potential health-promoting functions among intestinal commensal strains and identified several appealing novel candidates for the management of chronic diseases, notably obesity and inflammatory bowel diseases.}, }
@article {pmid33802197, year = {2021}, author = {Mariaule, V and Kriaa, A and Soussou, S and Rhimi, S and Boudaya, H and Hernandez, J and Maguin, E and Lesner, A and Rhimi, M}, title = {Digestive Inflammation: Role of Proteolytic Dysregulation.}, journal = {International journal of molecular sciences}, volume = {22}, number = {6}, pages = {}, pmid = {33802197}, issn = {1422-0067}, support = {Titan-ANR number ANR-18-CE18-0019-03//Agence Nationale de la Recherche/ ; SerpinGuTarget ANR-CE16-0018-01//Agence Nationale de la Recherche/ ; CMCU-PHC Utique (No. 19G0819)-Campus France (41786NC)//Campus France/ ; Twinning European project MICAfrica 952583//Horizon 2020/ ; }, mesh = {Animals ; Humans ; Inflammation/enzymology/pathology ; Inflammatory Bowel Diseases/*enzymology/pathology ; Matrix Metalloproteinases/*metabolism ; *Proteolysis ; Serine Proteases/*metabolism ; }, abstract = {Dysregulation of the proteolytic balance is often associated with diseases. Serine proteases and matrix metalloproteases are involved in a multitude of biological processes and notably in the inflammatory response. Within the framework of digestive inflammation, several studies have stressed the role of serine proteases and matrix metalloproteases (MMPs) as key actors in its pathogenesis and pointed to the unbalance between these proteases and their respective inhibitors. Substantial efforts have been made in developing new inhibitors, some of which have reached clinical trial phases, notwithstanding that unwanted side effects remain a major issue. However, studies on the proteolytic imbalance and inhibitors conception are directed toward host serine/MMPs proteases revealing a hitherto overlooked factor, the potential contribution of their bacterial counterpart. In this review, we highlight the role of proteolytic imbalance in human digestive inflammation focusing on serine proteases and MMPs and their respective inhibitors considering both host and bacterial origin.}, }
@article {pmid33785073, year = {2021}, author = {Bo, TB and Kohl, KD}, title = {Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {26}, pmid = {33785073}, issn = {2524-4671}, abstract = {Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.}, }
@article {pmid33767748, year = {2021}, author = {Zhu, L and Zhang, Z and Chen, H and Lamer, JT and Wang, J and Wei, W and Fu, L and Tang, M and Wang, C and Lu, G}, title = {Gut microbiomes of bigheaded carps and hybrids provide insights into invasion: A hologenome perspective.}, journal = {Evolutionary applications}, volume = {14}, number = {3}, pages = {735-745}, pmid = {33767748}, issn = {1752-4571}, abstract = {Gut microbiomes play an essential role in host survival and local adaptation and thus can facilitate the invasion of host species. Biological invasions have been shown to be linked to the genetic properties of alien host species. It is thus plausible that the holobiont, the host, and its associated microbiome act as an entity to drive invasion success. The bighead carp and silver carp (bigheaded carps), invasive species that exhibit extensive hybridization in the Mississippi River Basin (MRB), provided a unique model to test the holobiont hypothesis of invasion. Here, we investigated the microbiomes of foreguts and hindguts in bigheaded carps and their reciprocal hybrids reared in aquaculture ponds using 16S amplicons and the associated gene prediction. We found an admixed pattern in the gut microbiome community in bigheaded carp hybrids. The hybrid gut microbiomes showed special characteristics such as relatively high alpha diversity in the foregut, an increasing dissimilarity between foreguts and hindguts, and a remarkable proportion of genes coding for putative enzymes related to their digestion of main food resources (Cyanobacteria, cellulose, and chitin). The pond-reared hybrids had advantageous features in genes coding for putative enzymes related to their diet. The above results collectively suggested that the gut microbiomes of hybrids could be beneficial to their local adaptation (e.g., food resource utilization), which might have facilitated their invasion in the MRB. The gut microbial findings, along with the intrinsic genomic features likely associated with life-history traits revealed in our recent study, provide preliminary evidence supporting the holobiont hypothesis of invasion.}, }
@article {pmid33766108, year = {2021}, author = {Keller-Costa, T and Lago-Lestón, A and Saraiva, JP and Toscan, R and Silva, SG and Gonçalves, J and Cox, CJ and Kyrpides, N and Nunes da Rocha, U and Costa, R}, title = {Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {72}, pmid = {33766108}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*classification/*genetics ; Dysbiosis ; *Host-Pathogen Interactions ; Metagenome/*genetics ; *Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella.<br><br>RESULTS: Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host's immune system.<br><br>CONCLUSIONS: This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. Video Abstract.}, }
@article {pmid33758981, year = {2022}, author = {Campos, AB and Cavalcante, LC and de Azevedo, AR and Loiola, M and Silva, AET and Ara, A and Meirelles, PM}, title = {CPR and DPANN Have an Overlooked Role in Corals' Microbial Community Structure.}, journal = {Microbial ecology}, volume = {83}, number = {1}, pages = {252-255}, pmid = {33758981}, issn = {1432-184X}, support = {11268//Ministério da Ciência, Tecnologia, Inovações e Comunicações/ ; Serra-1709-17818//Instituto Serrapilheira/ ; 132261/2018-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.301758/2018-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; Archaea/genetics ; Bacteria/genetics ; *Cardiopulmonary Resuscitation ; *Microbiota ; }, abstract = {Understanding how microbial communities are structured in coral holobionts is important to estimate local and global impacts and provide efficient environment management strategies. Several studies investigated the relationship between corals and their microbial communities, including the environmental drivers of shifts in this relationship, associated with diseases and coral cover loss. However, these studies are often geographically or taxonomically restricted and usually focused on the most abundant microbial groups, neglecting the rare biosphere, including archaea in the group DPANN and the recently discovered bacterial members of the candidate phyla radiation (CPR). Although it is known that rare microbes can play essential roles in several environments, we still lack understanding about which taxa comprise the rare biosphere of corals' microbiome. Here, we investigated the host-related and technical factors influencing coral microbial community structure and the importance of CPR and DPANN in this context by analyzing more than a hundred coral metagenomes from independent studies worldwide. We show that coral genera are the main biotic factor shaping coral microbial communities. We also detected several CPR and DPANN phyla comprising corals' rare biosphere for the first time and showed that they significantly contribute to shaping coral microbial communities.}, }
@article {pmid33754443, year = {2021}, author = {Baum, L and Nguyen, MTHD and Jia, Y and Biazik, J and Thomas, T}, title = {Characterization of a novel roseophage and the morphological and transcriptional response of the sponge symbiont Ruegeria AU67 to infection.}, journal = {Environmental microbiology}, volume = {23}, number = {5}, pages = {2532-2549}, doi = {10.1111/1462-2920.15474}, pmid = {33754443}, issn = {1462-2920}, mesh = {Animals ; *Bacteriophages/genetics ; Porifera/*microbiology ; *Rhodobacteraceae/virology ; *Siphoviridae ; }, abstract = {Sponges have recently been recognized to contain complex communities of bacteriophages; however, little is known about how they interact with their bacterial hosts. Here, we isolated a novel phage, called Ruegeria phage Tedan, and characterized its impact on the bacterial sponge symbiont Ruegeria AU67 on a morphological and molecular level. Phage Tedan was structurally, genomically and phylogenetically characterized to be affiliated with the genus Xiamenvirus of the family Siphoviridae. Through microscopic observations and transcriptomic analysis, we show that phage Tedan upon infection induces a process leading to metabolic and morphological changes in its host. These changes would render Ruegeria AU67 better adapted to inhabit the sponge holobiont due to an improved utilization of ecologically relevant energy and carbon sources as well as a potential impediment of phagocytosis by the sponge through cellular enlargement. An increased survival or better growth of the bacterium in the sponge environment will likely benefit the phage reproduction. Our results point towards the possibility that phages from host-associated environments require, and have thus evolved, different strategies to interact with their host when compared to those phages from free-living or planktonic environments.}, }
@article {pmid33749821, year = {2021}, author = {Lemay, MA and Davis, KM and Martone, PT and Parfrey, LW}, title = {Kelp-associated Microbiota are Structured by Host Anatomy1.}, journal = {Journal of phycology}, volume = {57}, number = {4}, pages = {1119-1130}, doi = {10.1111/jpy.13169}, pmid = {33749821}, issn = {1529-8817}, mesh = {Bacteria/genetics ; *Kelp ; *Laminaria ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Seaweed-associated microbiota are essential for the health and resilience of nearshore ecosystems, marine biogeochemical cycling, and host health. Yet much remains unknown about the ecology of seaweed-microbe symbioses. In this study, we quantified fine-scale patterns of microbial community structure across distinct anatomical regions of the kelp Laminaria setchellii. These anatomical regions represent a gradient of tissue ages: perennial holdfasts can be several years old, whereas stipe epicortex and blades are younger annual structures. Within blades, new growth occurs at the base, while the blade tips may be several months old and undergoing senescence. We hypothesized that microbial communities will differ across anatomical regions (holdfast, stipe, blade base, and blade tip), such that younger tissues will harbor fewer microbes that are more consistent across replicate individuals. Our data support this hypothesis, with the composition of bacterial (16S rRNA gene) and microeukaryote (18S rRNA gene) communities showing significant differences across the four anatomical regions, with the surfaces of older tissues (holdfast and blade tips) harboring significantly greater microbial richness compared to the younger tissues of the meristematic region. Additional samples collected from the surfaces of new L. setchellii recruits (<1y old) also showed differences in microbial community structure across anatomical regions, which demonstrates that these microbial differences are established early. We also observed this pattern in two additional algal species, suggesting that microbial community structure across host anatomy may be a common feature of the seaweed microbiome.}, }
@article {pmid33732246, year = {2021}, author = {Fiuza, BSD and Fonseca, HF and Meirelles, PM and Marques, CR and da Silva, TM and Figueiredo, CA}, title = {Understanding Asthma and Allergies by the Lens of Biodiversity and Epigenetic Changes.}, journal = {Frontiers in immunology}, volume = {12}, number = {}, pages = {623737}, pmid = {33732246}, issn = {1664-3224}, mesh = {Animals ; Asthma/*genetics/*immunology/metabolism ; Bacteria/immunology ; Chromatin Assembly and Disassembly ; DNA Methylation ; Environmental Exposure/adverse effects ; *Epigenesis, Genetic ; Genetic Predisposition to Disease ; Helminths/immunology ; Host-Pathogen Interactions ; Humans ; Hygiene Hypothesis ; Hypersensitivity/*genetics/*immunology/metabolism ; *Immunogenetic Phenomena ; Microbiota/*immunology ; Risk Assessment ; Risk Factors ; Viruses/immunology ; }, abstract = {Exposure to different organisms (bacteria, mold, virus, protozoan, helminths, among others) can induce epigenetic changes affecting the modulation of immune responses and consequently increasing the susceptibility to inflammatory diseases. Epigenomic regulatory features are highly affected during embryonic development and are responsible for the expression or repression of different genes associated with cell development and targeting/conducting immune responses. The well-known, "window of opportunity" that includes maternal and post-natal environmental exposures, which include maternal infections, microbiota, diet, drugs, and pollutant exposures are of fundamental importance to immune modulation and these events are almost always accompanied by epigenetic changes. Recently, it has been shown that these alterations could be involved in both risk and protection of allergic diseases through mechanisms, such as DNA methylation and histone modifications, which can enhance Th2 responses and maintain memory Th2 cells or decrease Treg cells differentiation. In addition, epigenetic changes may differ according to the microbial agent involved and may even influence different asthma or allergy phenotypes. In this review, we discuss how exposure to different organisms, including bacteria, viruses, and helminths can lead to epigenetic modulations and how this correlates with allergic diseases considering different genetic backgrounds of several ancestral populations.}, }
@article {pmid33715441, year = {2021}, author = {Cornwell, BH and Hernández, L}, title = {Genetic structure in the endosymbiont Breviolum 'muscatinei' is correlated with geographical location, environment and host species.}, journal = {Proceedings. Biological sciences}, volume = {288}, number = {1946}, pages = {20202896}, pmid = {33715441}, issn = {1471-2954}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Ecosystem ; Genetic Structures ; *Sea Anemones ; Symbiosis ; }, abstract = {Corals and cnidarians form symbioses with dinoflagellates across a wide range of habitats from the tropics to temperate zones. Notably, these partnerships create the foundation of coral reef ecosystems and are at risk of breaking down due to climate change. This symbiosis couples the fitness of the partners, where adaptations in one species can benefit the holobiont. However, the scales over which each partner can match their current-and future-environment are largely unknown. We investigated population genetic patterns of temperate anemones (Anthopleura spp.) and their endosymbiont Breviolum 'muscatinei', across an extensive geographical range to identify the spatial scales over which local adaptation is possible. Similar to previously published results, two solitary host species exhibited isolation by distance across hundreds of kilometres. However, symbionts exhibited genetic structure across multiple spatial scales, from geographical location to depth in the intertidal zone, and host species, suggesting that symbiont populations are more likely than their hosts to adaptively mitigate the impact of increasing temperatures.}, }
@article {pmid33705688, year = {2021}, author = {Buffington, SA and Dooling, SW and Sgritta, M and Noecker, C and Murillo, OD and Felice, DF and Turnbaugh, PJ and Costa-Mattioli, M}, title = {Dissecting the contribution of host genetics and the microbiome in complex behaviors.}, journal = {Cell}, volume = {184}, number = {7}, pages = {1740-1756.e16}, pmid = {33705688}, issn = {1097-4172}, support = {T32 AI060537/AI/NIAID NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R01 MH112356/MH/NIMH NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Biopterin/analogs &amp; derivatives/metabolism ; Disease Models, Animal ; Excitatory Postsynaptic Potentials ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Lactobacillus reuteri/metabolism/physiology ; *Locomotion ; Membrane Proteins/deficiency/genetics ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Nerve Tissue Proteins/deficiency/genetics ; Neurodevelopmental Disorders/genetics/microbiology/pathology/therapy ; Principal Component Analysis ; Psychomotor Agitation/pathology ; *Social Behavior ; Synaptic Transmission ; }, abstract = {The core symptoms of many neurological disorders have traditionally been thought to be caused by genetic variants affecting brain development and function. However, the gut microbiome, another important source of variation, can also influence specific behaviors. Thus, it is critical to unravel the contributions of host genetic variation, the microbiome, and their interactions to complex behaviors. Unexpectedly, we discovered that different maladaptive behaviors are interdependently regulated by the microbiome and host genes in the Cntnap2-/- model for neurodevelopmental disorders. The hyperactivity phenotype of Cntnap2-/- mice is caused by host genetics, whereas the social-behavior phenotype is mediated by the gut microbiome. Interestingly, specific microbial intervention selectively rescued the social deficits in Cntnap2-/- mice through upregulation of metabolites in the tetrahydrobiopterin synthesis pathway. Our findings that behavioral abnormalities could have distinct origins (host genetic versus microbial) may change the way we think about neurological disorders and how to treat them.}, }
@article {pmid33687778, year = {2021}, author = {Borrero de Acuña, JM and Bernal, P}, title = {Plant holobiont interactions mediated by the type VI secretion system and the membrane vesicles: promising tools for a greener agriculture.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {1830-1836}, doi = {10.1111/1462-2920.15457}, pmid = {33687778}, issn = {1462-2920}, mesh = {Agriculture ; Crops, Agricultural ; *Microbiota ; Plant Development ; Plant Roots ; Soil Microbiology ; *Type VI Secretion Systems ; }, abstract = {A deeper understanding of the complex relationship between plants and their microbiota is allowing researchers to appreciate a plethora of possibilities to improve crops using chemical-free alternatives based on beneficial microorganisms. An increase in crop yield from the promotion of plant growth or even simultaneous protection of the plants from the attack of phytopathogens can be achieved in the presence of different plant-associated microorganisms known as plant-growth-promoting rhizobacteria (PGPR) and biocontrol agents (BCAs), respectively. Thus, the study of the great diversity of plant-microbe and microbe-microbe interactions is an attention-grabbing topic covering studies of interactions since the plant seed and through all developmental stages, from root to shoot. The intricate communication systems that plant holobionts co-evolved has resulted in many different strategies and interplays between these organisms shaping the bacterial communities and the plant fitness simultaneously. Herein, we emphasize two understudied delivery systems existing in plant-associated bacteria: the type VI secretion system (T6SS) and the membrane vesicles with a huge potential to boost a highly demanded and necessary green agriculture.}, }
@article {pmid33675372, year = {2021}, author = {Varasteh, T and Tschoeke, D and Garcia, G and Lima, AS and Moreira, APB and Thompson, C and Thompson, F}, title = {Insights into the genomic repertoire of Aquimarina litoralis CCMR20, a symbiont of coral Mussismilia braziliensis.}, journal = {Archives of microbiology}, volume = {203}, number = {5}, pages = {2743-2746}, pmid = {33675372}, issn = {1432-072X}, mesh = {Animals ; Anthozoa/*microbiology ; Brazil ; Coral Reefs ; Flavobacteriaceae/*genetics ; Genome, Bacterial/*genetics ; Genomics ; Symbiosis/*genetics ; }, abstract = {Aquimarina litoralis CCMR20 originated from the coral Mussismilia braziliensis (Sebastião Gomes Reef, Brazil, summer 2010). To gain new insights into the genomic repertoire associated with symbioses, we obtained the genome sequence of this strains using Illumina sequencing. CCMR20 has a genome size of 6.3 Mb, 32.6%GC, and 5513 genes (37 tRNA and 4 rRNA). A more fine-grained examination of the gene repertoire of CCMR20 disclosed genes engaged with symbiosis (heterotrophic carbon metabolism, CAZymes, B-vitamins group, carotenoid pigment and antioxidant molecules production). Genomic evidence further expand the possible relevance of this symbiont in the health of Mussismilia holobiont.Whole Genome Shotgun project has been deposited at DDBJ/ENA/GeneBank under the accession number WEKL00000000.}, }
@article {pmid33671759, year = {2021}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Musella, M and Quero, GM and Prada, F and Mancuso, A and Seyfarth, AM and Turroni, S and Candela, M and Biagi, E}, title = {Impact of Marine Aquaculture on the Microbiome Associated with Nearby Holobionts: The Case of Patella caerulea Living in Proximity of Sea Bream Aquaculture Cages.}, journal = {Microorganisms}, volume = {9}, number = {2}, pages = {}, pmid = {33671759}, issn = {2076-2607}, support = {818290//Horizon 2020/ ; }, abstract = {Aquaculture plays a major role in the coastal economy of the Mediterranean Sea. This raises the issue of the impact of fish cages on the surrounding environment. Here, we explore the impact of aquaculture on the composition of the digestive gland microbiome of a representative locally dwelling wild holobiont, the grazer gastropod Patella caerulea, at an aquaculture facility located in Southern Sicily, Italy. The microbiome was assessed in individuals collected on sea bream aquaculture cages and on a rocky coastal tract located about 1.2 km from the cages, as the control site. Patella caerulea microbiome variations were explained in the broad marine metacommunity context, assessing the water and sediment microbiome composition at both sites, and characterizing the microbiome associated with the farmed sea bream. The P. caerulea digestive gland microbiome at the aquaculture site was characterized by a lower diversity, the loss of microorganisms sensitive to heavy metal contamination, and by the acquisition of fish pathogens and parasites. However, we also observed possible adaptive responses of the P. caerulea digestive gland microbiome at the aquaculture site, including the acquisition of putative bacteria able to deal with metal and sulfide accumulation, highlighting the inherent microbiome potential to drive the host acclimation to stressful conditions.}, }
@article {pmid33669823, year = {2021}, author = {Saati-Santamaría, Z and Rivas, R and Kolařik, M and García-Fraile, P}, title = {A New Perspective of Pseudomonas-Host Interactions: Distribution and Potential Ecological Functions of the Genus Pseudomonas within the Bark Beetle Holobiont.}, journal = {Biology}, volume = {10}, number = {2}, pages = {}, pmid = {33669823}, issn = {2079-7737}, support = {19-09072S//Grantová agentura České republiky (GAČR)/ ; CLU-2018-04//Excellence Unit of the Spanish-Portuguese Institute for Agricultural Research (CIALE)/ ; }, abstract = {Symbiosis between microbes and insects has been raised as a promising area for understanding biological implications of microbe-host interactions. Among them, the association between fungi and bark beetles has been generally recognized as essential for the bark beetle ecology. However, many works investigating bark beetle bacterial communities and their functions usually meet in a common finding: Pseudomonas is a broadly represented genus within this holobiont and it may provide beneficial roles to its host. Thus, we aimed to review available research on this microbe-host interaction and point out the probable relevance of Pseudomonas strains for these insects, in order to guide future research toward a deeper analysis of the importance of these bacteria for the beetle's life cycle.}, }
@article {pmid33665032, year = {2021}, author = {Dittami, SM and Arboleda, E and Auguet, JC and Bigalke, A and Briand, E and Cárdenas, P and Cardini, U and Decelle, J and Engelen, AH and Eveillard, D and Gachon, CMM and Griffiths, SM and Harder, T and Kayal, E and Kazamia, E and Lallier, FH and Medina, M and Marzinelli, EM and Morganti, TM and Núñez Pons, L and Prado, S and Pintado, J and Saha, M and Selosse, MA and Skillings, D and Stock, W and Sunagawa, S and Toulza, E and Vorobev, A and Leblanc, C and Not, F}, title = {A community perspective on the concept of marine holobionts: current status, challenges, and future directions.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10911}, pmid = {33665032}, issn = {2167-8359}, support = {U17 CE002001/CE/NCIPC CDC HHS/United States ; }, abstract = {Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.}, }
@article {pmid33660094, year = {2021}, author = {Onyango, CA and Glassom, D and MacDonald, A}, title = {De novo assembly of the transcriptome of scleractinian coral, Anomastraea irregularis and analyses of its response to thermal stress.}, journal = {Molecular biology reports}, volume = {48}, number = {3}, pages = {2083-2092}, pmid = {33660094}, issn = {1573-4978}, mesh = {Animals ; Anthozoa/*genetics/*physiology ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; Heat-Shock Response/*genetics ; Molecular Sequence Annotation ; Principal Component Analysis ; *Sequence Analysis, RNA ; Transcriptome/*genetics ; }, abstract = {Rising seawater temperatures cause coral bleaching. The molecular responses of the coral holobiont under stress conditions, determine the success of the symbiosis. Anomastraea irregularis is a hard coral commonly found in the harsh intertidal zones of the south coast of KwaZulu-Natal (KZN), South Africa, where it thrives at the very margins of hard coral distribution in the Western Indian Ocean. To identify the possible molecular and cellular mechanisms underlying its resilience to heat stress, experimental and control nubbins were exposed to temperatures of 29 and 19 °C respectively for 24 h. The transcriptome was assembled de novo from 42.8 million quality controlled 63 bp paired-end short sequence reads obtained via RNA sequencing (RNA-seq). The assembly yielded 333,057 contigs (> 500 bp = 55,626, Largest = 6341 bp N50 = 747 bp). 1362 (1.23%) of the transcripts were significantly differentially expressed between heat stressed and control samples. Log fold change magnitudes among individual genes ranged from - 4.6 to 7.2. Overall, the heat stress response in the A. irregularis constituted a protective response involving up regulation of apoptosis and SUMOylation. Gene ontology (GO) analyses revealed that heat stress in the coral affected the metabolism, protein synthesis, photosynthesis, transport and cytoskeleton. This is the first study to produce a reference transcriptome of this coral species and analyze its response to heat stress. The assembled transcriptome also presents a valuable resource for further transcriptomic and genomic studies.}, }
@article {pmid33643235, year = {2021}, author = {Storo, R and Easson, C and Shivji, M and Lopez, JV}, title = {Microbiome Analyses Demonstrate Specific Communities Within Five Shark Species.}, journal = {Frontiers in microbiology}, volume = {12}, number = {}, pages = {605285}, pmid = {33643235}, issn = {1664-302X}, abstract = {Profiles of symbiotic microbial communities ("microbiomes") can provide insight into the natural history and ecology of their hosts. Using high throughput DNA sequencing of the 16S rRNA V4 region, microbiomes of five shark species in South Florida (nurse, lemon, sandbar, Caribbean reef, and tiger) have been characterized for the first time. The microbiomes show species specific microbiome composition, distinct from surrounding seawater. Shark anatomical location (gills, teeth, skin, cloaca) affected the diversity of microbiomes. An in-depth analysis of teeth communities revealed species specific microbial communities. For example, the genus Haemophilus, explained 7.0% of the differences of the teeth microbiomes of lemon and Caribbean reef sharks. Lemon shark teeth communities (n = 11) contained a high abundance of both Vibrio (10.8 ± 26.0%) and Corynebacterium (1.6 ± 5.1%), genera that can include human pathogenic taxa. The Vibrio (2.8 ± 6.34%) and Kordia (3.1 ± 6.0%) genera and Salmonella enterica (2.6 ± 6.4%) were the most abundant members of nurse shark teeth microbial communities. The Vibrio genus was highly represented in the sandbar shark (54.0 ± 46.0%) and tiger shark (5.8 ± 12.3%) teeth microbiomes. The prevalence of genera containing potential human pathogens could be informative in shark bite treatment protocols and future research to confirm or deny human pathogenicity. We conclude that South Florida sharks host species specific microbiomes that are distinct from their surrounding environment and vary due to differences in microbial community composition among shark species and diversity and composition among anatomical locations. Additionally, when considering the confounding effects of both species and location, microbial community diversity and composition varies.}, }
@article {pmid33624265, year = {2021}, author = {Choi, K and Khan, R and Lee, SW}, title = {Dissection of plant microbiota and plant-microbiome interactions.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {59}, number = {3}, pages = {281-291}, pmid = {33624265}, issn = {1976-3794}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Microbial Interactions ; *Microbiota ; Plant Physiological Phenomena ; Plants/*microbiology ; Soil Microbiology ; }, abstract = {Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.}, }
@article {pmid33608555, year = {2021}, author = {Lan, Y and Sun, J and Chen, C and Sun, Y and Zhou, Y and Yang, Y and Zhang, W and Li, R and Zhou, K and Wong, WC and Kwan, YH and Cheng, A and Bougouffa, S and Van Dover, CL and Qiu, JW and Qian, PY}, title = {Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis.}, journal = {Nature communications}, volume = {12}, number = {1}, pages = {1165}, pmid = {33608555}, issn = {2041-1723}, mesh = {Animals ; Bacteria/*genetics/metabolism ; Gammaproteobacteria/genetics/metabolism ; Gene Expression ; Genome, Bacterial ; Genomics ; Hydrothermal Vents/*microbiology ; Phylogeny ; Snails/*genetics/metabolism/*microbiology ; Sulfur/metabolism ; Symbiosis/*genetics/physiology ; Transcriptome ; }, abstract = {Animals endemic to deep-sea hydrothermal vents often form obligatory symbioses with bacteria, maintained by intricate host-symbiont interactions. Most genomic studies on holobionts have not investigated both sides to similar depths. Here, we report dual symbiosis in the peltospirid snail Gigantopelta aegis with two gammaproteobacterial endosymbionts: a sulfur oxidiser and a methane oxidiser. We assemble high-quality genomes for all three parties, including a chromosome-level host genome. Hologenomic analyses reveal mutualism with nutritional complementarity and metabolic co-dependency, highly versatile in transporting and using chemical energy. Gigantopelta aegis likely remodels its immune system to facilitate dual symbiosis. Comparisons with Chrysomallon squamiferum, a confamilial snail with a single sulfur-oxidising gammaproteobacterial endosymbiont, show that their sulfur-oxidising endosymbionts are phylogenetically distant. This is consistent with previous findings that they evolved endosymbiosis convergently. Notably, the two sulfur-oxidisers share the same capabilities in biosynthesising nutrients lacking in the host genomes, potentially a key criterion in symbiont selection.}, }
@article {pmid33604175, year = {2021}, author = {Nguyen, M and Wemheuer, B and Laffy, PW and Webster, NS and Thomas, T}, title = {Taxonomic, functional and expression analysis of viral communities associated with marine sponges.}, journal = {PeerJ}, volume = {9}, number = {}, pages = {e10715}, pmid = {33604175}, issn = {2167-8359}, abstract = {Viruses play an essential role in shaping the structure and function of ecological communities. Marine sponges have the capacity to filter large volumes of 'virus-laden' seawater through their bodies and host dense communities of microbial symbionts, which are likely accessible to viral infection. However, despite the potential of sponges and their symbionts to act as viral reservoirs, little is known about the sponge-associated virome. Here we address this knowledge gap by analysing metagenomic and (meta-) transcriptomic datasets from several sponge species to determine what viruses are present and elucidate their predicted and expressed functionality. Sponges were found to carry diverse, abundant and active bacteriophages as well as eukaryotic viruses belonging to the Megavirales and Phycodnaviridae. These viruses contain and express auxiliary metabolic genes (AMGs) for photosynthesis and vitamin synthesis as well as for the production of antimicrobials and the defence against toxins. These viral AMGs can therefore contribute to the metabolic capacities of their hosts and also potentially enhance the survival of infected cells. This suggest that viruses may play a key role in regulating the abundance and activities of members of the sponge holobiont.}, }
@article {pmid33603147, year = {2021}, author = {Jahn, MT and Lachnit, T and Markert, SM and Stigloher, C and Pita, L and Ribes, M and Dutilh, BE and Hentschel, U}, title = {Lifestyle of sponge symbiont phages by host prediction and correlative microscopy.}, journal = {The ISME journal}, volume = {15}, number = {7}, pages = {2001-2011}, pmid = {33603147}, issn = {1751-7370}, mesh = {Animals ; *Bacteriophages/genetics ; Life Style ; *Microbiota ; Microscopy ; *Porifera ; Symbiosis ; }, abstract = {Bacteriophages (phages) are ubiquitous elements in nature, but their ecology and role in animals remains little understood. Sponges represent the oldest known extant animal-microbe symbiosis and are associated with dense and diverse microbial consortia. Here we investigate the tripartite interaction between phages, bacterial symbionts, and the sponge host. We combined imaging and bioinformatics to tackle important questions on who the phage hosts are and what the replication mode and spatial distribution within the animal is. This approach led to the discovery of distinct phage-microbe infection networks in sponge versus seawater microbiomes. A new correlative in situ imaging approach ('PhageFISH-CLEM') localised phages within bacterial symbiont cells, but also within phagocytotically active sponge cells. We postulate that the phagocytosis of free virions by sponge cells modulates phage-bacteria ratios and ultimately controls infection dynamics. Prediction of phage replication strategies indicated a distinct pattern, where lysogeny dominates the sponge microbiome, likely fostered by sponge host-mediated virion clearance, while lysis dominates in seawater. Collectively, this work provides new insights into phage ecology within sponges, highlighting the importance of tripartite animal-phage-bacterium interplay in holobiont functioning. We anticipate that our imaging approach will be instrumental to further understanding of viral distribution and cellular association in animal hosts.}, }
@article {pmid33602493, year = {2021}, author = {McFall-Ngai, M and Bosch, TCG}, title = {Animal development in the microbial world: The power of experimental model systems.}, journal = {Current topics in developmental biology}, volume = {141}, number = {}, pages = {371-397}, pmid = {33602493}, issn = {1557-8933}, support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; R01 AI050661/AI/NIAID NIH HHS/United States ; R01 GM135254/GM/NIGMS NIH HHS/United States ; R01 OD011024/OD/NIH HHS/United States ; R37 AI050661/AI/NIAID NIH HHS/United States ; }, mesh = {Aliivibrio fischeri ; Animals ; Decapodiformes/*embryology/*microbiology/physiology ; Embryo, Nonmammalian/microbiology ; Gene Expression Regulation ; Hydra/metabolism/*microbiology ; Light ; *Microbiota ; Symbiosis ; Wnt Signaling Pathway ; }, abstract = {The development of powerful model systems has been a critical strategy for understanding the mechanisms underlying the progression of an animal through its ontogeny. Here we provide two examples that allow deep and mechanistic insight into the development of specific animal systems. Species of the cnidarian genus Hydra have provided excellent models for studying host-microbe interactions and how metaorganisms function in vivo. Studies of the Hawaiian bobtail squid Euprymna scolopes and its luminous bacterial partner Vibrio fischeri have been used for over 30 years to understand the impact of a broad array of levels, from ecology to genomics, on the development and persistence of symbiosis. These examples provide an integrated perspective of how developmental processes work and evolve within the context of a microbial world, a new view that opens vast horizons for developmental biology research. The Hydra and the squid systems also lend an example of how profound insights can be discovered by taking advantage of the "experiments" that evolution had done in shaping conserved developmental processes.}, }
@article {pmid33583434, year = {2021}, author = {Hudspith, M and Rix, L and Achlatis, M and Bougoure, J and Guagliardo, P and Clode, PL and Webster, NS and Muyzer, G and Pernice, M and de Goeij, JM}, title = {Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {44}, pmid = {33583434}, issn = {2049-2618}, mesh = {Animals ; Carbon/metabolism ; Microbiota/*physiology ; Nitrogen/metabolism ; Nutrients/*metabolism ; Porifera/*metabolism/*microbiology ; *Symbiosis ; }, abstract = {BACKGROUND: Sponges are increasingly recognised as key ecosystem engineers in many aquatic habitats. They play an important role in nutrient cycling due to their unrivalled capacity for processing both dissolved and particulate organic matter (DOM and POM) and the exceptional metabolic repertoire of their diverse and abundant microbial communities. Functional studies determining the role of host and microbiome in organic nutrient uptake and exchange, however, are limited. Therefore, we coupled pulse-chase isotopic tracer techniques with nanoscale secondary ion mass spectrometry (NanoSIMS) to visualise the uptake and translocation of 13C- and 15N-labelled dissolved and particulate organic food at subcellular level in the high microbial abundance sponge Plakortis angulospiculatus and the low microbial abundance sponge Halisarca caerulea.<br><br>RESULTS: The two sponge species showed significant enrichment of DOM- and POM-derived 13C and 15N into their tissue over time. Microbial symbionts were actively involved in the assimilation of DOM, but host filtering cells (choanocytes) appeared to be the primary site of DOM and POM uptake in both sponge species overall, via pinocytosis and phagocytosis, respectively. Translocation of carbon and nitrogen from choanocytes to microbial symbionts occurred over time, irrespective of microbial abundance, reflecting recycling of host waste products by the microbiome.<br><br>CONCLUSIONS: Here, we provide empirical evidence indicating that the prokaryotic communities of a high and a low microbial abundance sponge obtain nutritional benefits from their host-associated lifestyle. The metabolic interaction between the highly efficient filter-feeding host and its microbial symbionts likely provides a competitive advantage to the sponge holobiont in the oligotrophic environments in which they thrive, by retaining and recycling limiting nutrients. Sponges present a unique model to link nutritional symbiotic interactions to holobiont function, and, via cascading effects, ecosystem functioning, in one of the earliest metazoan-microbe symbioses. Video abstract.}, }
@article {pmid33576852, year = {2021}, author = {Zhou, G and Tong, H and Cai, L and Huang, H}, title = {Transgenerational Effects on the Coral Pocillopora damicornis Microbiome Under Ocean Acidification.}, journal = {Microbial ecology}, volume = {82}, number = {3}, pages = {572-580}, pmid = {33576852}, issn = {1432-184X}, support = {41876192//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; Oceans and Seas ; Seawater ; }, abstract = {Reef-building corals are inhabited by functionally diverse microorganisms which play important roles in coral health and persistence in the Anthropocene. However, our understanding of the complex associations within coral holobionts is largely limited, particularly transgenerational exposure to environmental stress, like ocean acidification. Here we investigated the microbiome development of an ecologically important coral Pocillopora damicornis following transgenerational exposure to moderate and high pCO2 (partial pressure of CO2) levels, using amplicon sequencing and analysis. Our results showed that the Symbiodiniaceae community structures in adult and juvenile had similar patterns, all of which were dominated by Durusdinium spp., previously known as clade D. Conversely, prokaryotic communities varied between adults and juveniles, possibly driven by the effect of host development. Surprisingly, there were no significant changes in both Symbiodiniaceae and prokaryotic communities with different pCO2 treatments, which was independent of the life history stage. This study shows that ocean acidification has no significant effect on P. damicornis microbiome, and warrants further research to test whether transgenerational acclimation exists in coral holobiont to projected future climate change.}, }
@article {pmid33548192, year = {2021}, author = {Iha, C and Dougan, KE and Varela, JA and Avila, V and Jackson, CJ and Bogaert, KA and Chen, Y and Judd, LM and Wick, R and Holt, KE and Pasella, MM and Ricci, F and Repetti, SI and Medina, M and Marcelino, VR and Chan, CX and Verbruggen, H}, title = {Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium.}, journal = {Current biology : CB}, volume = {31}, number = {7}, pages = {1393-1402.e5}, doi = {10.1016/j.cub.2021.01.018}, pmid = {33548192}, issn = {1879-0445}, mesh = {Adaptation, Biological/*genetics ; Animals ; *Anthozoa ; Chlorophyta/*genetics ; *Genomics ; *Symbiosis ; }, abstract = {The green alga Ostreobium is an important coral holobiont member, playing key roles in skeletal decalcification and providing photosynthate to bleached corals that have lost their dinoflagellate endosymbionts. Ostreobium lives in the coral's skeleton, a low-light environment with variable pH and O2 availability. We present the Ostreobium nuclear genome and a metatranscriptomic analysis of healthy and bleached corals to improve our understanding of Ostreobium's adaptations to its extreme environment and its roles as a coral holobiont member. The Ostreobium genome has 10,663 predicted protein-coding genes and shows adaptations for life in low and variable light conditions and other stressors in the endolithic environment. This alga presents a rich repertoire of light-harvesting complex proteins but lacks many genes for photoprotection and photoreceptors. It also has a large arsenal of genes for oxidative stress response. An expansion of extracellular peptidases suggests that Ostreobium may supplement its energy needs by feeding on the organic skeletal matrix, and a diverse set of fermentation pathways allows it to live in the anoxic skeleton at night. Ostreobium depends on other holobiont members for vitamin B12, and our metatranscriptomes identify potential bacterial sources. Metatranscriptomes showed Ostreobium becoming a dominant agent of photosynthesis in bleached corals and provided evidence for variable responses among coral samples and different Ostreobium genotypes. Our work provides a comprehensive understanding of the adaptations of Ostreobium to its extreme environment and an important genomic resource to improve our comprehension of coral holobiont resilience, bleaching, and recovery.}, }
@article {pmid33546771, year = {2021}, author = {Piccinni, MZ and Watts, JEM and Fourny, M and Guille, M and Robson, SC}, title = {The skin microbiome of Xenopus laevis and the effects of husbandry conditions.}, journal = {Animal microbiome}, volume = {3}, number = {1}, pages = {17}, pmid = {33546771}, issn = {2524-4671}, support = {212942/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/R014841/1//Biotechnology and Biological Sciences Research Council (GB)/ ; E3//Research England/ ; E3//Research England/ ; }, abstract = {BACKGROUND: Historically the main source of laboratory Xenopus laevis was the environment. The increase in genetically altered animals and evolving governmental constraints around using wild-caught animals for research has led to the establishment of resource centres that supply animals and reagents worldwide, such as the European Xenopus Resource Centre. In the last decade, centres were encouraged to keep animals in a "low microbial load" or "clean" state, where embryos are surface sterilized before entering the housing system; instead of the conventional, "standard" conditions where frogs and embryos are kept without prior surface treatment. Despite Xenopus laevis having been kept in captivity for almost a century, surprisingly little is known about the frogs as a holobiont and how changing the microbiome may affect resistance to disease. This study examines how the different treatment conditions, "clean" and "standard" husbandry in recirculating housing, affects the skin microbiome of tadpoles and female adults. This is particularly important when considering the potential for poor welfare caused by a change in husbandry method as animals move from resource centres to smaller research colonies.<br><br>RESULTS: We found strong evidence for developmental control of the surface microbiome on Xenopus laevis; adults had extremely similar microbial communities independent of their housing, while both tadpole and environmental microbiome communities were less resilient and showed greater diversity.<br><br>CONCLUSIONS: Our findings suggest that the adult Xenopus laevis microbiome is controlled and selected by the host. This indicates that the surface microbiome of adult Xenopus laevis is stable and defined independently of the environment in which it is housed, suggesting that the use of clean husbandry conditions poses little risk to the skin microbiome when transferring adult frogs to research laboratories. This will have important implications for frog health applicable to Xenopus laevis research centres throughout the world.}, }
@article {pmid33542710, year = {2020}, author = {Marzocchi, U and Bonaglia, S and Zaiko, A and Quero, GM and Vybernaite-Lubiene, I and Politi, T and Samuiloviene, A and Zilius, M and Bartoli, M and Cardini, U}, title = {Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {610269}, pmid = {33542710}, issn = {1664-302X}, abstract = {Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.}, }
@article {pmid33537923, year = {2021}, author = {Overby, HB and Ferguson, JF}, title = {Gut Microbiota-Derived Short-Chain Fatty Acids Facilitate Microbiota:Host Cross talk and Modulate Obesity and Hypertension.}, journal = {Current hypertension reports}, volume = {23}, number = {2}, pages = {8}, pmid = {33537923}, issn = {1534-3111}, support = {R01 DK117144/DK/NIDDK NIH HHS/United States ; R01DK117144/NH/NIH HHS/United States ; }, mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; *Hypertension ; *Microbiota ; Obesity ; }, abstract = {PURPOSE OF REVIEW: The purpose of this review is to summarize the evidence supporting a role of short-chain fatty acids (SCFAs) as messengers facilitating cross talk between the host and gut microbiota and discuss the effects of altered SCFA signaling in obesity and hypertension.<br><br>RECENT FINDINGS: Recent evidence suggests there to be a significant contribution of gut microbiota-derived SCFAs to microbe:host communication and host metabolism. SCFA production within the intestine modulates intestinal pH, microbial composition, and intestinal barrier integrity. SCFA signaling through host receptors, such as PPARγ and GPCRs, modulates host health and disease physiology. Alterations in SCFA signaling and downstream effects on inflammation are implicated in the development of obesity and hypertension. SCFAs are crucial components of the holobiont relationship; in the proper environment, they support normal gut, immune, and metabolic function. Dysregulation of microbial SCFA signaling affects downstream host metabolism, with implications in obesity and hypertension.}, }
@article {pmid33523848, year = {2021}, author = {Williams, A and Chiles, EN and Conetta, D and Pathmanathan, JS and Cleves, PA and Putnam, HM and Su, X and Bhattacharya, D}, title = {Metabolomic shifts associated with heat stress in coral holobionts.}, journal = {Science advances}, volume = {7}, number = {1}, pages = {}, pmid = {33523848}, issn = {2375-2548}, support = {P30 CA072720/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/physiology ; Coral Reefs ; *Dinoflagellida/physiology ; Dipeptides ; Heat-Shock Response ; *Sea Anemones ; Symbiosis ; }, abstract = {Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is "coral bleaching," usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral.}, }
@article {pmid33519751, year = {2020}, author = {Alibrandi, P and Schnell, S and Perotto, S and Cardinale, M}, title = {Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {604964}, pmid = {33519751}, issn = {1664-302X}, abstract = {The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.}, }
@article {pmid33504360, year = {2021}, author = {Wicaksono, WA and Kusstatscher, P and Erschen, S and Reisenhofer-Graber, T and Grube, M and Cernava, T and Berg, G}, title = {Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome.}, journal = {Microbiome}, volume = {9}, number = {1}, pages = {29}, pmid = {33504360}, issn = {2049-2618}, mesh = {Anti-Infective Agents/*pharmacology ; Ascomycota/*drug effects/*genetics ; Colistin/pharmacology ; Drug Resistance, Microbial/*drug effects/*genetics ; Glycine/analogs &amp; derivatives/pharmacology ; Microbiota/*drug effects/*genetics ; Pyrazines/pharmacology ; RNA, Ribosomal, 16S/genetics ; Tetracycline/pharmacology ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets.<br><br>RESULTS: The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 108 16S rRNA gene copies ng-1 DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential.<br><br>CONCLUSIONS: Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.}, }
@article {pmid33500473, year = {2021}, author = {Sivaguru, M and Todorov, LG and Fouke, CE and Munro, CMO and Fouke, KW and Fouke, KE and Baughman, ME and Fouke, BW}, title = {Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature.}, journal = {Scientific reports}, volume = {11}, number = {1}, pages = {2230}, pmid = {33500473}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/physiology ; Climate Change ; Dinoflagellida/physiology ; Female ; Magnetic Resonance Angiography ; Male ; Photosynthesis/physiology ; Sleep Wake Disorders/*physiopathology ; }, abstract = {The Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.}, }
@article {pmid33500354, year = {2021}, author = {Rädecker, N and Pogoreutz, C and Gegner, HM and Cárdenas, A and Roth, F and Bougoure, J and Guagliardo, P and Wild, C and Pernice, M and Raina, JB and Meibom, A and Voolstra, CR}, title = {Heat stress destabilizes symbiotic nutrient cycling in corals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {118}, number = {5}, pages = {}, pmid = {33500354}, issn = {1091-6490}, mesh = {Amino Acids/metabolism ; Ammonium Compounds/metabolism ; Animals ; Anthozoa/genetics/*physiology ; Carbon/metabolism ; Gene Expression Regulation ; Heat-Shock Response/*physiology ; Models, Biological ; Nitrogen/metabolism ; *Nutrients ; Oxidative Stress ; Photosynthesis ; Symbiosis/*physiology ; }, abstract = {Recurrent mass bleaching events are pushing coral reefs worldwide to the brink of ecological collapse. While the symptoms and consequences of this breakdown of the coral-algal symbiosis have been extensively characterized, our understanding of the underlying causes remains incomplete. Here, we investigated the nutrient fluxes and the physiological as well as molecular responses of the widespread coral Stylophora pistillata to heat stress prior to the onset of bleaching to identify processes involved in the breakdown of the coral-algal symbiosis. We show that altered nutrient cycling during heat stress is a primary driver of the functional breakdown of the symbiosis. Heat stress increased the metabolic energy demand of the coral host, which was compensated by the catabolic degradation of amino acids. The resulting shift from net uptake to release of ammonium by the coral holobiont subsequently promoted the growth of algal symbionts and retention of photosynthates. Together, these processes form a feedback loop that will gradually lead to the decoupling of carbon translocation from the symbiont to the host. Energy limitation and altered symbiotic nutrient cycling are thus key factors in the early heat stress response, directly contributing to the breakdown of the coral-algal symbiosis. Interpreting the stability of the coral holobiont in light of its metabolic interactions provides a missing link in our understanding of the environmental drivers of bleaching and may ultimately help uncover fundamental processes underpinning the functioning of endosymbioses in general.}, }
@article {pmid33499978, year = {2020}, author = {Zanotti, AA and Gregoracci, GB and Capel, KCC and Kitahara, MV}, title = {Microbiome of the Southwestern Atlantic invasive scleractinian coral, Tubastraea tagusensis.}, journal = {Animal microbiome}, volume = {2}, number = {1}, pages = {29}, pmid = {33499978}, issn = {2524-4671}, support = {2014/01332-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 301436/2018-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {BACKGROUND: Commonly known as sun-coral, Tubastraea tagusensis is an azooxanthellate scleractinian coral that successfully invaded the Southwestern Atlantic causing significant seascape changes. Today it is reported to over 3500 km along the Brazilian coast, with several rocky shores displaying high substrate coverage. Apart from its singular invasiveness capacity, the documentation and, therefore, understanding of the role of symbiotic microorganisms in the sun-coral invasion is still scarce. However, in general, the broad and constant relationship between corals and microorganisms led to the development of co-evolution hypotheses. As such, it has been shown that the microbial community responds to environmental factors, adjustment of the holobiont, adapting its microbiome, and improving the hosts' fitness in a short space of time. Here we describe the microbial community (i.e. Bacteria) associated with sun-coral larvae and adult colonies from a locality displaying a high invasion development.<br><br>RESULTS: The usage of high throughput sequencing indicates a great diversity of Bacteria associated with T. tagusensis, with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Planctomycetes, and Firmicutes corresponding to the majority of the microbiome in all samples. However, T. tagusensis' microbial core consists of only eight genera for colonies, and, within them, three are also present in the sequenced larvae. Overall, the microbiome from colonies sampled at different depths did not show significant differences. The microbiome of the larvae suggests a partial vertical transfer of the microbial core in this species.<br><br>CONCLUSION: Although diverse, the microbiome core of adult Tubastraea tagusensis is composed of only eight genera, of which three are transferred from the mother colony to their larvae. The remaining bacteria genera are acquired from the seawater, indicating that they might play a role in the host fitness and, therefore, facilitate the sun-coral invasion in the Southwestern Atlantic.}, }
@article {pmid33488540, year = {2020}, author = {Freitas-Silva, J and de Oliveira, BFR and Vigoder, FM and Muricy, G and Dobson, ADW and Laport, MS}, title = {Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha).}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {592735}, pmid = {33488540}, issn = {1664-302X}, abstract = {Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.}, }
@article {pmid33484584, year = {2021}, author = {Eckert, EM and Anicic, N and Fontaneto, D}, title = {Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment.}, journal = {Molecular ecology}, volume = {30}, number = {6}, pages = {1545-1558}, doi = {10.1111/mec.15815}, pmid = {33484584}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Fresh Water ; *Microbiota/genetics ; Zooplankton/genetics ; }, abstract = {The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co-evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species-specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of "core" microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co-evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host-microbiome association to originate and persist.}, }
@article {pmid33479490, year = {2021}, author = {Bonthond, G and Bayer, T and Krueger-Hadfield, SA and Stärck, N and Wang, G and Nakaoka, M and Künzel, S and Weinberger, F}, title = {The role of host promiscuity in the invasion process of a seaweed holobiont.}, journal = {The ISME journal}, volume = {15}, number = {6}, pages = {1668-1679}, pmid = {33479490}, issn = {1751-7370}, mesh = {Humans ; Introduced Species ; *Microbiota ; *Rhodophyta ; *Seaweed ; }, abstract = {Invasive species are co-introduced with microbiota from their native range and also interact with microbiota found in the novel environment to which they are introduced. Host flexibility toward microbiota, or host promiscuity, is an important trait underlying terrestrial plant invasions. To test whether host promiscuity may be important in macroalgal invasions, we experimentally simulated an invasion in a common garden setting, using the widespread invasive macroalga Agarophyton vermiculophyllum as a model invasive seaweed holobiont. After disturbing the microbiota of individuals from native and non-native populations with antibiotics, we monitored the microbial succession trajectories in the presence of a new source of microbes. Microbial communities were strongly impacted by the treatment and changed compositionally and in terms of diversity but recovered functionally by the end of the experiment in most respects. Beta-diversity in disturbed holobionts strongly decreased, indicating that different populations configure more similar -or more common- microbial communities when exposed to the same conditions. This decline in beta-diversity occurred not only more rapidly, but was also more pronounced in non-native populations, while individuals from native populations retained communities more similar to those observed in the field. This study demonstrates that microbial communities of non-native A. vermiculophyllum are more flexibly adjusted to the environment and suggests that an intraspecific increase in host promiscuity has promoted the invasion process of A. vermiculophyllum. This phenomenon may be important among invasive macroalgal holobionts in general.}, }
@article {pmid33440837, year = {2021}, author = {Bredon, M and Depuydt, E and Brisson, L and Moulin, L and Charles, C and Haenn, S and Moumen, B and Bouchon, D}, title = {Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod.}, journal = {Microorganisms}, volume = {9}, number = {1}, pages = {}, pmid = {33440837}, issn = {2076-2607}, support = {BiodivUP//State-Region Planning Contracts (CPER), European Regional Development Fund (FEDER)/ ; }, abstract = {The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host's diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the "eco-holobiont" conceptualization of macroorganisms.}, }
@article {pmid33436514, year = {2021}, author = {Fagorzi, C and Bacci, G and Huang, R and Cangioli, L and Checcucci, A and Fini, M and Perrin, E and Natali, C and diCenzo, GC and Mengoni, A}, title = {Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis.}, journal = {mSystems}, volume = {6}, number = {1}, pages = {}, pmid = {33436514}, issn = {2379-5077}, abstract = {Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.}, }
@article {pmid33435275, year = {2021}, author = {Mannaa, M and Seo, YS}, title = {Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm.}, journal = {Plants (Basel, Switzerland)}, volume = {10}, number = {1}, pages = {}, pmid = {33435275}, issn = {2223-7747}, abstract = {Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes-differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions-are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant's biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen-one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen-one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.}, }
@article {pmid33434804, year = {2021}, author = {Zhang, Y and Yang, Q and Zhang, Y and Ahmad, M and Ling, J and Tang, X and Dong, J}, title = {Shifts in abundance and network complexity of coral bacteria in response to elevated ammonium stress.}, journal = {The Science of the total environment}, volume = {768}, number = {}, pages = {144631}, doi = {10.1016/j.scitotenv.2020.144631}, pmid = {33434804}, issn = {1879-1026}, mesh = {*Ammonium Compounds ; Animals ; *Anthozoa ; Bacteria/genetics ; Chlorophyll A ; Coral Reefs ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Coral bacteria are highly dynamic and acutely affected by host health and environmental conditions. However, there is limited knowledge of how the dynamics of coral-associated bacterial communities and interactions among bacterial members change in response to dissolved inorganic nutrient stressors. Here, we used high-throughput sequencing of the 16S rRNA gene to examine dynamic changes in coral-associated bacterial communities under elevated ammonium stress. Short-term exposure to high levels of ammonium does not significantly harm coral holobiont. Physiological parameters such as carbohydrate, chlorophyll a, and lipid content of coral holobiont were not affected. After three weeks of elevated ammonium stress, however, the coral-associated bacterial community changed significantly. The abundance of certain bacterial populations increased significantly, with enrichment of pathogenic and opportunistic bacteria and a decrease in defensive and core bacteria. Keystone bacterial species in the co-occurrence network changed considerably. Under elevated ammonium stress, the abundance of keystone species associated with corals was lower and the complexity of keystone bacterial relationships decreased significantly. Our results indicate that bacteria respond to elevated ammonium stress through changes in abundance and co-occurrence among bacterial members. This precedes visual symptoms of changes in coral physiological conditions and could be used as an early warning indicator of elevated ammonium stress in coastal coral reef management.}, }
@article {pmid33417693, year = {2021}, author = {Bonacolta, AM and Connelly, MT and Rosales, SM and Del Campo, J and Traylor-Knowles, N}, title = {The starlet sea anemone, Nematostella vectensis, possesses body region-specific bacterial associations with spirochetes dominating the capitulum.}, journal = {FEMS microbiology letters}, volume = {368}, number = {3}, pages = {}, doi = {10.1093/femsle/fnab002}, pmid = {33417693}, issn = {1574-6968}, mesh = {Animals ; Bacteria/*classification/genetics ; Biodiversity ; Host Microbial Interactions/*physiology ; Microbiota/genetics ; Phylogeny ; Sea Anemones/*microbiology ; Spirochaetales/*genetics ; }, abstract = {Sampling of different body regions can reveal highly specialized bacterial associations within the holobiont and facilitate identification of core microbial symbionts that would otherwise be overlooked by bulk sampling methods. Here, we characterized compartment-specific associations present within the model cnidarian Nematostella vectensis by dividing its morphology into three distinct microhabitats. This sampling design allowed us to uncover a capitulum-specific dominance of spirochetes within N. vectensis. Bacteria from the family Spirochaetaceae made up 66% of the community in the capitulum, while only representing 1.2% and 0.1% of the communities in the mesenteries and physa, respectively. A phylogenetic analysis of the predominant spirochete sequence recovered from N. vectensis showed a close relation to spirochetes previously recovered from wild N. vectensis. These sequences clustered closer to the recently described genus Oceanispirochaeta, rather than Spirochaeta perfilievii, supporting them as members of this clade. This suggests a prevalent and yet uncharacterized association between N. vectensis and spirochetes from the order Spirochaetales.}, }
@article {pmid33409285, year = {2020}, author = {Martinez, S and Kolodny, Y and Shemesh, E and Scucchia, F and Nevo, R and Levin-Zaidman, S and Paltiel, Y and Keren, N and Tchernov, D and Mass, T}, title = {Energy Sources of the Depth-Generalist Mixotrophic Coral Stylophora pistillata.}, journal = {Frontiers in Marine Science}, volume = {7}, number = {}, pages = {988}, pmid = {33409285}, issn = {2296-7745}, support = {755876/ERC_/European Research Council/International ; }, abstract = {Energy sources of corals, ultimately sunlight and plankton availability, change dramatically from shallow to mesophotic (30-150 m) reefs. Depth-generalist corals, those that occupy both of these two distinct ecosystems, are adapted to cope with such extremely diverse conditions. In this study, we investigated the trophic strategy of the depth-generalist hermatypic coral Stylophora pistillata and the ability of mesophotic colonies to adapt to shallow reefs. We compared symbiont genera composition, photosynthetic traits and the holobiont trophic position and carbon sources, calculated from amino acids compound-specific stable isotope analysis (AA-CSIA), of shallow, mesophotic and translocated corals. This species harbors different Symbiodiniaceae genera at the two depths: Cladocopium goreaui (dominant in mesophotic colonies) and Symbiodinium microadriaticum (dominant in shallow colonies) with a limited change after transplantation. This allowed us to determine which traits stem from hosting different symbiont species compositions across the depth gradient. Calculation of holobiont trophic position based on amino acid δ15N revealed that heterotrophy represents the same portion of the total energy budget in both depths, in contrast to the dogma that predation is higher in corals growing in low light conditions. Photosynthesis is the major carbon source to corals growing at both depths, but the photosynthetic rate is higher in the shallow reef corals, implicating both higher energy consumption and higher predation rate in the shallow habitat. In the corals transplanted from deep to shallow reef, we observed extensive photo-acclimation by the Symbiodiniaceae cells, including substantial cellular morphological modifications, increased cellular chlorophyll a, lower antennae to photosystems ratios and carbon signature similar to the local shallow colonies. In contrast, non-photochemical quenching remains low and does not increase to cope with the high light regime of the shallow reef. Furthermore, host acclimation is much slower in these deep-to-shallow transplanted corals as evident from the lower trophic position and tissue density compared to the shallow-water corals, even after long-term transplantation (18 months). Our results suggest that while mesophotic reefs could serve as a potential refuge for shallow corals, the transition is complex, as even after a year and a half the acclimation is only partial.}, }
@article {pmid33392741, year = {2021}, author = {Taulé, C and Vaz-Jauri, P and Battistoni, F}, title = {Insights into the early stages of plant-endophytic bacteria interaction.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {37}, number = {1}, pages = {13}, pmid = {33392741}, issn = {1573-0972}, mesh = {Bacteria ; *Bacterial Physiological Phenomena ; Endophytes/*physiology ; Host Microbial Interactions/*physiology ; Microbiota ; Plant Development ; Plant Roots/microbiology ; Plants/*microbiology ; Seeds/growth &amp; development/microbiology ; Soil ; Soil Microbiology ; }, abstract = {The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.}, }
@article {pmid33389691, year = {2021}, author = {Miquel, PA and Hwang, SY}, title = {On biological individuation.}, journal = {Theory in biosciences = Theorie in den Biowissenschaften}, volume = {}, number = {}, pages = {}, pmid = {33389691}, issn = {1611-7530}, abstract = {In this paper, we understand the emergence of life as a pure individuation process. Individuation already occurs in open thermodynamics systems near equilibrium. We understand such open systems, as already recursively characterized (R1) by the relation between their internal properties, and their boundary conditions. Second, global properties emerge in such physical systems. We interpret this change as the fact that their structure is the recursive result of their operations (R2). We propose a simulation of the emergence of life in Earth by a mapping (R) through which (R1R2) operators are applied to themselves, so that RN = (R1R2)N. We suggest that under specific thermodynamic (open systems out of equilibrium) and chemical conditions (autocatalysis, kinetic dynamic stability), this mapping can go up to a limit characterized by a fixed-point equation: [Formula: see text]. In this equation, ([Formula: see text]) symbolizes a regime of permanent resonance characterizing the biosphere, as open from inside, by the recursive differential relation between the biosphere and all its holobionts. As such the biosphere is closed on itself as a pure differential entity. ([Formula: see text]) symbolizes the regime of permanent change characterizing the emergence of evolution in the biosphere. As such the biosphere is closed on itself, by the principle of descent with modifications, and by the fact that every holobiont evolves in a niche, while evolving with it.}, }
@article {pmid33342999, year = {2021}, author = {Babbin, AR and Tamasi, T and Dumit, D and Weber, L and Rodríguez, MVI and Schwartz, SL and Armenteros, M and Wankel, SD and Apprill, A}, title = {Discovery and quantification of anaerobic nitrogen metabolisms among oxygenated tropical Cuban stony corals.}, journal = {The ISME journal}, volume = {15}, number = {4}, pages = {1222-1235}, pmid = {33342999}, issn = {1751-7370}, mesh = {Anaerobiosis ; Animals ; *Anthozoa ; Coral Reefs ; *Microbiota ; Nitrogen ; }, abstract = {Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm-2 d-1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.}, }
@article {pmid33327517, year = {2020}, author = {Menaa, F and Wijesinghe, PAUI and Thiripuranathar, G and Uzair, B and Iqbal, H and Khan, BA and Menaa, B}, title = {Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions.}, journal = {Marine drugs}, volume = {18}, number = {12}, pages = {}, pmid = {33327517}, issn = {1660-3397}, mesh = {Animals ; *Ecology ; Humans ; *Industry ; *Microbiota ; Seaweed/*chemistry ; }, abstract = {Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)-microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.}, }
@article {pmid33324385, year = {2020}, author = {Mironov, T and Sabaneyeva, E}, title = {A Robust Symbiotic Relationship Between the Ciliate Paramecium multimicronucleatum and the Bacterium Ca. Trichorickettsia Mobilis.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {603335}, pmid = {33324385}, issn = {1664-302X}, abstract = {Close reciprocal interactions in symbiotic systems have suggested the holobiont concept, in which the host and its microbiota are considered as a single entity. Ciliates are known for their ability to form symbiotic associations with prokaryotes. Relationships between the partners in such systems vary from mutualism to parasitism and differ significantly in their robustness. We assessed the viability of the ciliate Paramecium multimicronucleatum and its ability to maintain its intranuclear endosymbiont Ca. Trichorickettsia mobilis (Rickettsiaceae) after treatment with antibiotics characterized by different mode of action, such as ampicillin, streptomycin, chloramphenicol, tetracycline. The presence of endosymbionts in the host cell was determined by means of living cell observations made using differential interference contrast or fluorescence in situ hybridization with the species-specific oligonucleotide probe (FISH). Administration of antibiotics traditionally used in treatments of rickettsioses, tetracycline and chloramphenicol, depending on the concentration used and the ciliate strain treated, either caused death of both, infected and control cells, or did not affect the ability of the host to maintain the intranuclear endosymbiont. The surviving cells always manifested motile bacteria in the macronucleus. Streptomycin treatment never led to the loss of endosymbionts in any of the four infected strains, and nearly all ciliates remained viable. Ampicillin treatment never caused host cell death, but resulted in formation of filamentous and immobile oval bacterial forms. Under repeated ampicillin treatments, a part of endosymbionts was registered in the host cytoplasm, as evidenced both by FISH and transmission electron microscopy. Endosymbionts located in the host cytoplasm were enclosed in vacuoles, apparently, corresponding to autophagosomes. Nevertheless, the bacteria seemed to persist in this compartment and might cause relapse of the infection. Although the antibiotic sensitivity profile of Trichorickettsia seems to resemble that of other representatives of Rickettsiaceae, causative agents of severe diseases in humans, neither of the antibiotic treatments used in this study resulted in an aposymbiotic cell line, apparently, due to the protists' sensitivity to tetracyclines, the drugs of preference in rickettsiosis treatment. The observed robustness of this symbiotic system makes it a good model for further elaboration of the holobiont concept.}, }
@article {pmid33322780, year = {2020}, author = {Oliveira, BFR and Lopes, IR and Canellas, ALB and Muricy, G and Dobson, ADW and Laport, MS}, title = {Not That Close to Mommy: Horizontal Transmission Seeds the Microbiome Associated with the Marine Sponge Plakina cyanorosea.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33322780}, issn = {2076-2607}, abstract = {Marine sponges are excellent examples of invertebrate-microbe symbioses. In this holobiont, the partnership has elegantly evolved by either transmitting key microbial associates through the host germline and/or capturing microorganisms from the surrounding seawater. We report here on the prokaryotic microbiota during different developmental stages of Plakina cyanorosea and their surrounding environmental samples by a 16S rRNA metabarcoding approach. In comparison with their source adults, larvae housed slightly richer and more diverse microbial communities, which are structurally more related to the environmental microbiota. In addition to the thaumarchaeal Nitrosopumilus, parental sponges were broadly dominated by Alpha- and Gamma-proteobacteria, while the offspring were particularly enriched in the Vibrionales, Alteromonodales, Enterobacterales orders and the Clostridia and Bacteroidia classes. An enterobacterial operational taxonomic unit (OTU) was the dominant member of the strict core microbiota. The most abundant and unique OTUs were not significantly enriched amongst the microbiomes from host specimens included in the sponge microbiome project. In a wider context, Oscarella and Plakina are the sponge genera with higher divergence in their associated microbiota compared to their Homoscleromorpha counterparts. Our results indicate that P. cyanorosea is a low microbial abundance sponge (LMA), which appears to heavily depend on the horizontal transmission of its microbial partners that likely help the sponge host in the adaptation to its habitat.}, }
@article {pmid33322411, year = {2020}, author = {Bombin, A and Cunneely, O and Eickman, K and Bombin, S and Ruesy, A and Su, M and Myers, A and Cowan, R and Reed, L}, title = {Influence of Lab Adapted Natural Diet and Microbiota on Life History and Metabolic Phenotype of Drosophila melanogaster.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33322411}, issn = {2076-2607}, support = {DEB 1737869//National Science Foundation/ ; R01GM098856//National Institute for Health Research/ ; }, abstract = {Symbiotic microbiota can help its host to overcome nutritional challenges, which is consistent with a holobiont theory of evolution. Our project investigated the effects produced by the microbiota community, acquired from the environment and horizontal transfer, on metabolic traits related to obesity. The study applied a novel approach of raising Drosophila melanogaster, from ten wild-derived genetic lines on naturally fermented peaches, preserving genuine microbial conditions. Larvae raised on the natural and standard lab diets were significantly different in every tested phenotype. Frozen peach food provided nutritional conditions similar to the natural ones and preserved key microbial taxa necessary for survival and development. On the peach diet, the presence of parental microbiota increased the weight and development rate. Larvae raised on each tested diet formed microbial communities distinct from each other. The effect that individual microbial taxa produced on the host varied significantly with changing environmental and genetic conditions, occasionally to the degree of opposite correlations.}, }
@article {pmid33321044, year = {2021}, author = {Peixoto, RS and Sweet, M and Villela, HDM and Cardoso, P and Thomas, T and Voolstra, CR and Høj, L and Bourne, DG}, title = {Coral Probiotics: Premise, Promise, Prospects.}, journal = {Annual review of animal biosciences}, volume = {9}, number = {}, pages = {265-288}, doi = {10.1146/annurev-animal-090120-115444}, pmid = {33321044}, issn = {2165-8110}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Dinoflagellida ; Microbiota ; *Probiotics ; Symbiosis ; }, abstract = {The use of Beneficial Microorganisms for Corals (BMCs) has been proposed recently as a tool for the improvement of coral health, with knowledge in this research topic advancing rapidly. BMCs are defined as consortia of microorganisms that contribute to coral health through mechanisms that include (a) promoting coral nutrition and growth, (b) mitigating stress and impacts of toxic compounds, (c) deterring pathogens, and (d) benefiting early life-stage development. Here, we review the current proposed BMC approach and outline the studies that have proven its potential to increase coral resilience to stress. We revisit and expand the list of putative beneficial microorganisms associated with corals and their proposed mechanismsthat facilitate improved host performance. Further, we discuss the caveats and bottlenecks affecting the efficacy of BMCs and close by focusing on the next steps to facilitate application at larger scales that can improve outcomes for corals and reefs globally.}, }
@article {pmid33316299, year = {2021}, author = {Sukhoverkhov, AV and Gontier, N}, title = {Non-genetic inheritance: Evolution above the organismal level.}, journal = {Bio Systems}, volume = {200}, number = {}, pages = {104325}, doi = {10.1016/j.biosystems.2020.104325}, pmid = {33316299}, issn = {1872-8324}, mesh = {Adaptation, Physiological/*physiology ; Animals ; *Biological Evolution ; Humans ; Inheritance Patterns/*physiology ; *Models, Theoretical ; Phenotype ; *Social Behavior ; }, abstract = {The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less on community system traits (synergetic/organizational traits) that characterize transgenerational biological, ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of interacting populations, and for which the individual members can belong to the same or to different species. Examples of communities include biofilms, ant colonies, symbiotic associations resulting in holobiont formation, and human societies. The proposed model of evolution at the level of communities revises classic theorizing on the major transitions in evolution by analyzing the interplay between community/social traits and individual traits, and how this brings forth ideas of top-down regulations of bottom-up evolutionary processes (collaboration of downward and upward causation). The work demonstrates that such interplay also includes reticulate interactions and reticulate causation. In this regard, we exemplify how community systems provide various non-genetic 'scaffoldings', 'constraints', and 'affordances' for individual and sociocultural evolutionary development. Such research complements prevailing models that focus on the vertical transmission of heritable information, from parent to offspring, with research that instead focusses on horizontal, oblique and even reverse information transmission, going from offspring to parent. We call this reversed information transfer the 'offspring effect' to contrast it from the 'parental effect'. We argue that the proposed approach to inheritance is effective for modelling cumulative and distributed developmental process and for explaining the biological origins and evolution of language.}, }
@article {pmid33309942, year = {2021}, author = {Wang, X and Feng, H and Wang, Y and Wang, M and Xie, X and Chang, H and Wang, L and Qu, J and Sun, K and He, W and Wang, C and Dai, C and Chu, Z and Tian, C and Yu, N and Zhang, X and Liu, H and Wang, E}, title = {Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia-legume symbiosis.}, journal = {Molecular plant}, volume = {14}, number = {3}, pages = {503-516}, doi = {10.1016/j.molp.2020.12.002}, pmid = {33309942}, issn = {1752-9867}, mesh = {Microbiota/physiology ; Mycorrhizae/*physiology ; RNA, Ribosomal, 16S/genetics ; Rhizobium/physiology ; Rhizosphere ; Symbiosis/genetics/physiology ; }, abstract = {Plants establish symbioses with mutualistic fungi, such as arbuscular mycorrhizal (AM) fungi, and bacteria, such as rhizobia, to exchange key nutrients and thrive. Plants and symbionts have coevolved and represent vital components of terrestrial ecosystems. Plants employ an ancestral AM signaling pathway to establish intracellular symbioses, including the legume-rhizobia symbiosis, in their roots. Nevertheless, the relationship between the AM and rhizobial symbioses in native soil is poorly understood. Here, we examined how these distinct symbioses affect root-associated bacterial communities in Medicago truncatula by performing quantitative microbiota profiling (QMP) of 16S rRNA genes. We found that M. truncatula mutants that cannot establish AM or rhizobia symbiosis have an altered microbial load (quantitative abundance) in the rhizosphere and roots, and in particular that AM symbiosis is required to assemble a normal quantitative root-associated microbiota in native soil. Moreover, quantitative microbial co-abundance network analyses revealed that AM symbiosis affects Rhizobiales hubs among plant microbiota and benefits the plant holobiont. Through QMP of rhizobial rpoB and AM fungal SSU rRNA genes, we revealed a new layer of interaction whereby AM symbiosis promotes rhizobia accumulation in the rhizosphere of M. truncatula. We further showed that AM symbiosis-conditioned microbial communities within the M. truncatula rhizosphere could promote nodulation in different legume plants in native soil. Given that the AM and rhizobial symbioses are critical for crop growth, our findings might inform strategies to improve agricultural management. Moreover, our work sheds light on the co-evolution of these intracellular symbioses during plant adaptation to native soil conditions.}, }
@article {pmid33281689, year = {2020}, author = {Robinson, JM and Cameron, R}, title = {The Holobiont Blindspot: Relating Host-Microbiome Interactions to Cognitive Biases and the Concept of the "Umwelt".}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {591071}, pmid = {33281689}, issn = {1664-1078}, abstract = {Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, we discuss the host's microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host-microbiome (collectively termed a "holobiont") interactions in a given behavior, may underpin a potentially important cognitive bias - which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking - that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited.}, }
@article {pmid33274469, year = {2021}, author = {Sharifi, R and Ryu, CM}, title = {Social networking in crop plants: Wired and wireless cross-plant communications.}, journal = {Plant, cell &amp; environment}, volume = {44}, number = {4}, pages = {1095-1110}, pmid = {33274469}, issn = {1365-3040}, mesh = {Communication ; Crops, Agricultural/*physiology ; Ecology ; Plant Defense Against Herbivory ; Plant Immunity ; *Plant Physiological Phenomena ; Plants/metabolism ; }, abstract = {The plant-associated microbial community (microbiome) has an important role in plant-plant communications. Plants decipher their complex habitat situations by sensing the environmental stimuli and molecular patterns and associated with microbes, herbivores and dangers. Perception of these cues generates inter/intracellular signals that induce modifications of plant metabolism and physiology. Signals can also be transferred between plants via different mechanisms, which we classify as wired- and wireless communications. Wired communications involve direct signal transfers between plants mediated by mycorrhizal hyphae and parasitic plant stems. Wireless communications involve plant volatile emissions and root exudates elicited by microbes/insects, which enable inter-plant signalling without physical contact. These producer-plant signals induce microbiome adaptation in receiver plants via facilitative or competitive mechanisms. Receiver plants eavesdrop to anticipate responses to improve fitness against stresses. An emerging body of information in plant-plant communication can be leveraged to improve integrated crop management under field conditions.}, }
@article {pmid33265911, year = {2020}, author = {Saha, M and Dove, S and Weinberger, F}, title = {Chemically Mediated Microbial "Gardening" Capacity of a Seaweed Holobiont Is Dynamic.}, journal = {Microorganisms}, volume = {8}, number = {12}, pages = {}, pmid = {33265911}, issn = {2076-2607}, support = {CP1215//DFG Excellence Cluster Future Ocean/ ; }, abstract = {Terrestrial plants are known to "garden" the microbiota of their rhizosphere via released metabolites (that can attract beneficial microbes and deter pathogenic microbes). Such a "gardening" capacity is also known to be dynamic in plants. Although microbial "gardening" has been recently demonstrated for seaweeds, we do not know whether this capacity is a dynamic property in any aquatic flora like in terrestrial plants. Here, we tested the dynamic microbial "gardening" capacity of seaweeds using the model invasive red seaweed Agarophyton vermiculophyllum. Following an initial extraction of surface-associated metabolites (immediately after field collection), we conducted a long-term mesocosm experiment for 5 months to test the effect of two different salinities (low = 8.5 and medium = 16.5) on the microbial "gardening" capacity of the alga over time. We tested "gardening" capacity of A. vermiculophyllum originating from two different salinity levels (after 5 months treatments) in settlement assays against three disease causing pathogenic bacteria and seven protective bacteria. We also compared the capacity of the alga with field-collected samples. Abiotic factors like low salinity significantly increased the capacity of the alga to deter colonization by pathogenic bacteria while medium salinity significantly decreased the capacity of the alga over time when compared to field-collected samples. However, capacity to attract beneficial bacteria significantly decreased at both tested salinity levels when compared to field-collected samples. Dynamic microbial "gardening" capacity of a seaweed to attract beneficial bacteria and deter pathogenic bacteria is demonstrated for the first time. Such a dynamic capacity as found in the current study could also be applicable to other aquatic host-microbe interactions. Our results may provide an attractive direction of research towards manipulation of salinity and other abiotic factors leading to better defended A. vermiculophyllum towards pathogenic bacteria thereby enhancing sustained production of healthy A. vermiculophyllum in farms.}, }
@article {pmid33263887, year = {2020}, author = {Ye, S and Siemann, E}, title = {Endosymbiont-Mediated Adaptive Responses to Stress in Holobionts.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {559-580}, pmid = {33263887}, issn = {0080-1844}, mesh = {Adaptation, Biological ; Animals ; Aquatic Organisms/*microbiology ; Bacteria ; Climate Change ; Ecosystem ; *Host Microbial Interactions ; Insecta/*microbiology ; Plants/*microbiology ; Stress, Physiological ; *Symbiosis ; }, abstract = {Endosymbiosis is found in all types of ecosystems and it can be sensitive to environmental changes due to the intimate interaction between the endosymbiont and the host. Indeed, global climate change disturbs the local ambient environment and threatens endosymbiotic species, and in some cases leads to local ecosystem collapse. Recent studies have revealed that the endosymbiont can affect holobiont (endosymbiont and host together) stress tolerance as much as the host does, and manipulation of the microbial partners in holobionts may mitigate the impacts of the environmental stress. Here, we first show how the endosymbiont presence affects holobiont stress tolerance by discussing three well-studied endosymbiotic systems, which include plant-fungi, aquatic organism-algae, and insect-bacteria systems. We then review how holobionts are able to alter their stress tolerance via associated endosymbionts by changing their endosymbiont composition, by adaptation of their endosymbionts, or by acclimation of their endosymbionts. Finally, we discuss how different transmission modes (vertical or horizontal transmission) might affect the adaptability of holobionts. We propose that the endosymbiont is a good target for modifying holobiont stress tolerance, which makes it critical to more fully investigate the role of endosymbionts in the adaptive responses of holobionts to stress.}, }
@article {pmid33263873, year = {2020}, author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M}, title = {Phenotype Heritability in Holobionts: An Evolutionary Model.}, journal = {Results and problems in cell differentiation}, volume = {69}, number = {}, pages = {199-223}, pmid = {33263873}, issn = {0080-1844}, mesh = {*Biological Evolution ; Genome ; Genomics ; *Host Microbial Interactions ; *Inheritance Patterns ; *Microbiota/genetics ; *Phenotype ; }, abstract = {Many complex diseases are expressed with high incidence only in certain populations. Genealogy studies determine that these diseases are inherited with a high probability. However, genetic studies have been unable to identify the genomic signatures responsible for such heritability, as identifying the genetic variants that make a population prone to a given disease is not enough to explain its high occurrence within the population. This gap is known as the missing heritability problem. We know that the microbiota plays a very important role in determining many important phenotypic characteristics of its host, in particular the complex diseases for which the missing heritability occurs. Therefore, when computing the heritability of a phenotype, it is important to consider not only the genetic variation in the host but also in its microbiota. Here we test this hypothesis by studying an evolutionary model based on gene regulatory networks. Our results show that the holobiont (the host plus its microbiota) is capable of generating a much larger variability than the host alone, greatly reducing the missing heritability of the phenotype. This result strongly suggests that a considerably large part of the missing heritability can be attributed to the microbiome.}, }
@article {pmid33249664, year = {2021}, author = {Porro, B and Zamoum, T and Mallien, C and Hume, BCC and Voolstra, CR and Röttinger, E and Furla, P and Forcioli, D}, title = {Horizontal acquisition of Symbiodiniaceae in the Anemonia viridis (Cnidaria, Anthozoa) species complex.}, journal = {Molecular ecology}, volume = {30}, number = {2}, pages = {391-405}, doi = {10.1111/mec.15755}, pmid = {33249664}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; *Dinoflagellida ; Mediterranean Sea ; *Sea Anemones/genetics ; Symbiosis/genetics ; }, abstract = {All metazoans are in fact holobionts, resulting from the association of several organisms, and organismal adaptation is then due to the composite response of this association to the environment. Deciphering the mechanisms of symbiont acquisition in a holobiont is therefore essential to understanding the extent of its adaptive capacities. In cnidarians, some species acquire their photosynthetic symbionts directly from their parents (vertical transmission) but may also acquire symbionts from the environment (horizontal acquisition) at the adult stage. The Mediterranean snakelocks sea anemone, Anemonia viridis (Forskål, 1775), passes down symbionts from one generation to the next by vertical transmission, but the capacity for such horizontal acquisition is still unexplored. To unravel the flexibility of the association between the different host lineages identified in A. viridis and its Symbiodiniaceae, we genotyped both the animal hosts and their symbiont communities in members of host clones in five different locations in the North Western Mediterranean Sea. The composition of within-host-symbiont populations was more dependent on the geographical origin of the hosts than their membership to a given lineage or even to a given clone. Additionally, similarities in host-symbiont communities were greater among genets (i.e. among different clones) than among ramets (i.e. among members of the same given clonal genotype). Taken together, our results demonstrate that A. viridis may form associations with a range of symbiotic dinoflagellates and suggest a capacity for horizontal acquisition. A mixed-mode transmission strategy in A. viridis, as we posit here, may help explain the large phenotypic plasticity that characterizes this anemone.}, }
@article {pmid33246955, year = {2020}, author = {Cooke, I and Ying, H and Forêt, S and Bongaerts, P and Strugnell, JM and Simakov, O and Zhang, J and Field, MA and Rodriguez-Lanetty, M and Bell, SC and Bourne, DG and van Oppen, MJ and Ragan, MA and Miller, DJ}, title = {Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts.}, journal = {Science advances}, volume = {6}, number = {48}, pages = {}, pmid = {33246955}, issn = {2375-2548}, abstract = {Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species' responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.}, }
@article {pmid33243513, year = {2021}, author = {Calegario, G and Freitas, L and Appolinario, LR and Venas, T and Arruda, T and Otsuki, K and Masi, B and Omachi, C and Moreira, AP and Soares, AC and Rezende, CE and Garcia, G and Tschoeke, D and Thompson, C and Thompson, FL}, title = {Conserved rhodolith microbiomes across environmental gradients of the Great Amazon Reef.}, journal = {The Science of the total environment}, volume = {760}, number = {}, pages = {143411}, doi = {10.1016/j.scitotenv.2020.143411}, pmid = {33243513}, issn = {1879-1026}, mesh = {Coral Reefs ; Metagenome ; *Microbiota ; Photosynthesis ; *Rhodophyta ; Seawater ; }, abstract = {The Great Amazon Reef System (GARS) covers an estimated area of 56,000 km2 off the mouth of the Amazon River. Living rhodolith holobionts are major benthic components of the GARS. However, it is unclear whether environmental conditions modulate the rhodolith microbiomes. Previous studies suggest that environmental parameters such as light, temperature, depth, and nutrients are drivers of rhodolith health. However, it is unclear whether rhodoliths from different sectors (northern, central, and southern) from the GARS have different microbiomes. We analysed metagenomes of rhodoliths (n = 10) and seawater (n = 6), obtained from the three sectors, by illumina shotgun sequencing (total read counts: 25.73 million). Suspended particulate material and isotopic composition of dissolved organic carbon (δ13C) indicated a strong influence of the Amazon river plume over the entire study area. However, photosynthetically active radiation at the bottom (PARb) was higher in the southern sector reefs, ranging from 10.1 to 14.3 E.m-2 day-1. The coralline calcareous red algae (CCA) Corallina caespitosa, Corallina officinalis, Lithophyllum cabiochiae, and Hapalidiales were present in the three sectors and in most rhodolith samples. Rhodolith microbiomes were very homogeneous across the studied area and differed significantly from seawater microbiomes. However, some subtle differences were found when comparing the rhodolith microbiomes from the northern and central sectors to the ones from the southern. Consistent with the higher light availability, two phyla were more abundant in rhodolith microbiomes from southern sites (Bacteroidetes, and Cyanobacteria). In addition, two functional categories were enhanced in southern rhodolith microbiomes (iron acquisition and metabolism, and photosynthesis). Phycobiliprotein-coding genes were also more abundant in southern locations, while the functional categories of respiration and sulfur metabolism were enhanced in northern and central rhodolith microbiomes, consistent with higher nutrient loads. The results confirm the conserved nature of rhodolith microbiomes even under pronounced environmental gradients. Subtle taxonomic and functional differences observed in rhodolith microbiomes may enable rhodoliths to thrive in changing environmental conditions.}, }
@article {pmid33240603, year = {2020}, author = {Aichelman, HE and Barshis, DJ}, title = {Adaptive divergence, neutral panmixia, and algal symbiont population structure in the temperate coral Astrangia poculata along the Mid-Atlantic United States.}, journal = {PeerJ}, volume = {8}, number = {}, pages = {e10201}, pmid = {33240603}, issn = {2167-8359}, abstract = {Astrangia poculata is a temperate scleractinian coral that exists in facultative symbiosis with the dinoflagellate alga Breviolum psygmophilum across a range spanning the Gulf of Mexico to Cape Cod, Massachusetts. Our previous work on metabolic thermal performance of Virginia (VA) and Rhode Island (RI) populations of A. poculata revealed physiological signatures of cold (RI) and warm (VA) adaptation of these populations to their respective local thermal environments. Here, we used whole-transcriptome sequencing (mRNA-Seq) to evaluate genetic differences and identify potential loci involved in the adaptive signature of VA and RI populations. Sequencing data from 40 A. poculata individuals, including 10 colonies from each population and symbiotic state (VA-white, VA-brown, RI-white, and RI-brown), yielded a total of 1,808 host-associated and 59 algal symbiont-associated single nucleotide polymorphisms (SNPs) post filtration. Fst outlier analysis identified 66 putative high outlier SNPs in the coral host and 4 in the algal symbiont. Differentiation of VA and RI populations in the coral host was driven by putatively adaptive loci, not neutral divergence (Fst = 0.16, p = 0.001 and Fst = 0.002, p = 0.269 for outlier and neutral SNPs respectively). In contrast, we found evidence of neutral population differentiation in B. psygmophilum (Fst = 0.093, p = 0.001). Several putatively adaptive host loci occur on genes previously associated with the coral stress response. In the symbiont, three of four putatively adaptive loci are associated with photosystem proteins. The opposing pattern of neutral differentiation in B. psygmophilum, but not the A. poculata host, reflects the contrasting dynamics of coral host and algal symbiont population connectivity, dispersal, and gene by environment interactions.}, }
@article {pmid33225561, year = {2021}, author = {Garcias-Bonet, N and Eguíluz, VM and Díaz-Rúa, R and Duarte, CM}, title = {Host-association as major driver of microbiome structure and composition in Red Sea seagrass ecosystems.}, journal = {Environmental microbiology}, volume = {23}, number = {4}, pages = {2021-2034}, doi = {10.1111/1462-2920.15334}, pmid = {33225561}, issn = {1462-2920}, mesh = {Bacteria/genetics ; Bacteroidetes ; Firmicutes ; Indian Ocean ; *Microbiota ; }, abstract = {The role of the microbiome in sustaining seagrasses has recently been highlighted. However, our understanding of the seagrass microbiome lacks behind that of other organisms. Here, we analyse the endophytic and total bacterial communities of leaves, rhizomes, and roots of six Red Sea seagrass species and their sediments. The structure of seagrass bacterial communities revealed that the 1% most abundant OTUs accounted for 87.9% and 74.8% of the total numbers of reads in sediment and plant tissue samples, respectively. We found taxonomically distinct bacterial communities in vegetated and bare sediments. Yet, our results suggest that lifestyle (i.e. free-living or host-association) is the main driver of bacterial community composition. Seagrass bacterial communities were tissue- and species-specific and differed from those of surrounding sediments. We identified OTUs belonging to genera related to N and S cycles in roots, and members of Actinobacteria, Bacteroidetes, and Firmicutes phyla as particularly enriched in root endosphere. The finding of highly similar OTUs in well-defined sub-clusters by network analysis suggests the co-occurrence of highly connected key members within Red Sea seagrass bacterial communities. These results provide key information towards the understanding of the role of microorganisms in seagrass ecosystem functioning framed under the seagrass holobiont concept.}, }
@article {pmid33222325, year = {2021}, author = {Grottoli, AG and Toonen, RJ and van Woesik, R and Vega Thurber, R and Warner, ME and McLachlan, RH and Price, JT and Bahr, KD and Baums, IB and Castillo, KD and Coffroth, MA and Cunning, R and Dobson, KL and Donahue, MJ and Hench, JL and Iglesias-Prieto, R and Kemp, DW and Kenkel, CD and Kline, DI and Kuffner, IB and Matthews, JL and Mayfield, AB and Padilla-Gamiño, JL and Palumbi, S and Voolstra, CR and Weis, VM and Wu, HC}, title = {Increasing comparability among coral bleaching experiments.}, journal = {Ecological applications : a publication of the Ecological Society of America}, volume = {31}, number = {4}, pages = {e02262}, pmid = {33222325}, issn = {1051-0761}, support = {NSF-1838667//National Science Foundation/ ; }, mesh = {Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Temperature ; }, abstract = {Coral bleaching is the single largest global threat to coral reefs worldwide. Integrating the diverse body of work on coral bleaching is critical to understanding and combating this global problem. Yet investigating the drivers, patterns, and processes of coral bleaching poses a major challenge. A recent review of published experiments revealed a wide range of experimental variables used across studies. Such a wide range of approaches enhances discovery, but without full transparency in the experimental and analytical methods used, can also make comparisons among studies challenging. To increase comparability but not stifle innovation, we propose a common framework for coral bleaching experiments that includes consideration of coral provenance, experimental conditions, and husbandry. For example, reporting the number of genets used, collection site conditions, the experimental temperature offset(s) from the maximum monthly mean (MMM) of the collection site, experimental light conditions, flow, and the feeding regime will greatly facilitate comparability across studies. Similarly, quantifying common response variables of endosymbiont (Symbiodiniaceae) and holobiont phenotypes (i.e., color, chlorophyll, endosymbiont cell density, mortality, and skeletal growth) could further facilitate cross-study comparisons. While no single bleaching experiment can provide the data necessary to determine global coral responses of all corals to current and future ocean warming, linking studies through a common framework as outlined here, would help increase comparability among experiments, facilitate synthetic insights into the causes and underlying mechanisms of coral bleaching, and reveal unique bleaching responses among genets, species, and regions. Such a collaborative framework that fosters transparency in methods used would strengthen comparisons among studies that can help inform coral reef management and facilitate conservation strategies to mitigate coral bleaching worldwide.}, }
@article {pmid33220182, year = {2021}, author = {Song, H and Hewitt, OH and Degnan, SM}, title = {Arginine Biosynthesis by a Bacterial Symbiont Enables Nitric Oxide Production and Facilitates Larval Settlement in the Marine-Sponge Host.}, journal = {Current biology : CB}, volume = {31}, number = {2}, pages = {433-437.e3}, doi = {10.1016/j.cub.2020.10.051}, pmid = {33220182}, issn = {1879-0445}, mesh = {Animals ; Aquatic Organisms/*growth &amp; development/metabolism/microbiology ; Arginine/biosynthesis ; Bacteria/*metabolism ; Citrulline/metabolism ; Larva/*growth &amp; development/metabolism/microbiology ; Metamorphosis, Biological ; Nitric Oxide/biosynthesis ; Porifera/*growth &amp; development/metabolism/microbiology ; Seawater/chemistry ; Symbiosis/*physiology ; }, abstract = {Larval settlement and metamorphosis are regulated by nitric oxide (NO) signaling in a wide diversity of marine invertebrates.1-10 It is thus surprising that, in most invertebrates, the substrate for NO synthesis-arginine-cannot be biosynthesized but instead must be exogenously sourced.11 In the sponge Amphimedon queenslandica, vertically inherited proteobacterial symbionts in the larva are able to biosynthesize arginine.12,13 Here, we test the hypothesis that symbionts provide arginine to the sponge host so that nitric oxide synthase expressed in the larva can produce NO, which regulates metamorphosis,8 and the byproduct citrulline (Figure 1). First, we find support for an arginine-citrulline biosynthetic loop in this sponge larval holobiont by using stable isotope tracing. In symbionts, incorporated 13C-citrulline decreases as 13C-arginine increases, consistent with the use of exogenous citrulline for arginine synthesis. In contrast, 13C-citrulline accumulates in larvae as 13C-arginine decreases, demonstrating the uptake of exogenous arginine and its conversion to NO and citrulline. Second, we show that, although Amphimedon larvae can derive arginine directly from seawater, normal settlement and metamorphosis can occur in artificial sea water lacking arginine. Together, these results support holobiont complementation of the arginine-citrulline loop and NO biosynthesis in Amphimedon larvae, suggesting a critical role for bacterial symbionts in the development of this marine sponge. Given that NO regulates settlement and metamorphosis in diverse animal phyla1-10 and arginine is procured externally in most animals,11 we propose that symbionts might play an equally critical regulatory role in this essential life cycle transition in other metazoans.}, }
@article {pmid33205966, year = {2020}, author = {Kelly, VW and Liang, BK and Sirk, SJ}, title = {Living Therapeutics: The Next Frontier of Precision Medicine.}, journal = {ACS synthetic biology}, volume = {9}, number = {12}, pages = {3184-3201}, doi = {10.1021/acssynbio.0c00444}, pmid = {33205966}, issn = {2161-5063}, mesh = {Antigens/genetics/metabolism ; Bacteria/genetics/metabolism ; Dysbiosis ; Gastrointestinal Microbiome ; Genetic Engineering ; Humans ; Metabolic Diseases/therapy ; Metabolic Engineering ; *Precision Medicine ; Probiotics/administration &amp; dosage ; }, abstract = {Modern medicine has long studied the mechanism and impact of pathogenic microbes on human hosts, but has only recently shifted attention toward the complex and vital roles that commensal and probiotic microbes play in both health and dysbiosis. Fueled by an enhanced appreciation of the human-microbe holobiont, the past decade has yielded countless insights and established many new avenues of investigation in this area. In this review, we discuss advances, limitations, and emerging frontiers for microbes as agents of health maintenance, disease prevention, and cure. We highlight the flexibility of microbial therapeutics across disease states, with special consideration for the rational engineering of microbes toward precision medicine outcomes. As the field advances, we anticipate that tools of synthetic biology will be increasingly employed to engineer functional living therapeutics with the potential to address longstanding limitations of traditional drugs.}, }
@article {pmid33193706, year = {2020}, author = {Djemiel, C and Goulas, E and Badalato, N and Chabbert, B and Hawkins, S and Grec, S}, title = {Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {581664}, pmid = {33193706}, issn = {1664-8021}, abstract = {The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.}, }
@article {pmid33141656, year = {2020}, author = {Parras-Moltó, M and Aguirre de Cárcer, D}, title = {A comprehensive human minimal gut metagenome extends the host's metabolic potential.}, journal = {Microbial genomics}, volume = {6}, number = {11}, pages = {}, pmid = {33141656}, issn = {2057-5858}, mesh = {Bacteria/*genetics/metabolism ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Metagenome/*genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Accumulating evidence suggests that humans could be considered as holobionts in which the gut microbiota play essential functions. Initial metagenomic studies reported a pattern of shared genes in the gut microbiome of different individuals, leading to the definition of the minimal gut metagenome as the set of microbial genes necessary for homeostasis and present in all healthy individuals. This study analyses the minimal gut metagenome of the most comprehensive dataset available, including individuals from agriculturalist and industrialist societies, also embodying highly diverse ethnic and geographical backgrounds. The outcome, based on metagenomic predictions for community composition data, resulted in a minimal metagenome comprising 3412 genes, mapping to 1856 reactions and 128 metabolic pathways predicted to occur across all individuals. These results were substantiated by the analysis of two additional datasets describing the microbial community compositions of larger Western cohorts, as well as a substantial shotgun metagenomics dataset. Subsequent analyses showed the plausible metabolic complementarity provided by the minimal gut metagenome to the human genome.}, }
@article {pmid33140282, year = {2021}, author = {Mote, S and Gupta, V and De, K and Nanajkar, M and Damare, SR and Ingole, B}, title = {Bacterial diversity associated with a newly described bioeroding sponge, Cliona thomasi, from the coral reefs on the West Coast of India.}, journal = {Folia microbiologica}, volume = {66}, number = {2}, pages = {203-211}, pmid = {33140282}, issn = {1874-9356}, support = {GAP 2871//Rajiv Gandhi Science and Technology Commission, Government of Maharashtra/ ; }, mesh = {Animals ; Bacteria/genetics ; *Coral Reefs ; Ecosystem ; India ; *Porifera ; }, abstract = {The bacterial diversity associated with eroding sponges belonging to the Cliona viridis species complex is scarcely known. Cliona thomasi described from the West Coast of India is a new introduction to the viridis species complex. In this study, we determined the bacterial diversity associated with C. thomasi using next-generation sequencing. The results revealed the dominance of Proteobacteria followed by Cyanobacteria, Actinobacteria and Firmicutes. Among Proteobacteria, the Alphaproteobacteria were found to be the most dominant class. Furthermore, at the genus level, Rhodothalassium were highly abundant followed by Endozoicomonas in sponge samples. The beta-diversity and species richness measures showed remarkably lower diversity in Cliona thomasi than the ambient environment. The determined lower bacterial diversity in C. thomasi than the environmental samples, thus, categorized it as a low microbial abundance (LMA). Functional annotation of the C. thomasi-associated bacterial community indicates their possible role in photo-autotrophy, aerobic nitrification, coupling of sulphate reduction and sulphide oxidization. The present study unveils the bacterial diversity in bioeroding C. thomasi, which is a crucial step to determine the functions of the sponge holobiont in coral reef ecosystem.}, }
@article {pmid33138319, year = {2020}, author = {Boilard, A and Dubé, CE and Gruet, C and Mercière, A and Hernandez-Agreda, A and Derome, N}, title = {Defining Coral Bleaching as a Microbial Dysbiosis within the Coral Holobiont.}, journal = {Microorganisms}, volume = {8}, number = {11}, pages = {}, pmid = {33138319}, issn = {2076-2607}, support = {6333//Natural Sciences and Engineering Research Council of Canada/ ; }, abstract = {Coral microbiomes are critical to holobiont health and functioning, but the stability of host-microbial interactions is fragile, easily shifting from eubiosis to dysbiosis. The heat-induced breakdown of the symbiosis between the host and its dinoflagellate algae (that is, "bleaching"), is one of the most devastating outcomes for reef ecosystems. Yet, bleaching tolerance has been observed in some coral species. This review provides an overview of the holobiont's diversity, explores coral thermal tolerance in relation to their associated microorganisms, discusses the hypothesis of adaptive dysbiosis as a mechanism of environmental adaptation, mentions potential solutions to mitigate bleaching, and suggests new research avenues. More specifically, we define coral bleaching as the succession of three holobiont stages, where the microbiota can (i) maintain essential functions for holobiont homeostasis during stress and/or (ii) act as a buffer to mitigate bleaching by favoring the recruitment of thermally tolerant Symbiodiniaceae species (adaptive dysbiosis), and where (iii) environmental stressors exceed the buffering capacity of both microbial and dinoflagellate partners leading to coral death.}, }
@article {pmid33135084, year = {2020}, author = {Panelli, S and Corbella, M and Gazzola, A and Piralla, A and Girello, A and Rampelli, S and Candela, M and Cambieri, P}, title = {Tracking over time the developing gut microbiota in newborns admitted to a neonatal intensive care unit during an outbreak caused by ESBL-producing Klebsiella pneumoniae.}, journal = {The new microbiologica}, volume = {43}, number = {4}, pages = {186-190}, pmid = {33135084}, issn = {1121-7138}, mesh = {*Cross Infection/epidemiology ; Disease Outbreaks ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Intensive Care Units, Neonatal ; *Klebsiella Infections/epidemiology ; Klebsiella pneumoniae/enzymology/genetics ; beta-Lactamases/genetics ; }, abstract = {The establishment of gut microbiota is reportedly aberrant in newborns admitted to neonatal intensive care units (NICUs), with detrimental long-term health impacts. Here, we vertically tracked the developing gut bacterial communities of newborns hosted in an NICU during an outbreak sustained by ESBL Klebsiella pneumoniae and compared colonized and non-colonized patients. Most communities were highly variable from one sampling point to the next, and dominated by few taxa, often Proteobacteria and Enterobacteriaceae, with marked interindividual variability. This picture was retrieved independently of colonization status or clinical covariates. Our data support the emerging idea of preterm infants as a population in which no defined microbial signatures are clearly associated to clinical status. Instead, the strong pressure of the nosocomial environment, antibiotics and, in this case, the ongoing outbreak, possibly drive the evolution of microbiota patterns according to individual conditions, also in non-colonized patients.}, }
@article {pmid33127817, year = {2021}, author = {Goddard-Dwyer, M and López-Legentil, S and Erwin, PM}, title = {Microbiome Variability across the Native and Invasive Ranges of the Ascidian Clavelina oblonga.}, journal = {Applied and environmental microbiology}, volume = {87}, number = {2}, pages = {}, pmid = {33127817}, issn = {1098-5336}, mesh = {Animals ; Bacteria/genetics ; Brazil ; DNA Barcoding, Taxonomic ; Florida ; *Introduced Species ; Italy ; *Microbiota ; North Carolina ; RNA, Ribosomal, 16S/genetics ; Seawater ; South Carolina ; Spain ; Symbiosis ; Urochordata/genetics/*microbiology ; }, abstract = {Ascidians are prolific colonizers of new environments and possess a range of well-studied features that contribute to their successful spread, but the role of their symbiotic microbial communities in their long-term establishment is mostly unknown. In this study, we utilized next-generation amplicon sequencing to provide a comprehensive description of the microbiome in the colonial ascidian Clavelina oblonga and examined differences in the composition, diversity, and structure of symbiont communities in the host's native and invasive ranges. To identify host haplotypes, we sequenced a fragment of the mitochondrial gene cytochrome c oxidase subunit I (COI). C. oblonga harbored a diverse microbiome spanning 42 bacterial and three archaeal phyla. Colonies in the invasive range hosted significantly less diverse symbiont communities and exhibited lower COI haplotype diversity than colonies in the native range. Differences in microbiome structure were also detected across colonies in the native and invasive range, driven largely by novel bacteria representing symbiont lineages with putative roles in nitrogen cycling. Variability in symbiont composition was also observed among sites within each range. Together, these data suggest that C. oblonga hosts a dynamic microbiome resulting from (i) reductions in symbiont diversity due to founder effects in host populations and (ii) environmental selection of symbiont taxa in response to new habitats within a range. Further investigation is required to document the mechanisms behind these changes and to determine how changes in microbiome structure relate to holobiont function and the successful establishment of C. oblonga worldwide.IMPORTANCE Nonnative species destabilize coastal ecosystems and microbial symbionts may facilitate their spread by enhancing host survival and fitness. However, we know little of the microorganisms that live inside invasive species and whether they change as the host spreads to new areas. In this study, we investigated the microbial communities of an introduced ascidian (Clavelina oblonga) and tracked symbiont changes across locations within the host's native and invasive ranges. Ascidians in the invasive range had less-diverse microbiomes, as well as lower host haplotype diversity, suggesting that specific colonies reach new locations and carry select symbionts from native populations (i.e., founder effects). Further, ascidians in the invasive range hosted a different composition of symbionts, including microbes with the potential to aid in processes related to invasion success (e.g., nutrient cycling). We conclude that the putative functionality and observed flexibility of this introduced ascidian microbiome may represent an underappreciated factor in the successful establishment of nonnative species in new environments.}, }
@article {pmid33123099, year = {2020}, author = {van de Water, JAJM and Coppari, M and Enrichetti, F and Ferrier-Pagès, C and Bo, M}, title = {Local Conditions Influence the Prokaryotic Communities Associated With the Mesophotic Black Coral Antipathella subpinnata.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {537813}, pmid = {33123099}, issn = {1664-302X}, abstract = {Black corals are important habitat-forming species in the mesophotic and deep-sea zones of the world's oceans because of their arborescent colony structure and tendency to form animal forests. Although we have started unraveling the ecology of mesophotic black corals, the importance of the associated microbes to their health has remained unexplored. Here, we provide in-depth assessments of black coral-microbe symbioses by investigating the spatial and temporal stability of these associations, and make comparisons with a sympatric octocoral with similar colony structure. To this end, we collected samples of Antipathella subpinnata colonies from three mesophotic shoals situated along the Ligurian Coast of the Mediterranean Sea (Bordighera, Portofino, Savona) in the spring of 2017. At the Portofino shoal, samples of A. subpinnata and the gorgonian Eunicella cavolini were collected in November 2016 and May 2017. Bacterial communities were profiled using 16S rRNA gene amplicon sequencing. The bacterial community of E. cavolini was consistently dominated by Endozoicomonas. Contrastingly, the black coral microbiome was more diverse, and was primarily composed of numerous Bacteroidetes, Alpha- and Gammaproteobacterial taxa, putatively involved in all steps of the nitrogen and sulfur cycles. Compositional differences in the A. subpinnata microbiome existed between all locations and both time points, and no phylotypes were consistently associated with A. subpinnata. This highlights that local conditions may influence the bacterial community structure and potentially nutrient cycling within the A. subpinnata holobiont. But it also suggests that this coral holobiont possesses a high degree of microbiome flexibility, which may be a mechanism to acclimate to environmental change.}, }
@article {pmid33122700, year = {2020}, author = {Chakraborty, A and Ashraf, MZ and Modlinger, R and Synek, J and Schlyter, F and Roy, A}, title = {Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {18572}, pmid = {33122700}, issn = {2045-2322}, mesh = {Animals ; Bacteria/*classification/genetics/metabolism ; Coleoptera/metabolism/*microbiology ; Ecology ; Forests ; *Gastrointestinal Microbiome ; Nitrogen Fixation ; Phylogeny ; Trees/parasitology ; }, abstract = {Bark beetles often serve as forest damaging agents, causing landscape-level mortality. Understanding the biology and ecology of beetles are important for both, gathering knowledge about important forest insects and forest protection. Knowledge about the bark beetle gut-associated bacteria is one of the crucial yet surprisingly neglected areas of research with European tree-killing bark beetles. Hence, in this study, we survey the gut bacteriome from five Ips and one non-Ips bark beetles from Scolytinae. Results reveal 69 core bacterial genera among five Ips beetles that may perform conserved functions within the bark beetle holobiont. The most abundant bacterial genera from different bark beetle gut include Erwinia, Sodalis, Serratia, Tyzzerella, Raoultella, Rahnella, Wolbachia, Spiroplasma, Vibrio, and Pseudoxanthomonas. Notable differences in gut-associated bacterial community richness and diversity among the beetle species are observed. Furthermore, the impact of sampling location on the overall bark beetle gut bacterial community assemblage is also documented, which warrants further investigations. Nevertheless, our data expanded the current knowledge about core gut bacterial communities in Ips bark beetles and their putative function such as cellulose degradation, nitrogen fixation, detoxification of defensive plant compounds, and inhibition of pathogens, which could serve as a basis for further metatranscriptomics and metaproteomics investigations.}, }
@article {pmid33120157, year = {2021}, author = {da Silva Fonseca, J and Mies, M and Paranhos, A and Taniguchi, S and Güth, AZ and Bícego, MC and Marques, JA and Fernandes de Barros Marangoni, L and Bianchini, A}, title = {Isolated and combined effects of thermal stress and copper exposure on the trophic behavior and oxidative status of the reef-building coral Mussismilia harttii.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {268}, number = {Pt B}, pages = {115892}, doi = {10.1016/j.envpol.2020.115892}, pmid = {33120157}, issn = {1873-6424}, mesh = {Animals ; *Anthozoa ; Copper/toxicity ; Coral Reefs ; Oxidation-Reduction ; Oxidative Stress ; Symbiosis ; }, abstract = {Global warming and local disturbances such as pollution cause several impacts on coral reefs. Among them is the breakdown of the symbiosis between host corals and photosynthetic symbionts, which is often a consequence of oxidative stress. Therefore, we investigated if the combined effects of thermal stress and copper (Cu) exposure change the trophic behavior and oxidative status of the reef-building coral Mussismilia harttii. Coral fragments were exposed in a mesocosm system to three temperatures (25.0, 26.6 and 27.3 °C) and three Cu concentrations (2.9, 5.4 and 8.6 μg L-1). Samples were collected after 4 and 12 days of exposure. We then (i) performed fatty acid analysis by gas chromatography-mass spectrometry to quantify changes in stearidonic acid and docosapentaenoic acid (autotrophy markers) and cis-gondoic acid (heterotrophy marker), and (ii) assessed the oxidative status of both host and symbiont through analyses of lipid peroxidation (LPO) and total antioxidant capacity (TAC). Our findings show that trophic behavior was predominantly autotrophic and remained unchanged under individual and combined stressors for both 4- and 12-day experiments; for the latter, however, there was an increase in the heterotrophy marker. Results also show that 4 days was not enough to trigger changes in LPO or TAC for both coral and symbiont. However, the 12-day experiment showed a reduction in symbiont LPO associated with thermal stress alone, and the combination of stressors increased their TAC. For the coral, the isolated effects of increase in Cu and temperature led to an increase in LPO. The effects of combined stressors on trophic behavior and oxidative status were not much different than those from the isolated effects of each stressor. These findings highlight that host and symbionts respond differently to stress and are relevant as they show the physiological response of individual holobiont compartments to both global and local stressors.}, }
@article {pmid33117320, year = {2020}, author = {Cannicci, S and Fratini, S and Meriggi, N and Bacci, G and Iannucci, A and Mengoni, A and Cavalieri, D}, title = {To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {575372}, pmid = {33117320}, issn = {1664-302X}, abstract = {The transition to terrestrial environments by formerly aquatic species has occurred repeatedly in many animal phyla and lead to the vast diversity of extant terrestrial species. The differences between aquatic and terrestrial habitats are enormous and involved remarkable morphological and physiological changes. Convergent evolution of various traits is evident among phylogenetically distant taxa, but almost no information is available about the role of symbiotic microbiota in such transition. Here, we suggest that intertidal and terrestrial brachyuran crabs are a perfect model to study the evolutionary pathways and the ecological role of animal-microbiome symbioses, since their transition to land is happening right now, through a number of independent lineages. The microorganisms colonizing the gut of intertidal and terrestrial crabs are expected to play a major role to conquer the land, by reducing water losses and permitting the utilization of novel food sources. Indeed, it has been shown that the microbiomes hosted in the digestive system of terrestrial isopods has been critical to digest plant items, but nothing is known about the microbiomes present in the gut of truly terrestrial crabs. Other important physiological regulations that could be facilitated by microbiomes are nitrogen excretion and osmoregulation in the new environment. We also advocate for advances in comparative and functional genomics to uncover physiological aspects of these ongoing evolutionary processes. We think that the multidisciplinary study of microorganisms associated with terrestrial crabs will shed a completely new light on the biological and physiological processes involved in the sea-land transition.}, }
@article {pmid33117317, year = {2020}, author = {Cárdenas, A and Ye, J and Ziegler, M and Payet, JP and McMinds, R and Vega Thurber, R and Voolstra, CR}, title = {Coral-Associated Viral Assemblages From the Central Red Sea Align With Host Species and Contribute to Holobiont Genetic Diversity.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {572534}, pmid = {33117317}, issn = {1664-302X}, abstract = {Coral reefs are highly diverse marine ecosystems increasingly threatened on a global scale. The foundation species of reef ecosystems are stony corals that depend on their symbiotic microalgae and bacteria for aspects of their metabolism, immunity, and environmental adaptation. Conversely, the function of viruses in coral biology is less well understood, and we are missing an understanding of the diversity and function of coral viruses, particularly in understudied regions such as the Red Sea. Here we characterized coral-associated viruses using a large metagenomic and metatranscriptomic survey across 101 cnidarian samples from the central Red Sea. While DNA and RNA viral composition was different across coral hosts, biological traits such as coral life history strategy correlated with patterns of viral diversity. Coral holobionts were broadly associated with Mimiviridae and Phycodnaviridae that presumably infect protists and algal cells, respectively. Further, Myoviridae and Siphoviridae presumably target members of the bacterial phyla Actinobacteria, Firmicutes, and Proteobacteria, whereas Hepadnaviridae and Retroviridae might infect the coral host. Genes involved in bacterial virulence and auxiliary metabolic genes were common among the viral sequences, corroborating a contribution of viruses to the holobiont's genetic diversity. Our work provides a first insight into Red Sea coral DNA and RNA viral assemblages and reveals that viral diversity is consistent with global coral virome patterns.}, }
@article {pmid33087470, year = {2020}, author = {Mason, RAB and Wall, CB and Cunning, R and Dove, S and Gates, RD}, title = {High light alongside elevated P CO2 alleviates thermal depression of photosynthesis in a hard coral (Pocillopora acuta).}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 20}, pages = {}, doi = {10.1242/jeb.223198}, pmid = {33087470}, issn = {1477-9145}, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Chlorophyll A ; Coral Reefs ; Humans ; Hydrogen-Ion Concentration ; Oceans and Seas ; Photosynthesis ; Seawater ; Temperature ; }, abstract = {The absorbtion of human-emitted CO2 by the oceans (elevated P CO2) is projected to alter the physiological performance of coral reef organisms by perturbing seawater chemistry (i.e. ocean acidification). Simultaneously, greenhouse gas emissions are driving ocean warming and changes in irradiance (through turbidity and cloud cover), which have the potential to influence the effects of ocean acidification on coral reefs. Here, we explored whether physiological impacts of elevated P CO2 on a coral-algal symbiosis (Pocillopora acuta-Symbiodiniaceae) are mediated by light and/or temperature levels. In a 39 day experiment, elevated P CO2 (962 versus 431 µatm P CO2) had an interactive effect with midday light availability (400 versus 800 µmol photons m-2 s-1) and temperature (25 versus 29°C) on areal gross and net photosynthesis, for which a decline at 29°C was ameliorated under simultaneous high-P CO2 and high-light conditions. Light-enhanced dark respiration increased under elevated P CO2 and/or elevated temperature. Symbiont to host cell ratio and chlorophyll a per symbiont increased at elevated temperature, whilst symbiont areal density decreased. The ability of moderately strong light in the presence of elevated P CO2 to alleviate the temperature-induced decrease in photosynthesis suggests that higher substrate availability facilitates a greater ability for photochemical quenching, partially offsetting the impacts of high temperature on the photosynthetic apparatus. Future environmental changes that result in moderate increases in light levels could therefore assist the P. acuta holobiont to cope with the 'one-two punch' of rising temperatures in the presence of an acidifying ocean.}, }
@article {pmid33086747, year = {2020}, author = {Wojciech, L and Tan, KSW and Gascoigne, NRJ}, title = {Taming the Sentinels: Microbiome-Derived Metabolites and Polarization of T Cells.}, journal = {International journal of molecular sciences}, volume = {21}, number = {20}, pages = {}, pmid = {33086747}, issn = {1422-0067}, support = {NUHSRO/2019/049/T1/SEED-MAR/02//NUS Seed Grant/ ; NUHSRO/2020/110/T1/SEED-MAR/06//NUS Seed Grant/ ; R-571-000-037-114//MOE Tier-1/ ; }, mesh = {Animals ; *Cell Polarity ; Fatty Acids/metabolism ; Homeostasis ; Humans ; *Metabolome ; *Microbiota ; T-Lymphocytes/*cytology ; }, abstract = {A global increase in the prevalence of metabolic syndromes and digestive tract disorders, like food allergy or inflammatory bowel disease (IBD), has become a severe problem in the modern world. Recent decades have brought a growing body of evidence that links the gut microbiome's complexity with host physiology. Hence, understanding the mechanistic aspects underlying the synergy between the host and its associated gut microbiome are among the most crucial questions. The functionally diversified adaptive immune system plays a central role in maintaining gut and systemic immune homeostasis. The character of the reciprocal interactions between immune components and host-dwelling microbes or microbial consortia determines the outcome of the organisms' coexistence within the holobiont structure. It has become apparent that metabolic by-products of the microbiome constitute crucial multimodal transmitters within the host-microbiome interactome and, as such, contribute to immune homeostasis by fine-tuning of the adaptive arm of immune system. In this review, we will present recent insights and discoveries regarding the broad landscape of microbiome-derived metabolites, highlighting the role of these small compounds in the context of the balance between pro- and anti-inflammatory mechanisms orchestrated by the host T cell compartment.}, }
@article {pmid33071821, year = {2020}, author = {Goulet, TL and Erill, I and Ascunce, MS and Finley, SJ and Javan, GT}, title = {Conceptualization of the Holobiont Paradigm as It Pertains to Corals.}, journal = {Frontiers in physiology}, volume = {11}, number = {}, pages = {566968}, pmid = {33071821}, issn = {1664-042X}, abstract = {Corals' obligate association with unicellular dinoflagellates, family Symbiodiniaceae form the foundation of coral reefs. For nearly a century, researchers have delved into understanding the coral-algal mutualism from multiple levels of resolution and perspectives, and the questions and scope have evolved with each iteration of new techniques. Advances in genetic technologies not only aided in distinguishing between the multitude of Symbiodiniaceae but also illuminated the existence and diversity of other organisms constituting the coral microbiome. The coral therefore is a meta-organism, often referred to as the coral holobiont. In this review, we address the importance of including a holistic perspective to understanding the coral holobiont. We also discuss the ramifications of how different genotypic combinations of the coral consortium affect the holobiont entity. We highlight the paucity of data on most of the coral microbiome. Using Symbiodiniaceae data, we present evidence that the holobiont properties are not necessarily the sum of its parts. We then discuss the consequences of the holobiont attributes to the fitness of the holobiont and the myriad of organisms that contribute to it. Considering the complexity of host-symbiont genotypic combinations will aid in our understanding of coral resilience, robustness, acclimation, and/or adaptation in the face of environmental change and increasing perturbations.}, }
@article {pmid33071127, year = {2021}, author = {Chen, B and Yu, K and Liao, Z and Yu, X and Qin, Z and Liang, J and Wang, G and Wu, Q and Jiang, L}, title = {Microbiome community and complexity indicate environmental gradient acclimatisation and potential microbial interaction of endemic coral holobionts in the South China Sea.}, journal = {The Science of the total environment}, volume = {765}, number = {}, pages = {142690}, doi = {10.1016/j.scitotenv.2020.142690}, pmid = {33071127}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; China ; Coral Reefs ; *Dinoflagellida ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Regional acclimatisation and microbial interactions significantly influence the resilience of reef-building corals facing anthropogenic climate change, allowing them to adapt to environmental stresses. However, the connections between community structure and microbial interactions of the endemic coral microbiome and holobiont acclimatisation remain unclear. Herein, we used generation sequencing of internal transcribed spacer (ITS2) and 16S rRNA genes to investigate the microbiome composition (Symbiodiniaceae and bacteria) and associated potential interactions of endemic dominant coral holobionts (Pocillopora verrucosa and Turbinaria peltata) in the South China Sea (SCS). We found that shifts in Symbiodiniaceae and bacterial communities of P. verrucosa were associated with latitudinal gradient and climate zone changes, respectively. The C1 sub-clade consistently dominated the Symbiodiniaceae community in T. peltata; yet, the bacterial community structure was spatially heterogeneous. The relative abundance of the core microbiome among P. verrucosa holobionts was reduced in the biogeographical transition zone, while bacterial taxa associated with anthropogenic activity (Escherichia coli and Sphingomonas) were identified in the core microbiomes. Symbiodiniaceae and bacteria potentially interact in microbial co-occurrence networks. Further, increased bacterial, and Symbiodiniaceae α-diversity was associated with increased and decreased network complexity, respectively. Hence, Symbiodiniaceae and bacteria demonstrated different flexibility in latitudinal or climatic environmental regimes, which correlated with holobiont acclimatisation. Core microbiome analysis has indicated that the function of core bacterial microbiota might have changed in distinct environmental regimes, implying potential human activity in the coral habitats. Increased bacterial α diversity may lead to a decline in the stability of coral-microorganism symbioses, whereas rare Symbiodiniaceae may help to retain symbioses. Cladocopium, γ-proteobacteria, while α-proteobacteria may have been the primary drivers in the Symbiodiniaceae-bacterial interactions (SBIs). Our study highlights the association between microbiome shift in distinct environmental regimes and holobiont acclimatisation, while providing insights into the impact of SBIs on holobiont health and acclimatisation during climate change.}, }
@article {pmid33060749, year = {2020}, author = {Vega de Luna, F and Córdoba-Granados, JJ and Dang, KV and Roberty, S and Cardol, P}, title = {In vivo assessment of mitochondrial respiratory alternative oxidase activity and cyclic electron flow around photosystem I on small coral fragments.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {17514}, pmid = {33060749}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*physiology ; Chlorophyll A/*chemistry ; Electron Transport ; Energy Metabolism ; Fluorescence ; Genotype ; Light ; Mitochondria/*enzymology ; Mitochondrial Proteins/*chemistry ; Oxidation-Reduction ; Oxidoreductases/*chemistry ; Oxygen/chemistry ; Oxygen Consumption ; Photosynthesis ; Photosystem I Protein Complex ; Photosystem II Protein Complex ; Plant Proteins/*chemistry ; Spectrophotometry ; *Symbiosis ; }, abstract = {The mutualistic relationship existing between scleractinian corals and their photosynthetic endosymbionts involves a complex integration of the metabolic pathways within the holobiont. Respiration and photosynthesis are the most important of these processes and although they have been extensively studied, our understanding of their interactions and regulatory mechanisms is still limited. In this work we performed chlorophyll-a fluorescence, oxygen exchange and time-resolved absorption spectroscopy measurements on small and thin fragments (0.3 cm2) of the coral Stylophora pistillata. We showed that the capacity of mitochondrial alternative oxidase accounted for ca. 25% of total coral respiration, and that the high-light dependent oxygen uptake, commonly present in isolated Symbiodiniaceae, was negligible. The ratio between photosystem I (PSI) and photosystem II (PSII) active centers as well as their respective electron transport rates, indicated that PSI cyclic electron flow occurred in high light in S. pistillata and in some branching and lamellar coral species freshly collected in the field. Altogether, these results show the potential of applying advanced biophysical and spectroscopic methods on small coral fragments to understand the complex mechanisms of coral photosynthesis and respiration and their responses to environmental changes.}, }
@article {pmid33053643, year = {2020}, author = {Baquiran, JIP and Nada, MAL and Campos, CLD and Sayco, SLG and Cabaitan, PC and Rosenberg, Y and Ayalon, I and Levy, O and Conaco, C}, title = {The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution.}, journal = {Microorganisms}, volume = {8}, number = {10}, pages = {}, pmid = {33053643}, issn = {2076-2607}, support = {QMSR- MRRD-MEC-295-1449//Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development/ ; }, abstract = {Corals harbor a great diversity of symbiotic microorganisms that play pivotal roles in host nutrition, reproduction, and development. Changes in the ocean environment, such as increasing exposure to artificial light at night (ALAN), may alter these relationships and result in a decline in coral health. In this study, we examined the microbiome associated with gravid specimens of the reef-building coral Acropora digitifera. We also assessed the temporal effects of ALAN on the coral-associated microbial community using high-throughput sequencing of the 16S rRNA gene V4 hypervariable region. The A. digitifera microbial community was dominated by phyla Proteobacteria, Firmicutes, and Bacteroidetes. Exposure to ALAN had no large-scale effect on the coral microbiome, although taxa affiliated with Rhodobacteraceae, Caulobacteraceae, Burkholderiaceae, Lachnospiraceae, and Ruminococcaceae were significantly enriched in corals subjected to ALAN. We further noted an increase in the relative abundance of the family Endozoicomonadaceae (Endozoicomonas) as the spawning period approached, regardless of light treatment. These findings highlight the stability of the A. digitifera microbial community under short-term artificial light pollution and provide initial insights into the response of the collective holobiont to ALAN.}, }
@article {pmid33048474, year = {2020}, author = {de Oliveira, BFR and Freitas-Silva, J and Sánchez-Robinet, C and Laport, MS}, title = {Transmission of the sponge microbiome: moving towards a unified model.}, journal = {Environmental microbiology reports}, volume = {12}, number = {6}, pages = {619-638}, doi = {10.1111/1758-2229.12896}, pmid = {33048474}, issn = {1758-2229}, support = {140046/2020-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/International ; 140840/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/International ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/International ; E-26/203.320/2017//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro (FAPERJ)/International ; }, mesh = {Animals ; Bacteria/classification/genetics/*isolation &amp; purification ; *Bacterial Physiological Phenomena ; *Microbiota ; Models, Biological ; Phylogeny ; Porifera/growth &amp; development/*microbiology/physiology ; Symbiosis ; }, abstract = {Sponges have co-evolved for millions of years alongside several types of microorganisms, which aside from participating in the animal's diet, are mostly symbionts. Since most of the genetic repertoire in the holobiont genome is provided by microbes, it is expected that the host-associated microbiome will be at least partially heritable. Sponges can therefore acquire their symbionts in different ways. Both vertical transmission (VT) and horizontal transmission (HT) have different advantages and disadvantages in the life cycle of these invertebrates. However, a third mode of transmission, called leaky vertical transmission or mixed mode of transmission (MMT), which incorporates both VT and HT modes, has gained relevance and seems to be the most robust model. In that regard, the aim of this review is to present the evolving knowledge on these main modes of transmission of the sponge microbiome. Our conclusions lead us to suggest that MMT may be more common for all sponges, with its frequency varying across the transmission spectrum between species and the environment. This hybrid model supports the stable and specific transmission of these microbial partners and reinforces their assistance in the resilience of sponges over the years.}, }
@article {pmid33041996, year = {2020}, author = {Martino, D and Johnson, I and Leckman, JF}, title = {What Does Immunology Have to Do With Normal Brain Development and the Pathophysiology Underlying Tourette Syndrome and Related Neuropsychiatric Disorders?.}, journal = {Frontiers in neurology}, volume = {11}, number = {}, pages = {567407}, pmid = {33041996}, issn = {1664-2295}, abstract = {Objective: The goal of this article is to review the past decade's literature and provide a critical commentary on the involvement of immunological mechanisms in normal brain development, as well as its role in the pathophysiology of Tourette syndrome, other Chronic tic disorders (CTD), and related neuropsychiatric disorders including Obsessive-compulsive disorder (OCD) and Attention deficit hyperactivity disorder (ADHD). Methods: We conducted a literature search using the Medline/PubMed and EMBASE electronic databases to locate relevant articles and abstracts published between 2009 and 2020, using a comprehensive list of search terms related to immune mechanisms and the diseases of interest, including both clinical and animal model studies. Results: The cellular and molecular processes that constitute our "immune system" are crucial to normal brain development and the formation and maintenance of neural circuits. It is also increasingly evident that innate and adaptive systemic immune pathways, as well as neuroinflammatory mechanisms, play an important role in the pathobiology of at least a subset of individuals with Tourette syndrome and related neuropsychiatric disorders In the conceptual framework of the holobiont theory, emerging evidence points also to the importance of the "microbiota-gut-brain axis" in the pathobiology of these neurodevelopmental disorders. Conclusions: Neural development is an enormously complex and dynamic process. Immunological pathways are implicated in several early neurodevelopmental processes including the formation and refinement of neural circuits. Hyper-reactivity of systemic immune pathways and neuroinflammation may contribute to the natural fluctuations of the core behavioral features of CTD, OCD, and ADHD. There is still limited knowledge of the efficacy of direct and indirect (i.e., through environmental modifications) immune-modulatory interventions in the treatment of these disorders. Future research also needs to focus on the key molecular pathways through which dysbiosis of different tissue microbiota influence neuroimmune interactions in these disorders, and how microbiota modification could modify their natural history. It is also possible that valid biomarkers will emerge that will guide a more personalized approach to the treatment of these disorders.}, }
@article {pmid33036916, year = {2021}, author = {Middleton, H and Yergeau, É and Monard, C and Combier, JP and El Amrani, A}, title = {Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator.}, journal = {Trends in plant science}, volume = {26}, number = {2}, pages = {132-141}, doi = {10.1016/j.tplants.2020.09.005}, pmid = {33036916}, issn = {1878-4372}, mesh = {*MicroRNAs/genetics ; *Microbiota ; Plant Development ; Plants/genetics ; Rhizosphere ; Soil Microbiology ; }, abstract = {The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant-microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota. Through coevolution, plants and microbes have developed cross-kingdom communication channels. Here, we propose that miRNAs are crucial mediators of plant-microbe interactions and microbiota shaping in the rhizosphere. Moreover, we suggest, as an alternative to generally unsuccessful strategies based on microbial inoculants, miRNAs as a promising tool for novel holobiont engineering.}, }
@article {pmid33025575, year = {2021}, author = {Clowez, S and Renicke, C and Pringle, JR and Grossman, AR}, title = {Impact of Menthol on Growth and Photosynthetic Function of Breviolum Minutum (Dinoflagellata, Dinophyceae, Symbiodiniaceae) and Interactions with its Aiptasia Host.}, journal = {Journal of phycology}, volume = {57}, number = {1}, pages = {245-257}, doi = {10.1111/jpy.13081}, pmid = {33025575}, issn = {1529-8817}, mesh = {Animals ; *Dinoflagellida ; Menthol ; Photosynthesis ; *Sea Anemones ; Symbiosis ; }, abstract = {Environmental change, including global warming and chemical pollution, can compromise cnidarian-(e.g., coral-) dinoflagellate symbioses and cause coral bleaching. Understanding the mechanisms that regulate these symbioses will inform strategies for sustaining healthy coral-reef communities. A model system for corals is the symbiosis between the sea anemone Exaiptasia pallida (common name Aiptasia) and its dinoflagellate partners (family Symbiodiniaceae). To complement existing studies of the interactions between these organisms, we examined the impact of menthol, a reagent often used to render cnidarians aposymbiotic, on the dinoflagellate Breviolum minutum, both in culture and in hospite. In both environments, the growth and photosynthesis of this alga were compromised at either 100 or 300 µM menthol. We observed reduction in PSII and PSI functions, the abundances of reaction-center proteins, and, at 300 µM menthol, of total cellular proteins. Interestingly, for free-living algae exposed to 100 µM menthol, an initial decline in growth, photosynthetic activities, pigmentation, and protein abundances reversed after 5-15 d, eventually approaching control levels. This behavior was observed in cells maintained in continuous light, but not in cells experiencing a light-dark regimen, suggesting that B. minutum can detoxify menthol or acclimate and repair damaged photosynthetic complexes in a light- and/or energy-dependent manner. Extended exposures of cultured algae to 300 µM menthol ultimately resulted in algal death. Most symbiotic anemones were also unable to survive this menthol concentration for 30 d. Additionally, cells impaired for photosynthesis by pre-treatment with 300 µM menthol exhibited reduced efficiency in re-populating the anemone host.}, }
@article {pmid33011965, year = {2020}, author = {Riccio, P and Rossano, R}, title = {The human gut microbiota is neither an organ nor a commensal.}, journal = {FEBS letters}, volume = {594}, number = {20}, pages = {3262-3271}, doi = {10.1002/1873-3468.13946}, pmid = {33011965}, issn = {1873-3468}, mesh = {Biotransformation ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Humans ; *Symbiosis ; }, abstract = {The recent explosive increase in the number of works on gut microbiota has been accompanied by the spread of rather vague or improper definitions, chosen more for common use than for experimental evidence. Among them are those defining the human gut microbiota as an organ of our body or as a commensal. But, is the human gut microbiota an organ or a commensal? Here, we address this issue to spearhead a reflection on the real roles of the human gut microbiota in our life. Actually, the misuse of the vocabulary used to describe the properties and functions of the gut microbiota may generate confusion and cause misunderstandings both in the scientific community and among the general public.}, }
@article {pmid32990394, year = {2020}, author = {Massé, A and Tribollet, A and Meziane, T and Bourguet-Kondracki, ML and Yéprémian, C and Sève, C and Thiney, N and Longeon, A and Couté, A and Domart-Coulon, I}, title = {Functional diversity of microboring Ostreobium algae isolated from corals.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4825-4846}, doi = {10.1111/1462-2920.15256}, pmid = {32990394}, issn = {1462-2920}, support = {//Muséum national d'Histoire naturelle/ ; //Sorbonne-Université (UPMC)/ ; }, mesh = {Animals ; Anthozoa/*microbiology ; Carbon/metabolism ; Chlorophyta/genetics/growth &amp; development/metabolism/*physiology ; Coral Reefs ; Fatty Acids/analysis/metabolism ; Nitrogen/metabolism ; Photosynthesis ; Pigments, Biological/analysis ; }, abstract = {The filamentous chlorophyte Ostreobium sp. dominates shallow marine carbonate microboring communities, and is one of the major agents of reef bioerosion. While its large genetic diversity has emerged, its physiology remains little known, with unexplored relationship between genotypes and phenotypes (endolithic versus free-living growth forms). Here, we isolated nine strains affiliated to two lineages of Ostreobium (>8% sequence divergence of the plastid gene rbcL), one of which was assigned to the family Odoaceae, from the fast-growing coral host Pocillopora acuta Lamarck 1816. Free-living isolates maintained their bioerosive potential, colonizing pre-bleached coral carbonate skeletons. We compared phenotypes, highlighting shifts in pigment and fatty acid compositions, carbon to nitrogen ratios and stable isotope compositions (δ13 C and δ15 N). Our data show a pattern of higher chlorophyll b and lower arachidonic acid (20:4ω6) content in endolithic versus free-living Ostreobium. Photosynthetic carbon fixation and nitrate uptake, quantified via 8 h pulse-labeling with 13 C-bicarbonate and 15 N-nitrate, showed lower isotopic enrichment in endolithic compared to free-living filaments. Our results highlight the functional plasticity of Ostreobium phenotypes. The isotope tracer approach opens the way to further study the biogeochemical cycling and trophic ecology of these cryptic algae at coral holobiont and reef scales.}, }
@article {pmid32985530, year = {2020}, author = {Carradec, Q and Poulain, J and Boissin, E and Hume, BCC and Voolstra, CR and Ziegler, M and Engelen, S and Cruaud, C and Planes, S and Wincker, P}, title = {A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {15893}, pmid = {32985530}, issn = {2045-2322}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*genetics ; *Coral Reefs ; Microbiota/*genetics ; Nanopore Sequencing ; Symbiosis ; }, abstract = {Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.}, }
@article {pmid32984975, year = {2021}, author = {Schmidt, R and Saha, M}, title = {Infochemicals in terrestrial plants and seaweed holobionts: current and future trends.}, journal = {The New phytologist}, volume = {229}, number = {4}, pages = {1852-1860}, doi = {10.1111/nph.16957}, pmid = {32984975}, issn = {1469-8137}, mesh = {Climate Change ; Droughts ; Ecology ; Ecosystem ; Rhizosphere ; *Seaweed ; }, abstract = {Since the holobiont concept came into the limelight ten years ago, we have become aware that responses of holobionts to climate change stressors may be driven by shifts in the microbiota. However, the complex interactions underlying holobiont responses across aquatic and terrestrial ecosystems remain largely unresolved. One of the key factors driving these responses is the infochemical-mediated communication in the holobiont. In order to come up with a holistic picture, in this Viewpoint we compare mechanisms and infochemicals in the rhizosphere of plants and the eco-chemosphere of seaweeds in response to climate change stressors and other environmental stressors, including drought, warming and nutrient stress. Furthermore, we discuss the inclusion of chemical ecology concepts that are of crucial importance in driving holobiont survival, adaptation and/or holobiont breakdown. Infochemicals can thus be regarded as a 'missing link' in our understanding of holobiont response to climate change and should be investigated while investigating the responses of plant and seaweed holobionts to climate change. This will set the basis for improving our understanding of holobiont responses to climate change stressors across terrestrial and aquatic ecosystems.}, }
@article {pmid32975356, year = {2020}, author = {Klinges, G and Maher, RL and Vega Thurber, RL and Muller, EM}, title = {Parasitic 'Candidatus Aquarickettsia rohweri' is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress.}, journal = {Environmental microbiology}, volume = {22}, number = {12}, pages = {5341-5355}, pmid = {32975356}, issn = {1462-2920}, support = {1314109//Division of Graduate Education/ ; 1840998//Division of Graduate Education/ ; 1452538//Division of Ocean Sciences/ ; 1923836//Division of Ocean Sciences/ ; }, mesh = {Alphaproteobacteria/*physiology ; Animals ; Anthozoa/*microbiology/physiology ; Disease Resistance ; Disease Susceptibility/*microbiology ; Genotype ; *Heat-Shock Response ; Host Microbial Interactions ; Hot Temperature ; Microbiota/*genetics ; }, abstract = {Holobiont phenotype results from a combination of host and symbiont genotypes as well as from prevailing environmental conditions that alter the relationships among symbiotic members. Corals exemplify this concept, where shifts in the algal symbiont community can lead to some corals becoming more or less thermally tolerant. Despite linkage between coral bleaching and disease, the roles of symbiotic bacteria in holobiont resistance and susceptibility to disease remains less well understood. This study thus characterizes the microbiome of disease-resistant and -susceptible Acropora cervicornis coral genotypes (hereafter referred to simply as 'genotypes') before and after high temperature-mediated bleaching. We found that the intracellular bacterial parasite 'Ca. Aquarickettsia rohweri' was strikingly abundant in disease-susceptible genotypes. Disease-resistant genotypes, however, had notably more diverse and even communities, with correspondingly low abundances of 'Ca. Aquarickettsia'. Bleaching caused a dramatic reduction of 'Ca. Aquarickettsia' within disease-susceptible corals and led to an increase in bacterial community dispersion, as well as the proliferation of opportunists. Our data support the hypothesis that 'Ca. Aquarickettsia' species increase coral disease risk through two mechanisms: (i) the creation of host nutritional deficiencies leading to a compromised host-symbiont state and (ii) the opening of niche space for potential pathogens during thermal stress.}, }
@article {pmid32950795, year = {2020}, author = {Letourneau, ML and Hopkinson, BM and Fitt, WK and Medeiros, PM}, title = {Molecular composition and biodegradation of loggerhead sponge Spheciospongia vesparium exhalent dissolved organic matter.}, journal = {Marine environmental research}, volume = {162}, number = {}, pages = {105130}, doi = {10.1016/j.marenvres.2020.105130}, pmid = {32950795}, issn = {1879-0291}, mesh = {Biodegradation, Environmental ; Carbon ; Florida ; *Microbiota ; *Seawater ; }, abstract = {Sponges are critical components of marine reefs due to their high filtering capacity, wide abundance, and alteration of biogeochemical cycling. Here, we characterized dissolved organic matter (DOM) composition in the sponge holobiont exhalent seawater of a loggerhead sponge (Spheciospongia vesparium) and in ambient seawater in Florida Bay (USA), as well as the microbial responses to each DOM pool through dark incubations. The sponge holobiont removed 6% of the seawater dissolved organic carbon (DOC), utilizing compounds that were low in carbon and oxygen, yet high in nitrogen content relative to the ambient seawater. The microbial community accessed 7% of DOC from the ambient seawater during a 5-day incubation but only 1% of DOC from the sponge exhalent seawater, suggesting a decrease in lability possibly due to holobiont removal of nitrogen-rich compounds. If this holds true for other sponges, it may have important implications for DOM lability and cycling in coastal environments.}, }
@article {pmid32947881, year = {2020}, author = {Cuffaro, B and Assohoun, ALW and Boutillier, D and Súkeníková, L and Desramaut, J and Boudebbouze, S and Salomé-Desnoulez, S and Hrdý, J and Waligora-Dupriet, AJ and Maguin, E and Grangette, C}, title = {In Vitro Characterization of Gut Microbiota-Derived Commensal Strains: Selection of Parabacteroides distasonis Strains Alleviating TNBS-Induced Colitis in Mice.}, journal = {Cells}, volume = {9}, number = {9}, pages = {}, pmid = {32947881}, issn = {2073-4409}, mesh = {Adult ; Animals ; Bacteroidetes/*genetics/*immunology/isolation &amp; purification ; Caco-2 Cells ; Colitis/*chemically induced/immunology/*microbiology ; DNA, Bacterial/genetics/metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; Infant, Newborn ; Inflammatory Bowel Diseases/immunology/microbiology ; Intestinal Mucosa/immunology ; Mice ; Mice, Inbred BALB C ; Real-Time Polymerase Chain Reaction ; T-Lymphocytes, Regulatory/immunology ; Trinitrobenzenesulfonic Acid/*adverse effects ; }, abstract = {Alterations in the gut microbiota composition and diversity seem to play a role in the development of chronic diseases, including inflammatory bowel disease (IBD), leading to gut barrier disruption and induction of proinflammatory immune responses. This opens the door for the use of novel health-promoting bacteria. We selected five Parabacteroides distasonis strains isolated from human adult and neonates gut microbiota. We evaluated in vitro their immunomodulation capacities and their ability to reinforce the gut barrier and characterized in vivo their protective effects in an acute murine model of colitis. The in vitro beneficial activities were highly strain dependent: two strains exhibited a potent anti-inflammatory potential and restored the gut barrier while a third strain reinstated the epithelial barrier. While their survival to in vitro gastric conditions was variable, the levels of P. distasonis DNA were higher in the stools of bacteria-treated animals. The strains that were positively scored in vitro displayed a strong ability to rescue mice from colitis. We further showed that two strains primed dendritic cells to induce regulatory T lymphocytes from naïve CD4+ T cells. This study provides better insights on the functionality of commensal bacteria and crucial clues to design live biotherapeutics able to target inflammatory chronic diseases such as IBD.}, }
@article {pmid32943577, year = {2020}, author = {Becker, DM and Silbiger, NJ}, title = {Nutrient and sediment loading affect multiple facets of functionality in a tropical branching coral.}, journal = {The Journal of experimental biology}, volume = {223}, number = {Pt 21}, pages = {}, doi = {10.1242/jeb.225045}, pmid = {32943577}, issn = {1477-9145}, mesh = {Animals ; *Anthozoa ; Chlorophyll A ; Coral Reefs ; Ecosystem ; Nutrients ; Polynesia ; }, abstract = {Coral reefs, one of the most diverse ecosystems in the world, face increasing pressures from global and local anthropogenic stressors. Therefore, a better understanding of the ecological ramifications of warming and land-based inputs (e.g. sedimentation and nutrient loading) on coral reef ecosystems is necessary. In this study, we measured how a natural nutrient and sedimentation gradient affected multiple facets of coral functionality, including endosymbiont and coral host response variables, holobiont metabolic responses and percent cover of Pocillopora acuta colonies in Mo'orea, French Polynesia. We used thermal performance curves to quantify the relationship between metabolic rates and temperature along the environmental gradient. We found that algal endosymbiont percent nitrogen content, endosymbiont densities and total chlorophyll a content increased with nutrient input, while endosymbiont nitrogen content per cell decreased, likely representing competition among the algal endosymbionts. Nutrient and sediment loading decreased coral metabolic responses to thermal stress in terms of their thermal performance and metabolic rate processes. The acute thermal optimum for dark respiration decreased, along with the maximal performance for gross photosynthetic and calcification rates. Gross photosynthetic and calcification rates normalized to a reference temperature (26.8°C) decreased along the gradient. Lastly, percent cover of P. acuta colonies decreased by nearly two orders of magnitude along the nutrient gradient. These findings illustrate that nutrient and sediment loading affect multiple levels of coral functionality. Understanding how local-scale anthropogenic stressors influence the responses of corals to temperature can inform coral reef management, particularly in relation to the mediation of land-based inputs into coastal coral reef ecosystems.}, }
@article {pmid32932829, year = {2020}, author = {Parisi, MG and Parrinello, D and Stabili, L and Cammarata, M}, title = {Cnidarian Immunity and the Repertoire of Defense Mechanisms in Anthozoans.}, journal = {Biology}, volume = {9}, number = {9}, pages = {}, pmid = {32932829}, issn = {2079-7737}, support = {PJ_RIC_FFABR_2017_161753 MGP//PJ_RIC_FFABR_2017_161753 MGP/ ; }, abstract = {Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes and gene families similar to those of the Bilateria. Evidence indicates that the Anthozoan innate immune system is not only involved in the disruption of harmful microorganisms, but is also crucial in structuring tissue-associated microbial communities that are essential components of the cnidarian holobiont and useful to the animal's health for several functions including metabolism, immune defense, development, and behavior. Here, we report on the current state of the art of Anthozoan immunity. Like other invertebrates, Anthozoans possess immune mechanisms based on self/non-self-recognition. Although lacking adaptive immunity, they use a diverse repertoire of immune receptor signaling pathways (PRRs) to recognize a broad array of conserved microorganism-associated molecular patterns (MAMP). The intracellular signaling cascades lead to gene transcription up to endpoints of release of molecules that kill the pathogens, defend the self by maintaining homeostasis, and modulate the wound repair process. The cells play a fundamental role in immunity, as they display phagocytic activities and secrete mucus, which acts as a physicochemical barrier preventing or slowing down the proliferation of potential invaders. Finally, we describe the current state of knowledge of some immune effectors in Anthozoan species, including the potential role of toxins and the inflammatory response in the Mediterranean Anthozoan Anemonia viridis following injection of various foreign particles differing in type and dimensions, including pathogenetic bacteria.}, }
@article {pmid32901388, year = {2021}, author = {González-Dominici, LI and Saati-Santamaría, Z and García-Fraile, P}, title = {Genome Analysis and Genomic Comparison of the Novel Species Arthrobacter ipsi Reveal Its Potential Protective Role in Its Bark Beetle Host.}, journal = {Microbial ecology}, volume = {81}, number = {2}, pages = {471-482}, pmid = {32901388}, issn = {1432-184X}, support = {19-09072S//Grantová Agentura České Republiky/ ; CLU-2018-04//Junta de Castilla y León (ES)/ ; }, mesh = {Animals ; Antibiosis ; Arthrobacter/classification/genetics/*physiology ; Coleoptera/*microbiology ; DNA, Bacterial/genetics ; Fungi/growth &amp; development ; Genes, Bacterial/genetics ; Genome, Bacterial/*genetics ; Host Microbial Interactions ; Phenotype ; Phylogeny ; Pinus/parasitology ; Plant Bark/*parasitology ; Plant Diseases/parasitology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {The pine engraver beetle, Ips acuminatus Gyll, is a bark beetle that causes important damages in Scots pine (Pinus sylvestris) forests and plantations. As almost all higher organisms, Ips acuminatus harbours a microbiome, although the role of most members of its microbiome is not well understood. As part of a work in which we analysed the bacterial diversity associated to Ips acuminatus, we isolated the strain Arthrobacter sp. IA7. In order to study its potential role within the bark beetle holobiont, we sequenced and explored its genome and performed a pan-genome analysis of the genus Arthrobacter, showing specific genes of strain IA7 that might be related with its particular role in its niche. Based on these investigations, we suggest several potential roles of the bacterium within the beetle. Analysis of genes related to secondary metabolism indicated potential antifungal capability, confirmed by the inhibition of several entomopathogenic fungal strains (Metarhizium anisopliae CCF0966, Lecanicillium muscarium CCF6041, L. muscarium CCF3297, Isaria fumosorosea CCF4401, I. farinosa CCF4808, Beauveria bassiana CCF4422 and B. brongniartii CCF1547). Phylogenetic analyses of the 16S rRNA gene, six concatenated housekeeping genes (tuf-secY-rpoB-recA-fusA-atpD) and genome sequences indicated that strain IA7 is closely related to A. globiformis NBRC 12137T but forms a new species within the genus Arthrobacter; this was confirmed by digital DNA-DNA hybridization (37.10%) and average nucleotide identity (ANIb) (88.9%). Based on phenotypic and genotypic features, we propose strain IA7T as the novel species Arthrobacter ipsi sp. nov. (type strain IA7T = CECT 30100T = LMG 31782T) and suggest its protective role for its host.}, }
@article {pmid32881650, year = {2020}, author = {Xie, H and Feng, X and Wang, M and Wang, Y and Kumar Awasthi, M and Xu, P}, title = {Implications of endophytic microbiota in Camellia sinensis: a review on current understanding and future insights.}, journal = {Bioengineered}, volume = {11}, number = {1}, pages = {1001-1015}, pmid = {32881650}, issn = {2165-5987}, mesh = {Camellia sinensis/genetics/*microbiology ; Gene Expression Regulation, Plant/genetics/physiology ; Microbiota ; }, abstract = {Endophytic fungi and bacteria are the most ubiquitous and representative commensal members that have been studied so far in various higher plants. Within colonization and interaction with their host plants, endophytic microbiota are reportedly to modulate not only the host's growth but also holobiont resilience to abiotic and biotic stresses, providing a natural reservoir and a promising solution for sustainable agricultural development challenged by global climate change. Moreover, possessing the talent to produce a wide array of high-value natural products, plant endophytic microbiota also serve as an alternative way for novel drug discovery. In this review, tea, one of the world's three largest nonalcoholic beverages and a worldwide economic woody crop, was highlighted in the context of endophytic microbiota. We explore the recent studies regarding isolation approaches, distribution characteristics and diversity, and also biological functions of endophytic microbiota in Camellia sinensis (L.) O. Kuntze. Profoundly, the future insight into interaction mechanism between endophytic microbiota and tea plants will shed light on in-depth exploration of tea microbial resources.}, }
@article {pmid32864518, year = {2020}, author = {Assefa, S and Köhler, G}, title = {Intestinal Microbiome and Metal Toxicity.}, journal = {Current opinion in toxicology}, volume = {19}, number = {}, pages = {21-27}, pmid = {32864518}, issn = {2468-2934}, support = {R15 GM110593/GM/NIGMS NIH HHS/United States ; }, abstract = {The human gut microbiome is considered critical for establishing and maintaining intestinal function and homeostasis throughout life. Evidence for bidirectional communication with the immune and nervous systems has spawned interest in the microbiome as a key factor for human and animal health. Consequently, appreciation of the microbiome as a target of xenobiotics, including environmental pollutants such as heavy metals, has risen steadily because disruption of a healthy microbiome (dysbiosis) has been linked to unfavorable health outcomes. Thus, toxicology must consider toxicant effects on the host's microbiome as an integral part of the holobiont. We discuss current findings on the impact of toxic metals on the composition, diversity, and function of the gut microbiome as well as the modulation of metal toxicity by the microbiome. Present limitations and future needs in elucidating microbiome-metal interactions and the potential of harnessing beneficial traits of the microbiota to counteract metal toxicity are also considered.}, }
@article {pmid32858775, year = {2020}, author = {Lindsay, EC and Metcalfe, NB and Llewellyn, MS}, title = {The potential role of the gut microbiota in shaping host energetics and metabolic rate.}, journal = {The Journal of animal ecology}, volume = {89}, number = {11}, pages = {2415-2426}, doi = {10.1111/1365-2656.13327}, pmid = {32858775}, issn = {1365-2656}, support = {BB/P001203/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Diet ; Fishes ; *Gastrointestinal Microbiome ; Symbiosis ; }, abstract = {It is increasingly recognized that symbiotic microbiota (especially those present in the gut) have important influences on the functioning of their host. Here, we review the interplay between this microbial community and the growth, metabolic rate and nutritional energy harvest of the host. We show how recent developments in experimental and analytical methods have allowed much easier characterization of the nature, and increasingly the functioning, of the gut microbiota. Manipulation studies that remove or augment gut microorganisms or transfer them between hosts have allowed unprecedented insights into their impact. Whilst much of the information to date has come from studies of laboratory model organisms, recent studies have used a more diverse range of host species, including those living in natural conditions, revealing their ecological relevance. The gut microbiota can provide the host with dietary nutrients that would be otherwise unobtainable, as well as allow the host flexibility in its capacity to cope with changing environments. The composition of the gut microbial community of a species can vary seasonally or when the host moves between environments (e.g. fresh and sea water in the case of migratory fish). It can also change with host diet choice, metabolic rate (or demands) and life stage. These changes in gut microbial community composition enable the host to live within different environments, adapt to seasonal changes in diet and maintain performance throughout its entire life history, highlighting the ecological relevance of the gut microbiota. Whilst it is evident that gut microbes can underpin host metabolic plasticity, the causal nature of associations between particular microorganisms and host performance is not always clear unless a manipulative approach has been used. Many studies have focussed on a correlative approach by characterizing microbial community composition, but there is now a need for more experimental studies in both wild and laboratory-based environments, to reveal the true role of gut microbiota in influencing the functioning of their hosts, including its capacity to tolerate environmental change. We highlight areas where these would be particularly fruitful in the context of ecological energetics.}, }
@article {pmid32858771, year = {2020}, author = {Kenkel, CD and Mocellin, VJL and Bay, LK}, title = {Global gene expression patterns in Porites white patch syndrome: Disentangling symbiont loss from the thermal stress response in reef-building coral.}, journal = {Molecular ecology}, volume = {29}, number = {20}, pages = {3907-3920}, doi = {10.1111/mec.15608}, pmid = {32858771}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Chlorophyll A ; Coral Reefs ; *Dinoflagellida/genetics ; Gene Expression ; Symbiosis/genetics ; }, abstract = {The mechanisms resulting in the breakdown of the coral symbiosis once the process of bleaching has been initiated remain unclear. Distinguishing the process of symbiont loss from the thermal stress response may shed light on the cellular and molecular pathways involved in each process. This study examined physiological changes and global gene expression patterns associated with white patch syndrome (WPS) in Porites lobata, which manifests in localized bleaching independent of thermal stress. In addition, a meta-analysis of global gene expression studies in other corals and anemones was used to contrast differential regulation as a result of disease and thermal stress from patterns correlated with symbiotic state. Symbiont density, chlorophyll a content, holobiont productivity, instant calcification rate, and total host protein content were uniformly reduced in WPS relative to healthy tissue. While expression patterns associated with WPS were secondary to fixed effects of source colony, specific functional enrichments combined with a lack of immune regulation suggest that the viral infection putatively giving rise to this condition affects symbiont rather than host cells. Expression in response to WPS also clustered independently of patterns in white syndrome impacted A. hyacinthus, further supporting a distinct aetiology of this syndrome. Expression patterns in WPS-affected tissues were significantly correlated with prior studies that examined short-term thermal stress responses independent of symbiotic state, suggesting that the majority of expression changes reflect a nonspecific stress response. Across studies, the magnitude and direction of expression change among particular functional enrichments suggests unique responses to stressor duration and highlights distinct responses to bleaching in an anemone model.}, }
@article {pmid32849407, year = {2020}, author = {Shiu, JH and Yu, SP and Fong, CL and Ding, JY and Tan, CJ and Fan, TY and Lu, CY and Tang, SL}, title = {Shifting in the Dominant Bacterial Group Endozoicomonas Is Independent of the Dissociation With Coral Symbiont Algae.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1791}, pmid = {32849407}, issn = {1664-302X}, abstract = {The coral-associated Endozoicomonas are dominant bacteria in the coral holobiont. Their relative abundance usually decreases with heat-induced coral bleaching and is proposed to be positively correlated with Symbiodiniaceae abundance. It remains unclear whether this phenomenon of decreased Endozoicomonas abundance is caused by temperature stress or a decreased abundance of Symbiodiniaceae. This study induced bleaching in the coral Euphyllia glabrescens using a dark treatment over 15 weeks. We examined shifts in Endozoicomonas abundance and experimentally reduced Symbiodiniaceae density. 16S rRNA gene amplicon sequencing was used to characterize the changes in bacterial community (incl. Endozoicomonas) over time, and the 16S rRNA gene copy number of Endozoicomonas was quantified by qPCR. We detected a high abundance of Endozoicomonas in E. glabrescens that underwent dark-induced bleaching. The results reveal that changes in the relative abundance of Endozoicomonas are unrelated to Symbiodiniaceae abundance, indicating that Endozoicomonas can be independent of Symbiodiniaceae in the coral holobiont.}, }
@article {pmid32831146, year = {2020}, author = {Wada, N and Yuasa, H and Kajitani, R and Gotoh, Y and Ogura, Y and Yoshimura, D and Toyoda, A and Tang, SL and Higashimura, Y and Sweatman, H and Forsman, Z and Bronstein, O and Eyal, G and Thongtham, N and Itoh, T and Hayashi, T and Yasuda, N}, title = {A ubiquitous subcuticular bacterial symbiont of a coral predator, the crown-of-thorns starfish, in the Indo-Pacific.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {123}, pmid = {32831146}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics/*isolation &amp; purification ; Coral Reefs ; Indian Ocean ; Male ; Pacific Ocean ; Phylogeny ; *Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Starfish/genetics/*microbiology/*physiology ; *Symbiosis ; }, abstract = {BACKGROUND: Population outbreaks of the crown-of-thorns starfish (Acanthaster planci sensu lato; COTS), a primary predator of reef-building corals in the Indo-Pacific Ocean, are a major threat to coral reefs. While biological and ecological knowledge of COTS has been accumulating since the 1960s, little is known about its associated bacteria. The aim of this study was to provide fundamental information on the dominant COTS-associated bacteria through a multifaceted molecular approach.<br><br>METHODS: A total of 205 COTS individuals from 17 locations throughout the Indo-Pacific Ocean were examined for the presence of COTS-associated bacteria. We conducted 16S rRNA metabarcoding of COTS to determine the bacterial profiles of different parts of the body and generated a full-length 16S rRNA gene sequence from a single dominant bacterium, which we designated COTS27. We performed phylogenetic analysis to determine the taxonomy, screening of COTS27 across the Indo-Pacific, FISH to visualize it within the COTS tissues, and reconstruction of the bacterial genome from the hologenome sequence data.<br><br>RESULTS: We discovered that a single bacterium exists at high densities in the subcuticular space in COTS forming a biofilm-like structure between the cuticle and the epidermis. COTS27 belongs to a clade that presumably represents a distinct order (so-called marine spirochetes) in the phylum Spirochaetes and is universally present in COTS throughout the Indo-Pacific Ocean. The reconstructed genome of COTS27 includes some genetic traits that are probably linked to adaptation to marine environments and evolution as an extracellular endosymbiont in subcuticular spaces.<br><br>CONCLUSIONS: COTS27 can be found in three allopatric COTS species, ranging from the northern Red Sea to the Pacific, implying that the symbiotic relationship arose before the speciation events (approximately 2 million years ago). The universal association of COTS27 with COTS and nearly mono-specific association at least with the Indo-Pacific COTS provides a useful model system for studying symbiont-host interactions in marine invertebrates and may have applications for coral reef conservation. Video Abstract.}, }
@article {pmid32827049, year = {2020}, author = {de Oliveira, BFR and Carr, CM and Dobson, ADW and Laport, MS}, title = {Harnessing the sponge microbiome for industrial biocatalysts.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {19}, pages = {8131-8154}, pmid = {32827049}, issn = {1432-0614}, support = {140840/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 304477/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.341847/2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; E-26/203.320/2017//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; SSPC-3, 12/RC/2275_2/SFI_/Science Foundation Ireland/Ireland ; SSPC-2, 12/RC/2275/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Bacteria/genetics ; Biotechnology ; Fungi ; *Microbiota ; Prospective Studies ; }, abstract = {Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.}, }
@article {pmid32811860, year = {2020}, author = {Zilius, M and Bonaglia, S and Broman, E and Chiozzini, VG and Samuiloviene, A and Nascimento, FJA and Cardini, U and Bartoli, M}, title = {N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {13966}, pmid = {32811860}, issn = {2045-2322}, mesh = {Animals ; Biofilms/growth &amp; development ; Brachyura/*metabolism/*microbiology ; Decapoda/metabolism/microbiology ; Ecosystem ; Microbiota/genetics ; Nitrogen/metabolism ; Nitrogen Cycle/genetics/physiology ; Nitrogen Fixation/*physiology ; RNA, Ribosomal, 16S/genetics ; Wetlands ; }, abstract = {Mangrove forests are among the most productive and diverse ecosystems on the planet, despite limited nitrogen (N) availability. Under such conditions, animal-microbe associations (holobionts) are often key to ecosystem functioning. Here, we investigated the role of fiddler crabs and their carapace-associated microbial biofilm as hotspots of microbial N transformations and sources of N within the mangrove ecosystem. 16S rRNA gene and metagenomic sequencing provided evidence of a microbial biofilm dominated by Cyanobacteria, Alphaproteobacteria, Actinobacteria, and Bacteroidota with a community encoding both aerobic and anaerobic pathways of the N cycle. Dinitrogen (N2) fixation was among the most commonly predicted process. Net N fluxes between the biofilm-covered crabs and the water and microbial N transformation rates in suspended biofilm slurries portray these holobionts as a net N2 sink, with N2 fixation exceeding N losses, and as a significant source of ammonium and dissolved organic N to the surrounding environment. N stable isotope natural abundances of fiddler crab carapace-associated biofilms were within the range expected for fixed N, further suggesting active microbial N2 fixation. These results extend our knowledge on the diversity of invertebrate-microbe associations, and provide a clear example of how animal microbiota can mediate a plethora of essential biogeochemical processes in mangrove ecosystems.}, }
@article {pmid32811423, year = {2020}, author = {Dunaj, SJ and Bettencourt, BR and Garb, JE and Brucker, RM}, title = {Spider phylosymbiosis: divergence of widow spider species and their tissues' microbiomes.}, journal = {BMC evolutionary biology}, volume = {20}, number = {1}, pages = {104}, pmid = {32811423}, issn = {1471-2148}, mesh = {Animals ; *Biological Evolution ; Female ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Spiders/*classification/*microbiology ; *Symbiosis ; }, abstract = {BACKGROUND: Microbiomes can have profound impacts on host biology and evolution, but to date, remain vastly understudied in spiders despite their unique and diverse predatory adaptations. This study evaluates closely related species of spiders and their host-microbe relationships in the context of phylosymbiosis, an eco-evolutionary pattern where the microbial community profile parallels the phylogeny of closely related host species. Using 16S rRNA gene amplicon sequencing, we characterized the microbiomes of five species with known phylogenetic relationships from the family Theridiidae, including multiple closely related widow spiders (L. hesperus, L. mactans, L. geometricus, S. grossa, and P. tepidariorum).<br><br>RESULTS: We compared whole animal and tissue-specific microbiomes (cephalothorax, fat bodies, venom glands, silk glands, and ovary) in the five species to better understand the relationship between spiders and their microbial symbionts. This showed a strong congruence of the microbiome beta-diversity of the whole spiders, cephalothorax, venom glands, and silk glands when compared to their host phylogeny. Our results support phylosymbiosis in these species and across their specialized tissues. The ovary tissue microbial dendrograms also parallel the widow phylogeny, suggesting vertical transfer of species-specific bacterial symbionts. By cross-validating with RNA sequencing data obtained from the venom glands, silk glands and ovaries of L. hesperus, L. geometricus, S. grossa, and P. tepidariorum we confirmed that several microbial symbionts of interest are viably active in the host.<br><br>CONCLUSION: Together these results provide evidence that supports the importance of host-microbe interactions and the significant role microbial communities may play in the evolution and adaptation of their hosts.}, }
@article {pmid32806647, year = {2020}, author = {Poquita-Du, RC and Goh, YL and Huang, D and Chou, LM and Todd, PA}, title = {Gene Expression and Photophysiological Changes in Pocillopora acuta Coral Holobiont Following Heat Stress and Recovery.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32806647}, issn = {2076-2607}, support = {MSRDP-P03//National Research Foundation Singapore/ ; MSRDP-P05//National Research Foundation Singapore/ ; }, abstract = {The ability of corals to withstand changes in their surroundings is a critical survival mechanism for coping with environmental stress. While many studies have examined responses of the coral holobiont to stressful conditions, its capacity to reverse responses and recover when the stressor is removed is not well-understood. In this study, we investigated among-colony responses of Pocillopora acuta from two sites with differing distance to the mainland (Kusu (closer to the mainland) and Raffles Lighthouse (further from the mainland)) to heat stress through differential expression analysis of target genes and quantification of photophysiological metrics. We then examined how these attributes were regulated after the stressor was removed to assess the recovery potential of P. acuta. The fragments that were subjected to heat stress (2 °C above ambient levels) generally exhibited significant reduction in their endosymbiont densities, but the extent of recovery following stress removal varied depending on natal site and colony. There were minimal changes in chl a concentration and maximum quantum yield (Fv/Fm, the proportion of variable fluorescence (Fv) to maximum fluorescence (Fm)) in heat-stressed corals, suggesting that the algal endosymbionts' Photosystem II was not severely compromised. Significant changes in gene expression levels of selected genes of interest (GOI) were observed following heat exposure and stress removal among sites and colonies, including Actin, calcium/calmodulin-dependent protein kinase type IV (Camk4), kinesin-like protein (KIF9), and small heat shock protein 16.1 (Hsp16.1). The most responsive GOIs were Actin, a major component of the cytoskeleton, and the adaptive immune-related Camk4 which both showed significant reduction following heat exposure and subsequent upregulation during the recovery phase. Our findings clearly demonstrate specific responses of P. acuta in both photophysiological attributes and gene expression levels, suggesting differential capacity of P. acuta corals to tolerate heat stress depending on the colony, so that certain colonies may be more resilient than others.}, }
@article {pmid32795355, year = {2020}, author = {Ronai, I and Greslehner, GP and Boem, F and Carlisle, J and Stencel, A and Suárez, J and Bayir, S and Bretting, W and Formosinho, J and Guerrero, AC and Morgan, WH and Prigot-Maurice, C and Rodeck, S and Vasse, M and Wallis, JM and Zacks, O}, title = {"Microbiota, symbiosis and individuality summer school" meeting report.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {117}, pmid = {32795355}, issn = {2049-2618}, mesh = {*Biomedical Research ; Europe ; Health ; Humans ; *Individuality ; *Interdisciplinary Studies ; *Microbiota ; *Schools ; Seasons ; *Symbiosis ; }, abstract = {How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.}, }
@article {pmid32794337, year = {2020}, author = {Berlanga-Clavero, MV and Molina-Santiago, C and de Vicente, A and Romero, D}, title = {More than words: the chemistry behind the interactions in the plant holobiont.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4532-4544}, doi = {10.1111/1462-2920.15197}, pmid = {32794337}, issn = {1462-2920}, support = {BacBio 637971//H2020 European Research Council/ ; PID2019-107724GB-I00//Ministerio de Ciencia e Innovación/ ; AGL2016-78662R//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; }, mesh = {Bacteria/*metabolism ; Germination/physiology ; Microbial Interactions/physiology ; Microbiota/physiology ; Plant Development/*physiology ; Plant Roots/microbiology ; Plants/metabolism/*microbiology ; Rhizosphere ; Seeds/growth &amp; development/microbiology ; Signal Transduction/physiology ; Symbiosis/*physiology ; Virulence Factors/metabolism ; }, abstract = {Plants and microbes have evolved sophisticated ways to communicate and coexist. The simplest interactions that occur in plant-associated habitats, i.e., those involved in disease detection, depend on the production of microbial pathogenic and virulence factors and the host's evolved immunological response. In contrast, microbes can also be beneficial for their host plants in a number of ways, including fighting pathogens and promoting plant growth. In order to clarify the mechanisms directly involved in these various plant-microbe interactions, we must still deepen our understanding of how these interkingdom communication systems, which are constantly modulated by resident microbial activity, are established and, most importantly, how their effects can span physically separated plant compartments. Efforts in this direction have revealed a complex and interconnected network of molecules and associated metabolic pathways that modulate plant-microbe and microbe-microbe communication pathways to regulate diverse ecological responses. Once sufficiently understood, these pathways will be biotechnologically exploitable, for example, in the use of beneficial microbes in sustainable agriculture. The aim of this review is to present the latest findings on the dazzlingly diverse arsenal of molecules that efficiently mediate specific microbe-microbe and microbe-plant communication pathways during plant development and on different plant organs.}, }
@article {pmid32788054, year = {2020}, author = {Triviño, V and Suárez, J}, title = {Holobionts: Ecological communities, hybrids, or biological individuals? A metaphysical perspective on multispecies systems.}, journal = {Studies in history and philosophy of biological and biomedical sciences}, volume = {84}, number = {}, pages = {101323}, doi = {10.1016/j.shpsc.2020.101323}, pmid = {32788054}, issn = {1879-2499}, mesh = {Animals ; Biological Evolution ; *Biota ; Invertebrates/*microbiology ; Metaphysics ; *Microbiota ; Plants/*microbiology ; *Symbiosis ; Vertebrates/*microbiology ; }, abstract = {Holobionts are symbiotic assemblages composed by a macrobe host (animal or plant) plus its symbiotic microbiota. In recent years, the ontological status of holobionts has created a great amount of controversy among philosophers and biologists: are holobionts biological individuals or are they rather ecological communities of independent individuals that interact together? Chiu and Eberl have recently developed an eco-immunity account of the holobiont wherein holobionts are neither biological individuals nor ecological communities, but hybrids between a host and its microbiota. According to their account, the microbiota is not a proper part of the holobiont. Yet, it should be regarded as a set of scaffolds that support the individuality of the host. In this paper, we approach Chiu and Eberl's account from a metaphysical perspective and argue that, contrary to what the authors claim, the eco-immunity account entails that the microorganisms that compose the host's microbiota are proper parts of the holobiont. Second, we argue that by claiming that holobionts are hybrids, and therefore, not biological individuals, the authors seem to be assuming a controversial position about the ontology of hybrids, which are conventionally characterized as a type of biological individual. In doing so, our paper aligns with the contemporary tendency to incorporate metaphysical resources to shed light on current biological debates and builds on that to provide additional support to the consideration of holobionts as biological individuals from an eco-immunity perspective.}, }
@article {pmid32772673, year = {2020}, author = {Fontaine, SS and Kohl, KD}, title = {Optimal integration between host physiology and functions of the gut microbiome.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190594}, pmid = {32772673}, issn = {1471-2970}, mesh = {Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Host Microbial Interactions/*physiology ; Invertebrates/microbiology/*physiology ; *Symbiosis ; Vertebrates/microbiology/*physiology ; }, abstract = {Host-associated microbial communities have profound impacts on animal physiological function, especially nutrition and metabolism. The hypothesis of 'symmorphosis', which posits that the physiological systems of animals are regulated precisely to meet, but not exceed, their imposed functional demands, has been used to understand the integration of physiological systems across levels of biological organization. Although this idea has been criticized, it is recognized as having important heuristic value, even as a null hypothesis, and may, therefore, be a useful tool in understanding how hosts evolve in response to the function of their microbiota. Here, through a hologenomic lens, we discuss how the idea of symmorphosis may be applied to host-microbe interactions. Specifically, we consider scenarios in which host physiology may have evolved to collaborate with the microbiota to perform important functions, and, on the other hand, situations in which services have been completely outsourced to the microbiota, resulting in relaxed selection on host pathways. Following this theoretical discussion, we finally suggest strategies by which these currently speculative ideas may be explicitly tested to further our understanding of host evolution in response to their associated microbial communities. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772672, year = {2020}, author = {van Oppen, MJH and Medina, M}, title = {Coral evolutionary responses to microbial symbioses.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190591}, pmid = {32772672}, issn = {1471-2970}, mesh = {Animals ; Anthozoa/metabolism/*microbiology ; *Biological Evolution ; Dinoflagellida/*physiology ; Global Warming ; *Microbiota ; *Symbiosis ; }, abstract = {This review explores how microbial symbioses may have influenced and continue to influence the evolution of reef-building corals (Cnidaria; Scleractinia). The coral holobiont comprises a diverse microbiome including dinoflagellate algae (Dinophyceae; Symbiodiniaceae), bacteria, archaea, fungi and viruses, but here we focus on the Symbiodiniaceae as knowledge of the impact of other microbial symbionts on coral evolution is scant. Symbiosis with Symbiodiniaceae has extended the coral's metabolic capacity through metabolic handoffs and horizontal gene transfer (HGT) and has contributed to the ecological success of these iconic organisms. It necessitated the prior existence or the evolution of a series of adaptations of the host to attract and select the right symbionts, to provide them with a suitable environment and to remove disfunctional symbionts. Signatures of microbial symbiosis in the coral genome include HGT from Symbiodiniaceae and bacteria, gene family expansions, and a broad repertoire of oxidative stress response and innate immunity genes. Symbiosis with Symbiodiniaceae has permitted corals to occupy oligotrophic waters as the algae provide most corals with the majority of their nutrition. However, the coral-Symbiodiniaceae symbiosis is sensitive to climate warming, which disrupts this intimate relationship, causing coral bleaching, mortality and a worldwide decline of coral reefs. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772670, year = {2020}, author = {Moeller, AH and Sanders, JG}, title = {Roles of the gut microbiota in the adaptive evolution of mammalian species.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190597}, pmid = {32772670}, issn = {1471-2970}, mesh = {*Adaptation, Biological ; Animals ; *Biological Evolution ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Mammals/*microbiology ; }, abstract = {Every mammalian species harbours a gut microbiota, and variation in the gut microbiota within mammalian species can have profound effects on host phenotypes. In this review, we summarize recent evidence that gut microbiotas have influenced the course of mammalian adaptation and diversification. Associations with gut microbiotas have: (i) promoted the diversification of mammalian species by enabling dietary transitions onto difficult-to-digest carbon sources and toxic food items; (ii) shaped the evolution of adaptive phenotypic plasticity in mammalian species through the amplification of signals from the external environment and from postnatal developmental processes; and (iii) generated selection for host mechanisms, including innate and adaptive immune mechanisms, to control the gut microbiota for the benefit of host fitness. The stability of specific gut microbiotas within host species lineages varies substantially across the mammalian phylogeny, and this variation may alter the ultimate evolutionary outcomes of relationships with gut microbiotas in different mammalian clades. In some mammalian species, including humans, relationships with host species-specific gut microbiotas appear to have led to the evolution of host dependence on the gut microbiota for certain functions. These studies implicate the gut microbiota as a significant environmental factor and selective agent shaping the adaptive evolution of mammalian diet, phenotypic plasticity, gastrointestinal morphology and immunity. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772660, year = {2020}, author = {Koskella, B and Bergelson, J}, title = {The study of host-microbiome (co)evolution across levels of selection.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {375}, number = {1808}, pages = {20190604}, pmid = {32772660}, issn = {1471-2970}, mesh = {*Biological Coevolution ; *Host Microbial Interactions ; *Microbiota ; *Selection, Genetic ; }, abstract = {Microorganismal diversity can be explained in large part by selection imposed from both the abiotic and biotic environments, including-in the case of host-associated microbiomes-interactions with eukaryotes. As such, the diversity of host-associated microbiomes can be usefully studied across a variety of scales: within a single host over time, among host genotypes within a population, between populations and among host species. A plethora of recent studies across these scales and across diverse systems are: (i) exemplifying the importance of the host genetics in shaping microbiome composition; (ii) uncovering the role of the microbiome in shaping key host phenotypes; and (iii) highlighting the dynamic nature of the microbiome. They have also raised a critical question: do these complex associations fit within our existing understanding of evolution and coevolution, or do these often intimate and seemingly cross-generational interactions follow novel evolutionary rules from those previously identified? Herein, we describe the known importance of (co)evolution in host-microbiome systems, placing the existing data within extant frameworks that have been developed over decades of study, and ask whether there are unique properties of host-microbiome systems that require a paradigm shift. By examining when and how selection can act on the host and its microbiome as a unit (termed, the holobiont), we find that the existing conceptual framework, which focuses on individuals, as well as interactions among individuals and groups, is generally well suited for understanding (co)evolutionary change in these intimate assemblages. This article is part of the theme issue 'The role of the microbiome in host evolution'.}, }
@article {pmid32772380, year = {2021}, author = {Ravanbakhsh, M and Kowalchuk, GA and Jousset, A}, title = {Targeted plant hologenome editing for plant trait enhancement.}, journal = {The New phytologist}, volume = {229}, number = {2}, pages = {1067-1077}, doi = {10.1111/nph.16867}, pmid = {32772380}, issn = {1469-8137}, mesh = {*Arabidopsis/genetics ; Ethylenes ; Genes, Plant ; Phenotype ; Plant Breeding ; }, abstract = {Breeding better crops is a cornerstone of global food security. While efforts in plant genetic improvement show promise, it is increasingly becoming apparent that the plant phenotype should be treated as a function of the holobiont, in which plant and microbial traits are deeply intertwined. Using a minimal holobiont model, we track ethylene production and plant nutritional value in response to alterations in plant ethylene synthesis (KO mutation in ETO1), which induces 1-aminocyclopropane-1-carboxylic acid (ACC) synthase 5 (ACS5), or microbial degradation of ACC (KO mutation in microbial acdS), preventing the breakdown of the plant ACC pool, the product of ACS5. We demonstrate that similar plant phenotypes can be generated by either specific mutations of plant-associated microbes or alterations in the plant genome. Specifically, we could equally increase plant nutritional value by either altering the plant ethylene synthesis gene ETO1, or the microbial gene acdS. Both mutations yielded a similar plant phenotype with increased ethylene production and higher shoot micronutrient concentrations. Restoring bacterial AcdS enzyme activity also rescued the plant wild-t8yp phenotype in an eto1 background. Plant and bacterial genes build an integrated plant-microbe regulatory network amenable to genetic improvement from both the plant and microbial sides.}, }
@article {pmid32767091, year = {2021}, author = {Vargas, S and Leiva, L and Wörheide, G}, title = {Short-Term Exposure to High-Temperature Water Causes a Shift in the Microbiome of the Common Aquarium Sponge Lendenfeldia chondrodes.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {213-222}, pmid = {32767091}, issn = {1432-184X}, mesh = {Animals ; Bacteroidetes/*classification/genetics/isolation &amp; purification ; Biodiversity ; Climate ; Climate Change ; Cyanobacteria/*classification/genetics/isolation &amp; purification ; Hot Temperature ; Microbiota/*genetics ; Planctomycetales/*classification/genetics/isolation &amp; purification ; Porifera/*microbiology ; Proteobacteria/*classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Thermotolerance/genetics ; }, abstract = {Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of cultured Lendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria. Lendenfeldia chondrodes exhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome of L. chondrodes to short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience of L. chondrodes and the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.}, }
@article {pmid32765431, year = {2020}, author = {Friel, AD and Neiswenter, SA and Seymour, CO and Bali, LR and McNamara, G and Leija, F and Jewell, J and Hedlund, BP}, title = {Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs (Limulus polyphemus) Into a Touch-Tank Exhibit.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1398}, pmid = {32765431}, issn = {1664-302X}, abstract = {The Atlantic horseshoe crab (Limulus polyphemus) is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adult L. polyphemus in a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. The wild population hosted diverse and distinct microbiomes on the carapace (260 ± 96 amplicon sequence variants or ASVs), cloaca (345 ± 77 ASVs), gills (309 ± 36 ASVs), and oral cavity (359 ± 37 ASVs), which were dominated by classes Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria. A rapid decline in richness across all body locations was observed within 1 month of captivity, with tank-acclimated (>2 years) animals having <5% of the initial microbiome richness and a nearly completely restructured microbial community. Tank-acclimated horseshoe crabs possessed distinct microbiomes that were highly uneven and low in species richness on the carapace (31 ± 7 ASVs), cloaca (53 ± 19 ASVs), gills (17 ± 2 ASVs), and oral cavity (31 ± 13 ASVs). The carapace, oral cavity, and gills of the tank-acclimated animals hosted abundant populations of Aeromonas (>60%) and Pseudomonas (>20%), both of which are known opportunistic pathogens of aquatic animals and can express chitinases, providing a plausible mechanism for the development of the carapace lesion pathology observed in this and other studies. The cloaca of the tank-acclimated animals was slightly more diverse than the other body locations with Aeromonas, Enterococcus, Shewanella, and Vagococcus dominating the community. These results provide an important baseline on the microbiomes of both wild and tank-acclimated horseshoe crabs and underscore the need to continue to investigate how native microbial populations may protect animals from pathogens.}, }
@article {pmid32762039, year = {2021}, author = {Lousada, MB and Lachnit, T and Edelkamp, J and Rouillé, T and Ajdic, D and Uchida, Y and Di Nardo, A and Bosch, TCG and Paus, R}, title = {Exploring the human hair follicle microbiome.}, journal = {The British journal of dermatology}, volume = {184}, number = {5}, pages = {802-815}, doi = {10.1111/bjd.19461}, pmid = {32762039}, issn = {1365-2133}, support = {//University of Miami/ ; //DFG CRC 1182 (TPC4.2)/ ; //Canadian Institute for Advanced Research (CIFAR)/ ; //DFG CRC 1182/ ; }, mesh = {*Alopecia Areata ; *Folliculitis ; Hair Follicle ; *Hidradenitis Suppurativa ; Humans ; *Microbiota ; }, abstract = {Human hair follicles (HFs) carry complex microbial communities that differ from the skin surface microbiota. This likely reflects that the HF epithelium differs from the epidermal barrier in that it provides a moist, less acidic, and relatively ultraviolet light-protected environment, part of which is immune-privileged, thus facilitating microbial survival. Here we review the current understanding of the human HF microbiome and its potential physiological and pathological functions, including in folliculitis, acne vulgaris, hidradenitis suppurativa, alopecia areata and cicatricial alopecias. While reviewing the main human HF bacteria (such as Propionibacteria, Corynebacteria, Staphylococci and Streptococci), viruses, fungi and parasites as human HF microbiome constituents, we advocate a broad view of the HF as an integral part of the human holobiont. Specifically, we explore how the human HF may manage its microbiome via the regulated production of antimicrobial peptides (such as cathelicidin, psoriasin, RNAse7 and dermcidin) by HF keratinocytes, how the microbiome may impact on cytokine and chemokine release from the HF, and examine hair growth-modulatory effects of antibiotics, and ask whether the microbiome affects hair growth in turn. We highlight major open questions and potential novel approaches to the management of hair diseases by targeting the HF microbiome.}, }
@article {pmid32743860, year = {2020}, author = {Duarte, CM and Ngugi, DK and Alam, I and Pearman, J and Kamau, A and Eguiluz, VM and Gojobori, T and Acinas, SG and Gasol, JM and Bajic, V and Irigoien, X}, title = {Sequencing effort dictates gene discovery in marine microbial metagenomes.}, journal = {Environmental microbiology}, volume = {22}, number = {11}, pages = {4589-4603}, pmid = {32743860}, issn = {1462-2920}, support = {//King Abdullah University of Science and Technology/ ; BB123456/NH/NIH HHS/United States ; AA123456/NH/NIH HHS/United States ; CSD2008-00077//Spanish Ministry of Science and Innovation/ ; }, mesh = {Alphaproteobacteria/genetics ; Aquatic Organisms/*genetics/microbiology ; Diatoms/genetics ; Flavobacteriaceae/genetics ; Gammaproteobacteria/genetics ; Genetic Association Studies ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing ; Indian Ocean ; Metagenome/*genetics ; Metagenomics/methods ; Plankton/*genetics/microbiology ; Water Microbiology ; }, abstract = {Massive metagenomic sequencing combined with gene prediction methods were previously used to compile the gene catalogue of the ocean and host-associated microbes. Global expeditions conducted over the past 15 years have sampled the ocean to build a catalogue of genes from pelagic microbes. Here we undertook a large sequencing effort of a perturbed Red Sea plankton community to uncover that the rate of gene discovery increases continuously with sequencing effort, with no indication that the retrieved 2.83 million non-redundant (complete) genes predicted from the experiment represented a nearly complete inventory of the genes present in the sampled community (i.e., no evidence of saturation). The underlying reason is the Pareto-like distribution of the abundance of genes in the plankton community, resulting in a very long tail of millions of genes present at remarkably low abundances, which can only be retrieved through massive sequencing. Microbial metagenomic projects retrieve a variable number of unique genes per Tera base-pair (Tbp), with a median value of 14.7 million unique genes per Tbp sequenced across projects. The increase in the rate of gene discovery in microbial metagenomes with sequencing effort implies that there is ample room for new gene discovery in further ocean and holobiont sequencing studies.}, }
@article {pmid32738355, year = {2020}, author = {Miller, WB and Baluška, F and Torday, JS}, title = {Cellular senomic measurements in Cognition-Based Evolution.}, journal = {Progress in biophysics and molecular biology}, volume = {156}, number = {}, pages = {20-33}, doi = {10.1016/j.pbiomolbio.2020.07.002}, pmid = {32738355}, issn = {1873-1732}, mesh = {Animals ; *Biological Evolution ; Biology/trends ; Cell Communication ; *Cognition ; Homeostasis ; Humans ; Models, Biological ; Thermodynamics ; }, abstract = {All living entities are cognitive and dependent on ambiguous information. Any assessment of that imprecision is necessarily a measuring function. Individual cells measure information to sustain self-referential homeostatic equipoise (self-identity) in juxtaposition to the external environment. The validity of that information is improved by its collective assessment. The reception of cellular information obliges thermodynamic reactions that initiate a self-reinforcing work channel. This expresses as natural cellular engineering and niche constructions which become the complex interrelated tissue ecologies of holobionts. Multicellularity is collaborative cellular information management directed towards the optimization of information quality through its collective measured assessment. Biology and its evolution can now be re-framed as the continuous process of self-referential cellular measurement in the perpetual defense of individual cellular self-identities through the collective form.}, }
@article {pmid32731457, year = {2020}, author = {Lifshitz, N and Hazanov, L and Fine, M and Yarden, O}, title = {Seasonal Variations in the Culturable Mycobiome of Acropora loripes along a Depth Gradient.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32731457}, issn = {2076-2607}, support = {888/19//Israel Science Foundation/ ; }, abstract = {Coral associated fungi are widespread, highly diverse and are part and parcel of the coral holobiont. To study how environmental conditions prevailing near the coral-host may affect fungal diversity, the culturable (isolated on potato dextrose agar) mycobiome associated with Acropora loripes colonies was seasonally sampled along a depth gradient in the Gulf of Aqaba. Fragments were sampled from both apparently healthy coral colonies as well as those exhibiting observable lesions. Based on phylogenetic analysis of 197 fungal sequences, Ascomycota were the most prevalent (91.9%). The abundance of fungi increased with increasing water depth, where corals sampled at 25 m yielded up to 70% more fungal colony forming units (CFUs) than those isolated at 6 m. Fungal diversity at 25 m was also markedly higher, with over 2-fold more fungal families represented. Diversity was also higher in lesioned coral samples, when compared to apparently healthy colonies. In winter, concurrent with water column mixing and increased levels of available nutrients, at the shallow depths, Saccharomytacea and Sporidiobolacea were more prevalent, while in spring and fall Trichocomacea (overall, the most prevalent family isolated throughout this study) were the most abundant taxa isolated at these depths as well as at deeper sampling sites. Our results highlight the dynamic nature of the culturable coral mycobiome and its sensitivity to environmental conditions and coral health.}, }
@article {pmid32727134, year = {2020}, author = {Biagi, E and Mengucci, C and Barone, M and Picone, G and Lucchi, A and Celi, P and Litta, G and Candela, M and Manfreda, G and Brigidi, P and Capozzi, F and De Cesare, A}, title = {Effects of Vitamin B2 Supplementation in Broilers Microbiota and Metabolome.}, journal = {Microorganisms}, volume = {8}, number = {8}, pages = {}, pmid = {32727134}, issn = {2076-2607}, support = {77/2018//Università di Bologna/ ; }, abstract = {The study of the microbiome in broiler chickens holds great promise for the development of strategies for health maintenance and performance improvement. Nutritional strategies aimed at modulating the microbiota-host relationship can improve chickens' immunological status and metabolic fitness. Here, we present the results of a pilot trial aimed at analyzing the effects of a nutritional strategy involving vitamin B2 supplementation on the ileum, caeca and litter microbiota of Ross 308 broilers, as well as on the metabolic profile of the caecal content. Three groups of chickens were administered control diets and diets supplemented with two different dosages of vitamin B2. Ileum, caeca, and litter samples were obtained from subgroups of birds at three time points along the productive cycle. Sequencing of the 16S rRNA V3-V4 region and NMR metabolomics were used to explore microbiota composition and the concentration of metabolites of interest, including short-chain fatty acids. Vitamin B2 supplementation significantly modulated caeca microbiota, with the highest dosage being more effective in increasing the abundance of health-promoting bacterial groups, including Bifidobacterium, resulting in boosted production of butyrate, a well-known health-promoting metabolite, in the caeca environment.}, }
@article {pmid32710518, year = {2020}, author = {Allgeier, JE and Andskog, MA and Hensel, E and Appaldo, R and Layman, C and Kemp, DW}, title = {Rewiring coral: Anthropogenic nutrients shift diverse coral-symbiont nutrient and carbon interactions toward symbiotic algal dominance.}, journal = {Global change biology}, volume = {26}, number = {10}, pages = {5588-5601}, doi = {10.1111/gcb.15230}, pmid = {32710518}, issn = {1365-2486}, support = {OCE #0746164//National Science Foundation/ ; OCE #2023507//National Science Foundation/ ; OCE #1948622//National Science Foundation/ ; //University of Alabama at Birmingham/ ; }, mesh = {Animals ; *Anthozoa ; Carbon ; Coral Reefs ; Nutrients ; Symbiosis ; }, abstract = {Improving coral reef conservation requires heightened understanding of the mechanisms by which coral cope with changing environmental conditions to maintain optimal health. We used a long-term (10 month) in situ experiment with two phylogenetically diverse scleractinians (Acropora palmata and Porites porites) to test how coral-symbiotic algal interactions changed under real-world conditions that were a priori expected to be beneficial (fish-mediated nutrients) and to be harmful, but non-lethal, for coral (fish + anthropogenic nutrients). Analyzing nine response variables of nutrient stoichiometry and stable isotopes per coral fragment, we found that nutrients from fish positively affected coral growth, and moderate doses of anthropogenic nutrients had no additional effects. While growing, coral maintained homeostasis in their nutrient pools, showing tolerance to the different nutrient regimes. Nonetheless, structural equation models revealed more nuanced relationships, showing that anthropogenic nutrients reduced the diversity of coral-symbiotic algal interactions and caused nutrient and carbon flow to be dominated by the symbiont. Our findings show that nutrient and carbon pathways are fundamentally "rewired" under anthropogenic nutrient regimes in ways that could increase corals' susceptibility to further stressors. We hypothesize that our experiment captured coral in a previously unrecognized transition state between mutualism and antagonism. These findings highlight a notable parallel between how anthropogenic nutrients promote symbiont dominance with the holobiont, and how they promote macroalgal dominance at the coral reef scale. Our findings suggest more realistic experimental conditions, including studies across gradients of anthropogenic nutrient enrichment as well as the incorporation of varied nutrient and energy pathways, may facilitate conservation efforts to mitigate coral loss.}, }
@article {pmid32686736, year = {2020}, author = {Fernandes de Barros Marangoni, L and Ferrier-Pagès, C and Rottier, C and Bianchini, A and Grover, R}, title = {Unravelling the different causes of nitrate and ammonium effects on coral bleaching.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {11975}, pmid = {32686736}, issn = {2045-2322}, mesh = {Ammonium Compounds/*pharmacology ; Analysis of Variance ; Animals ; Anthozoa/drug effects/*physiology ; Antioxidants/metabolism ; Calcification, Physiologic/drug effects ; Chlorophyll/metabolism ; Energy Metabolism/drug effects ; Lactic Acid/metabolism ; Lipid Peroxidation/drug effects ; Models, Biological ; Nitrates/*pharmacology ; Nitric Oxide/biosynthesis ; Nitrosation ; Oxidative Stress/drug effects ; Photosynthesis/drug effects ; Reactive Oxygen Species/metabolism ; Symbiosis/drug effects ; Tyrosine/metabolism ; }, abstract = {Mass coral bleaching represents one of the greatest threats to coral reefs and has mainly been attributed to seawater warming. However, reduced water quality can also interact with warming to increase coral bleaching, but this interaction depends on nutrient ratios and forms. In particular, nitrate (NO3-) enrichment reduces thermal tolerance while ammonium (NH4+) enrichment tends to benefit coral health. The biochemical mechanisms underpinning the different bleaching responses of corals exposed to DIN enrichment still need to be investigated. Here, we demonstrated that the coral Stylophora pistillata underwent a severe oxidative stress condition and reduced aerobic scope when exposed to NO3- enrichment combined with thermal stress. Such condition resulted in increased bleaching intensity compared to a low-nitrogen condition. On the contrary, NH4+ enrichment was able to amend the deleterious effects of thermal stress by favoring the oxidative status and energy metabolism of the coral holobiont. Overall, our results demonstrate that the opposite effects of nitrate and ammonium enrichment on coral bleaching are related to the effects on corals' energy/redox status. As nitrate loading in coastal waters is predicted to significantly increase in the future due to agriculture and land-based pollution, there is the need for urgent management actions to prevent increases in nitrate levels in seawater. In addition, the maintenance of important fish stocks, which provide corals with recycled nitrogen such as ammonium, should be favoured.}, }
@article {pmid32686311, year = {2021}, author = {Li, J and Long, L and Zou, Y and Zhang, S}, title = {Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont.}, journal = {Environmental microbiology}, volume = {23}, number = {2}, pages = {826-843}, pmid = {32686311}, issn = {1462-2920}, support = {2017A030306025//Guangdong Natural Science Funds for Distinguished Young Scholars/ ; 2017YFC0506303//National Key R&amp;D Program of China/ ; 41676155//National Natural Science Foundation of China/ ; 41890853//National Natural Science Foundation of China/ ; 2017396//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; Anthozoa/*genetics/growth &amp; development/*microbiology ; Bacteria/classification/*genetics/isolation &amp; purification ; Coral Reefs ; Dinoflagellida/genetics/physiology ; Hot Temperature ; *Microbiota ; Seawater/*chemistry/microbiology/parasitology ; Symbiosis ; Temperature ; Transcription, Genetic ; }, abstract = {A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease-associated bacteria increased at 32°C, which may affect immune responses in heat-stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non-selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.}, }
@article {pmid32684958, year = {2020}, author = {Angers, B and Perez, M and Menicucci, T and Leung, C}, title = {Sources of epigenetic variation and their applications in natural populations.}, journal = {Evolutionary applications}, volume = {13}, number = {6}, pages = {1262-1278}, pmid = {32684958}, issn = {1752-4571}, abstract = {Epigenetic processes manage gene expression and products in a real-time manner, allowing a single genome to display different phenotypes. In this paper, we discussed the relevance of assessing the different sources of epigenetic variation in natural populations. For a given genotype, the epigenetic variation could be environmentally induced or occur randomly. Strategies developed by organisms to face environmental fluctuations such as phenotypic plasticity and diversified bet-hedging rely, respectively, on these different sources. Random variation can also represent a proxy of developmental stability and can be used to assess how organisms deal with stressful environmental conditions. We then proposed the microbiome as an extension of the epigenotype of the host to assess the factors determining the establishment of the community of microorganisms. Finally, we discussed these perspectives in the applied context of conservation.}, }
@article {pmid32681284, year = {2021}, author = {Varasteh, T and Hamerski, L and Tschoeke, D and Lima, AS and Garcia, G and Cosenza, CAN and Thompson, C and Thompson, F}, title = {Conserved Pigment Profiles in Phylogenetically Diverse Symbiotic Bacteria Associated with the Corals Montastraea cavernosa and Mussismilia braziliensis.}, journal = {Microbial ecology}, volume = {81}, number = {1}, pages = {267-277}, pmid = {32681284}, issn = {1432-184X}, mesh = {Animals ; Anthozoa/*microbiology ; Antioxidants/*metabolism ; Bacteroidetes/genetics/isolation &amp; purification/*metabolism ; Brazil ; Carotenoids/metabolism ; Catalase/biosynthesis ; DNA, Bacterial/genetics ; Genome, Bacterial/genetics ; Oxidoreductases/biosynthesis ; Paracoccus/genetics/isolation &amp; purification/*metabolism ; Peroxidase/biosynthesis ; Pigments, Biological/genetics/*metabolism ; Pseudoalteromonas/genetics/isolation &amp; purification/*metabolism ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Symbiosis ; }, abstract = {Pigmented bacterial symbionts play major roles in the health of coral holobionts. However, there is scarce knowledge on the diversity of these microbes for several coral species. To gain further insights into holobiont health, pigmented bacterial isolates of Fabibacter pacificus (Bacteroidetes; n = 4), Paracoccus marcusii (Alphaproteobacteria; n = 1), and Pseudoalteromonas shioyasakiensis (Gammaproteobacteria; n = 1) were obtained from the corals Mussismilia braziliensis and Montastraea cavernosa in Abrolhos Bank, Brazil. Cultures of these bacterial symbionts produced strong antioxidant activity (catalase, peroxidase, and oxidase). To explore these bacterial isolates further, we identified their major pigments by HPLC and mass spectrometry. The six phylogenetically diverse symbionts had similar pigment patterns and produced myxol and keto-carotene. In addition, similar carotenoid gene clusters were confirmed in the whole genome sequences of these symbionts, which reinforce their antioxidant potential. This study highlights the possible roles of bacterial symbionts in Montastraea and Mussismilia holobionts.}, }
@article {pmid32676070, year = {2020}, author = {Mensch, B and Neulinger, SC and Künzel, S and Wahl, M and Schmitz, RA}, title = {Warming, but Not Acidification, Restructures Epibacterial Communities of the Baltic Macroalga Fucus vesiculosus With Seasonal Variability.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1471}, pmid = {32676070}, issn = {1664-302X}, abstract = {Due to ocean acidification and global warming, surface seawater of the western Baltic Sea is expected to reach an average of ∼1100 μatm pCO2 and an increase of ∼5°C by the year 2100. In four consecutive experiments (spanning 10-11 weeks each) in all seasons within 1 year, the abiotic factors temperature (+5°C above in situ) and pCO2 (adjusted to ∼1100 μatm) were tested for their single and combined effects on epibacterial communities of the brown macroalga Fucus vesiculosus and on bacteria present in the surrounding seawater. The experiments were set up in three biological replicates using the Kiel Outdoor Benthocosm facility (Kiel, Germany). Phylogenetic analyses of the respective microbiota were performed by bacterial 16S (V1-V2) rDNA Illumina MiSeq amplicon sequencing after 0, 4, 8, and 10/11 weeks per season. The results demonstrate (I) that the bacterial community composition varied in time and (II) that relationships between operational taxonomic units (OTUs) within an OTU association network were mainly governed by the habitat. (III) Neither single pCO2 nor pCO2:Temperature interaction effects were statistically significant. However, significant impact of ocean warming was detected varying among seasons. (IV) An indicator OTU (iOTU) analysis identified several iOTUs that were strongly influenced by temperature in spring, summer, and winter. In the warming treatments of these three seasons, we observed decreasing numbers of bacteria that are commonly associated with a healthy marine microbial community and-particularly during spring and summer-an increase in potentially pathogenic and bacteria related to intensified microfouling. This might lead to severe consequences for the F. vesiculosus holobiont finally affecting the marine ecosystem.}, }
@article {pmid32669465, year = {2020}, author = {Yergaliyev, TM and Alexander-Shani, R and Dimerets, H and Pivonia, S and Bird, DM and Rachmilevitch, S and Szitenberg, A}, title = {Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions.}, journal = {mSphere}, volume = {5}, number = {4}, pages = {}, pmid = {32669465}, issn = {2379-5042}, mesh = {Animals ; Bacteria/*classification/metabolism ; DNA Barcoding, Taxonomic ; Genetic Variation ; *Host Microbial Interactions ; *Microbiota ; Phylogeny ; Plant Roots/*microbiology/*parasitology ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil ; Soil Microbiology ; Tylenchoidea/*microbiology/physiology ; }, abstract = {Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode's chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles.IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode's life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.}, }
@article {pmid32664706, year = {2020}, author = {Malassigné, S and Valiente Moro, C and Luis, P}, title = {Mosquito Mycobiota: An Overview of Non-Entomopathogenic Fungal Interactions.}, journal = {Pathogens (Basel, Switzerland)}, volume = {9}, number = {7}, pages = {}, pmid = {32664706}, issn = {2076-0817}, support = {(IDEX Lyon - Université de Lyon)//Scientific Breakthrough Program Micro-be-have/ ; }, abstract = {The growing expansion of mosquito vectors leads to the emergence of vector-borne diseases in new geographic areas and causes major public health concerns. In the absence of effective preventive treatments against most pathogens transmitted, vector control remains one of the most suitable strategies to prevent mosquito-borne diseases. Insecticide overuse raises mosquito resistance and deleterious impacts on the environment and non-target species. Growing knowledge of mosquito biology has allowed the development of alternative control methods. Following the concept of holobiont, mosquito-microbiota interactions play an important role in mosquito biology. Associated microbiota is known to influence many aspects of mosquito biology such as development, survival, immunity or even vector competence. Mosquito-associated microbiota is composed of bacteria, fungi, protists, viruses and nematodes. While an increasing number of studies have focused on bacteria, other microbial partners like fungi have been largely neglected despite their huge diversity. A better knowledge of mosquito-mycobiota interactions offers new opportunities to develop innovative mosquito control strategies. Here, we review the recent advances concerning the impact of mosquito-associated fungi, and particularly nonpathogenic fungi, on life-history traits (development, survival, reproduction), vector competence and behavior of mosquitoes by focusing on Culex, Aedes and Anopheles species.}, }
@article {pmid32662980, year = {2020}, author = {Mohanty, I and Moore, SG and Yi, D and Biggs, JS and Gaul, DA and Garg, N and Agarwal, V}, title = {Precursor-Guided Mining of Marine Sponge Metabolomes Lends Insight into Biosynthesis of Pyrrole-Imidazole Alkaloids.}, journal = {ACS chemical biology}, volume = {15}, number = {8}, pages = {2185-2194}, pmid = {32662980}, issn = {1554-8937}, support = {K99 ES026620/ES/NIEHS NIH HHS/United States ; R00 ES026620/ES/NIEHS NIH HHS/United States ; }, mesh = {Alkaloids/*biosynthesis/*chemistry ; Animals ; Imidazoles/*chemistry ; *Metabolome ; Microbiota ; Phylogeny ; Porifera/*metabolism ; Pyrroles/*chemistry ; }, abstract = {Pyrrole-imidazole alkaloids are natural products isolated from marine sponges, holobiont metazoans that are associated with symbiotic microbiomes. Pyrrole-imidazole alkaloids have attracted attention due to their chemical complexity and their favorable pharmacological properties. However, insights into how these molecules are biosynthesized within the sponge holobionts are scarce. Here, we provide a multiomic profiling of the microbiome and metabolomic architectures of three sponge genera that are prolific producers of pyrrole-imidazole alkaloids. Using a retrobiosynthetic scheme as a guide, we mine the metabolomes of these sponges to detect intermediates in pyrrole-imidazole alkaloid biosynthesis. Our findings reveal that the nonproteinogenic amino acid homoarginine is a critical branch point that connects primary metabolite lysine to the production of pyrrole-imidazole alkaloids. These insights are derived from the polar metabolomes of these sponges which additionally reveal the presence of zwitterionic betaines that may serve important ecological roles in marine habitats. We also establish that metabolomic richness does not correlate with microbial diversity of the sponge holobiont for neither the polar nor the nonpolar metabolomes. Our findings now provide the biochemical foundation for genomic interrogation of the sponge holobiont to establish biogenetic routes for pyrrole-imidazole alkaloid production.}, }
@article {pmid32645351, year = {2020}, author = {Groussin, M and Mazel, F and Alm, EJ}, title = {Co-evolution and Co-speciation of Host-Gut Bacteria Systems.}, journal = {Cell host &amp; microbe}, volume = {28}, number = {1}, pages = {12-22}, doi = {10.1016/j.chom.2020.06.013}, pmid = {32645351}, issn = {1934-6069}, mesh = {Animals ; Bacteria/genetics/immunology ; *Biological Coevolution ; *Gastrointestinal Microbiome ; *Genetic Speciation ; Host Microbial Interactions ; Humans ; Mammals/genetics/immunology/microbiology ; Phylogeny ; *Symbiosis ; }, abstract = {Mammalian gut microbiomes profoundly influence host fitness, but the processes that drive the evolution of host-microbiome systems are poorly understood. Recent studies suggest that mammals and their individual gut symbionts can have parallel evolutionary histories, as represented by their congruent phylogenies. These "co-phylogenetic" patterns are signatures of ancient co-speciation events and illustrate the cohesiveness of the mammalian host-gut microbiome entity over evolutionary times. Theory predicts that co-speciation between mammals and their gut symbionts could result from their co-evolution. However, there is only limited evidence of such co-evolution. Here, we propose a model that explains cophylogenetic patterns without relying on co-evolution. Specifically, we suggest that individual gut bacteria are likely to diverge in patterns recapitulating host phylogeny when hosts undergo allopatric speciation, limiting inter-host bacterial dispersal and genomic recombination. We provide evidence that the model is empirically grounded and propose a series of observational and experimental approaches to test its validity.}, }
@article {pmid32635154, year = {2020}, author = {Bertazzon, N and Chitarra, W and Angelini, E and Nerva, L}, title = {Two New Putative Plant Viruses from Wood Metagenomics Analysis of an Esca Diseased Vineyard.}, journal = {Plants (Basel, Switzerland)}, volume = {9}, number = {7}, pages = {}, pmid = {32635154}, issn = {2223-7747}, support = {VITE 4.0//Cassa di Risparmio di Cuneo/ ; DiBIO - Subproject BIOPRIME//Ministero delle Politiche Agricole Alimentari e Forestali/ ; }, abstract = {The concept of plant as a holobiont is now spreading among the scientific community and the importance to study plant-associated microorganisms is becoming more and more necessary. Along with bacteria and fungi, also viruses can play important roles during the holobiont-environment interactions. In grapevine, viruses are studied mainly as pathological agents, and many species (more than 80) are known to be able to replicate inside its tissues. In this study two new viral species associated with grape wood tissues are presented, one belongs to the Potyviridae family and one to the Bunyavirales order. Due to the ability of potyviruses to enhance heterologous virus replication, it will be important to assess the presence of such a virus in the grapevine population to understand its ecological role. Furthermore, the association of the cogu-like virus with esca symptomatic samples opens new questions and the necessity of a more detailed characterization of this virus.}, }
@article {pmid32627905, year = {2020}, author = {Herrera, M and Klein, SG and Schmidt-Roach, S and Campana, S and Cziesielski, MJ and Chen, JE and Duarte, CM and Aranda, M}, title = {Unfamiliar partnerships limit cnidarian holobiont acclimation to warming.}, journal = {Global change biology}, volume = {26}, number = {10}, pages = {5539-5553}, pmid = {32627905}, issn = {1365-2486}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Heat-Shock Response ; Symbiosis ; }, abstract = {Enhancing the resilience of corals to rising temperatures is now a matter of urgency, leading to growing efforts to explore the use of heat tolerant symbiont species to improve their thermal resilience. The notion that adaptive traits can be retained by transferring the symbionts alone, however, challenges the holobiont concept, a fundamental paradigm in coral research. Holobiont traits are products of a specific community (holobiont) and all its co-evolutionary and local adaptations, which might limit the retention or transference of holobiont traits by exchanging only one partner. Here we evaluate how interchanging partners affect the short- and long-term performance of holobionts under heat stress using clonal lineages of the cnidarian model system Aiptasia (host and Symbiodiniaceae strains) originating from distinct thermal environments. Our results show that holobionts from more thermally variable environments have higher plasticity to heat stress, but this resilience could not be transferred to other host genotypes through the exchange of symbionts. Importantly, our findings highlight the role of the host in determining holobiont productivity in response to thermal stress and indicate that local adaptations of holobionts will likely limit the efficacy of interchanging unfamiliar compartments to enhance thermal tolerance.}, }
@article {pmid32620152, year = {2020}, author = {Clerissi, C and Guillou, L and Escoubas, JM and Toulza, E}, title = {Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {193}, pmid = {32620152}, issn = {1471-2180}, mesh = {Alveolata/*classification/genetics/isolation &amp; purification ; Animals ; Crassostrea/*parasitology ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; RNA, Ribosomal, 18S/*genetics ; Sequence Analysis, DNA/methods ; Stramenopiles/*classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: Microbiome of macroorganisms might directly or indirectly influence host development and homeostasis. Many studies focused on the diversity and distribution of prokaryotes within these assemblages, but the eukaryotic microbial compartment remains underexplored so far.<br><br>RESULTS: To tackle this issue, we compared blocking and excluding primers to analyze microeukaryotic communities associated with Crassostrea gigas oysters. High-throughput sequencing of 18S rRNA genes variable loops revealed that excluding primers performed better by not amplifying oyster DNA, whereas the blocking primer did not totally prevent host contaminations. However, blocking and excluding primers showed similar pattern of alpha and beta diversities when protist communities were sequenced using metabarcoding. Alveolata, Stramenopiles and Archaeplastida were the main protist phyla associated with oysters. In particular, Codonellopsis, Cyclotella, Gymnodinium, Polarella, Trichodina, and Woloszynskia were the dominant genera. The potential pathogen Alexandrium was also found in high abundances within some samples.<br><br>CONCLUSIONS: Our study revealed the main protist taxa within oysters as well as the occurrence of potential oyster pathogens. These new primer sets are promising tools to better understand oyster homeostasis and disease development, such as the Pacific Oyster Mortality Syndrome (POMS) targeting juveniles.}, }
@article {pmid32616905, year = {2020}, author = {Breusing, C and Mitchell, J and Delaney, J and Sylva, SP and Seewald, JS and Girguis, PR and Beinart, RA}, title = {Physiological dynamics of chemosynthetic symbionts in hydrothermal vent snails.}, journal = {The ISME journal}, volume = {14}, number = {10}, pages = {2568-2579}, pmid = {32616905}, issn = {1751-7370}, mesh = {Animals ; Ecosystem ; *Gammaproteobacteria/genetics ; *Hydrothermal Vents ; Phylogeny ; Symbiosis ; }, abstract = {Symbioses between invertebrate animals and chemosynthetic bacteria form the basis of hydrothermal vent ecosystems worldwide. In the Lau Basin, deep-sea vent snails of the genus Alviniconcha associate with either Gammaproteobacteria (A. kojimai, A. strummeri) or Campylobacteria (A. boucheti) that use sulfide and/or hydrogen as energy sources. While the A. boucheti host-symbiont combination (holobiont) dominates at vents with higher concentrations of sulfide and hydrogen, the A. kojimai and A. strummeri holobionts are more abundant at sites with lower concentrations of these reductants. We posit that adaptive differences in symbiont physiology and gene regulation might influence the observed niche partitioning between host taxa. To test this hypothesis, we used high-pressure respirometers to measure symbiont metabolic rates and examine changes in gene expression among holobionts exposed to in situ concentrations of hydrogen (H2: ~25 µM) or hydrogen sulfide (H2S: ~120 µM). The campylobacterial symbiont exhibited the lowest rate of H2S oxidation but the highest rate of H2 oxidation, with fewer transcriptional changes and less carbon fixation relative to the gammaproteobacterial symbionts under each experimental condition. These data reveal potential physiological adaptations among symbiont types, which may account for the observed net differences in metabolic activity and contribute to the observed niche segregation among holobionts.}, }
@article {pmid32614866, year = {2020}, author = {Vogel, MA and Mason, OU and Miller, TE}, title = {Host and environmental determinants of microbial community structure in the marine phyllosphere.}, journal = {PloS one}, volume = {15}, number = {7}, pages = {e0235441}, pmid = {32614866}, issn = {1932-6203}, mesh = {Bacteria/*classification/genetics ; Fresh Water/*microbiology ; Gulf of Mexico ; Host Microbial Interactions ; Hydrocharitaceae/*microbiology/physiology ; *Microbiota ; Phylogeny ; Plant Leaves/*microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Salinity ; Seawater/*microbiology ; Wetlands ; }, abstract = {Although seagrasses are economically and ecologically critical species, little is known about their blade surface microbial communities and how these communities relate to the plant host. To determine microbial community composition and diversity on seagrass blade surfaces and in the surrounding seawater,16S rRNA gene sequencing (iTag) was used for samples collected at five sites along a gradient of freshwater input in the northern Gulf of Mexico on three separate sampling dates. Additionally, seagrass surveys were performed and environmental parameters were measured to characterize host characteristics and the abiotic conditions at each site. Results showed that Thalassia testudinum (turtle grass) blades hosted unique microbial communities that were distinct in composition and diversity from the water column. Environmental conditions, including water depth, salinity, and temperature, influenced community structure as blade surface microbial communities varied among sites and sampling dates in correlation with changes in environmental parameters. Microbial community composition also correlated with seagrass host characteristics, including growth rates and blade nutrient composition. There is some evidence for a core community for T. testudinum as 21 microorganisms from five phyla (Cyanobacteria, Proteobacteria, Planctomycetes, Chloroflexi, and Bacteroidetes) were present in all blade surface samples. This study provides new insights and understanding of the processes that influence the structure of marine phyllosphere communities, how these microbial communities relate to their host, and their role as a part of the seagrass holobiont, which is an important contribution given the current decline of seagrass coverage worldwide.}, }
@article {pmid32612612, year = {2020}, author = {Dierking, K and Pita, L}, title = {Receptors Mediating Host-Microbiota Communication in the Metaorganism: The Invertebrate Perspective.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {1251}, pmid = {32612612}, issn = {1664-3224}, mesh = {Animals ; Biodiversity ; Homeostasis ; *Host Microbial Interactions/immunology ; Humans ; Invertebrates ; *Microbiota/immunology ; Protein Binding ; Receptors, Pattern Recognition/*metabolism ; *Signal Transduction ; Species Specificity ; }, abstract = {Multicellular organisms live in close association with a plethora of microorganism, which have a profound effect on multiple host functions. As such, the microbiota and its host form an intimate functional entity, termed the metaorganism or holobiont. But how does the metaorganism communicate? Which receptors recognize microbial signals, mediate the effect of the microbiota on host physiology or regulate microbiota composition and homeostasis? In this review we provide an overview on the function of different receptor classes in animal host-microbiota communication. We put a special focus on invertebrate hosts, including both traditional invertebrate models such as Drosophila melanogaster and Caenorhabditis elegans and "non-model" invertebrates in microbiota research. Finally, we highlight the potential of invertebrate systems in studying mechanism of host-microbiota interactions.}, }
@article {pmid32587579, year = {2020}, author = {Bourgin, M and Labarthe, S and Kriaa, A and Lhomme, M and Gérard, P and Lesnik, P and Laroche, B and Maguin, E and Rhimi, M}, title = {Exploring the Bacterial Impact on Cholesterol Cycle: A Numerical Study.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {1121}, pmid = {32587579}, issn = {1664-302X}, abstract = {High blood cholesterol levels are often associated with cardiovascular diseases. Therapeutic strategies, targeting different functions involved in cholesterol transport or synthesis, were developed to control cholesterolemia in human. However, the gut microbiota is also involved in cholesterol regulation by direct biotransformation of luminal cholesterol or conversion of bile salts, opening the way to the design of new strategies to manage cholesterol level. In this report, we developed for the first time a whole-body human model of cholesterol metabolism including the gut microbiota in order to investigate the relative impact of host and microbial pathways. We first used an animal model to investigate the ingested cholesterol distribution in vivo. Then, using in vitro bacterial growth experiments and metabolite measurements, we modeled the population dynamics of bacterial strains in the presence of cholesterol or bile salts, together with their bioconversion function. Next, after correct rescaling to mimic the activity of a complex microbiota, we developed a whole body model of cholesterol metabolism integrating host and microbiota mechanisms. This global model was validated with the animal experiments. Finally, the model was numerically explored to give a further insight into the different flux involved in cholesterol turn-over. According to this model, bacterial pathways appear as an important driver of cholesterol regulation, reinforcing the need for development of novel "bacteria-based" strategies for cholesterol management.}, }
@article {pmid32566125, year = {2020}, author = {Gacesa, R and Hung, JY and Bourne, DG and Long, PF}, title = {Horizontal transfer of a natterin-like toxin encoding gene within the holobiont of the reef building coral Acropora digitifera (Cnidaria: Anthozoa: Scleractinia) and across multiple animal linages.}, journal = {Journal of venom research}, volume = {10}, number = {}, pages = {7-12}, pmid = {32566125}, issn = {2044-0324}, abstract = {Phylogenetic evidence is provided for horizontal transfer of a natterin-like toxin encoding gene from fungi into the genome of the coral Acropora digitifera. Sequencing analysis of the coral tissues supported that a fungal taxon predicted to be the most likely gene donor was represented in the coral microbiome. Further bioinformatics data suggested widespread recruitment of the natterin-like gene into venomous terrestrial invertebrates, and repositioning of this gene to non-toxic functions in non-venomous teleost fish.}, }
@article {pmid32554943, year = {2020}, author = {Chiba, Y and Tomaru, Y and Shimabukuro, H and Kimura, K and Hirai, M and Takaki, Y and Hagiwara, D and Nunoura, T and Urayama, SI}, title = {Viral RNA Genomes Identified from Marine Macroalgae and a Diatom.}, journal = {Microbes and environments}, volume = {35}, number = {3}, pages = {}, pmid = {32554943}, issn = {1347-4405}, mesh = {Biodiversity ; Diatoms/*virology ; Double Stranded RNA Viruses/classification/*genetics/isolation &amp; purification ; Genome, Viral/*genetics ; Phylogeny ; Seawater/*virology ; Seaweed/*virology ; Viral Proteins/genetics ; Virome ; }, abstract = {Protists provide insights into the diversity and function of RNA viruses in marine systems. Among them, marine macroalgae are good targets for RNA virome analyses because they have a sufficient biomass in nature. However, RNA viruses in macroalgae have not yet been examined in detail, and only partial genome sequences have been reported for the majority of RNA viruses. Therefore, to obtain further insights into the distribution and diversity of RNA viruses associated with marine protists, we herein examined RNA viruses in macroalgae and a diatom. We report the putative complete genome sequences of six novel RNA viruses from two marine macroalgae and one diatom holobiont. Four viruses were not classified into established viral genera or families. Furthermore, a virus classified into Totiviridae showed a genome structure that has not yet been reported in this family. These results suggest that a number of distinct RNA viruses are widespread in a broad range of protists.}, }
@article {pmid32550573, year = {2019}, author = {Ul-Hasan, S and Rodríguez-Román, E and Reitzel, AM and Adams, RMM and Herzig, V and Nobile, CJ and Saviola, AJ and Trim, SA and Stiers, EE and Moschos, SA and Keiser, CN and Petras, D and Moran, Y and Colston, TJ}, title = {The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP).}, journal = {Toxicon: X}, volume = {4}, number = {}, pages = {100016}, pmid = {32550573}, issn = {2590-1710}, abstract = {Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium.}, }
@article {pmid32548850, year = {2020}, author = {Voolstra, CR and Ziegler, M}, title = {Adapting with Microbial Help: Microbiome Flexibility Facilitates Rapid Responses to Environmental Change.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {7}, pages = {e2000004}, doi = {10.1002/bies.202000004}, pmid = {32548850}, issn = {1521-1878}, mesh = {Adaptation, Physiological ; Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota ; Symbiosis ; }, abstract = {Animals and plants are metaorganisms and associate with microbes that affect their physiology, stress tolerance, and fitness. Here the hypothesis that alteration of the microbiome may constitute a fast-response mechanism to environmental change is examined. This is supported by recent reciprocal transplant experiments with reef corals, which have shown that their microbiome adapts to thermally variable habitats and changes over time when transplanted into different environments. Further, inoculation of corals with beneficial bacteria increases their stress tolerance. But corals differ in their ability to flexibly associate with different bacteria. How scales of microbiome flexibility may reflect different metaorganism adaptation mechanisms is discussed and future directions for research are pinpointed. It is posited that microbiome flexibility is a broad phenomenon that contributes to the ability of organisms to respond to environmental change. Importantly, adapting with microbial help may provide an alternate route to organismal adaptation that facilitates rapid responses.}, }
@article {pmid32544798, year = {2020}, author = {Zelante, T and Costantini, C and Romani, L}, title = {Microbiome-mediated regulation of anti-fungal immunity.}, journal = {Current opinion in microbiology}, volume = {58}, number = {}, pages = {8-14}, doi = {10.1016/j.mib.2020.05.002}, pmid = {32544798}, issn = {1879-0364}, mesh = {Animals ; Bacteria/classification/genetics/growth &amp; development/isolation &amp; purification ; Fungi/genetics/immunology/*physiology ; Humans ; Immunity ; *Microbiota ; Mycoses/*immunology/microbiology ; }, abstract = {Anti-fungal immunity is characterized by the continuous interplay between immune activation and immune regulation processes. These processes have now been clearly shown not only in animal pre-clinical models but also in humans. To create and maintain this immune homeostasis, reciprocal interactions among the host immune system, fungal pathogens, and the microbiome are crucial. Notably, the microbiome exerts multiple direct and indirect antifungal effects that are particularly aimed at minimizing host tissue damage. Thus, in this microbiome era, the architecture of 3D culture system or 'tissue organoids' might finally represent a simple but effective in vitro 'holobiont' to unravel the diverse interactions and adaptations that evolve to overcome fungal infections.}, }
@article {pmid32537770, year = {2020}, author = {Fields, C and Levin, M}, title = {Scale-Free Biology: Integrating Evolutionary and Developmental Thinking.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {42}, number = {8}, pages = {e1900228}, doi = {10.1002/bies.201900228}, pmid = {32537770}, issn = {1521-1878}, support = {12171//Paul G. Allen Frontiers Group/International ; TWCF0089/AB55//Templeton World Charity Foundation/International ; //Paul G. Allen Frontiers Group/International ; }, mesh = {*Biological Evolution ; *Developmental Biology ; Humans ; }, abstract = {When the history of life on earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life on earth can also be seen as the development of life on earth. Here, in reviewing this field, some potentially fruitful research directions suggested by this change in perspective are highlighted. Variation and selection become, for example, bidirectional information flows between scales, while the notions of "cooperation" and "competition" become scale relative. The language of communication, inference, and information processing becomes more useful than the language of causation to describe the interactions of both homogeneous and heterogeneous living systems at any scale. Emerging scale-free theoretical frameworks such as predictive coding and active inference provide conceptual tools for reconceptualizing biology as the study of a unified, multiscale dynamical system.}, }
@article {pmid32521261, year = {2020}, author = {Vandehoef, C and Molaei, M and Karpac, J}, title = {Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP.}, journal = {Cell reports}, volume = {31}, number = {10}, pages = {107736}, pmid = {32521261}, issn = {2211-1247}, support = {F30 DK117538/DK/NIDDK NIH HHS/United States ; P40 OD010949/OD/NIH HHS/United States ; R01 DK108930/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Animals, Genetically Modified ; Diet ; Drosophila Proteins/*metabolism ; Drosophila melanogaster/metabolism/*microbiology ; Female ; Intracellular Signaling Peptides and Proteins/*metabolism ; Male ; *Microbiota ; NF-kappa B/*metabolism ; Peptide Initiation Factors/*metabolism ; Signal Transduction ; }, abstract = {Dietary nutrients shape complex interactions between hosts and their commensal gut bacteria, further promoting flexibility in host-microbiota associations that can drive nutritional symbiosis. However, it remains less clear if diet-dependent host signaling mechanisms also influence these associations. Using Drosophila, we show here that nuclear factor κB (NF-κB)/Relish, an innate immune transcription factor emerging as a signaling node linking nutrient-immune-metabolic interactions, is vital to adapt gut microbiota species composition to host diet macronutrient composition. We find that Relish is required within midgut enterocytes to amplify host-Lactobacillus associations, an important bacterial mediator of nutritional symbiosis, and thus modulate microbiota composition in response to dietary adaptation. Relish limits diet-dependent transcriptional inducibility of the cap-dependent translation inhibitor 4E-BP/Thor to control microbiota composition. Furthermore, maintaining cap-dependent translation in response to dietary adaptation is critical to amplify host-Lactobacillus associations. These results highlight that NF-κB-dependent host signaling mechanisms, in coordination with host translation control, shape diet-microbiota interactions.}, }
@article {pmid32518251, year = {2020}, author = {Bovo, S and Utzeri, VJ and Ribani, A and Cabbri, R and Fontanesi, L}, title = {Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {9279}, pmid = {32518251}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Bees ; DNA, Environmental/*analysis/genetics ; Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Genome, Fungal/genetics ; Genome, Plant/genetics ; Genome, Protozoan/genetics ; Genome, Viral/genetics ; Honey/*analysis ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Honey bees are large-scale monitoring tools due to their extensive environmental exploration. In their activities and from the hive ecosystem complex, they get in close contact with many organisms whose traces can be transferred into the honey, which can represent an interesting reservoir of environmental DNA (eDNA) signatures and information useful to analyse the honey bee hologenome complexity. In this study, we tested a deep shotgun sequencing approach of honey DNA coupled with a specifically adapted bioinformatic pipeline. This methodology was applied to a few honey samples pointing out DNA sequences from 191 organisms spanning different kingdoms or phyla (viruses, bacteria, plants, fungi, protozoans, arthropods, mammals). Bacteria included the largest number of species. These multi-kingdom signatures listed common hive and honey bee gut microorganisms, honey bee pathogens, parasites and pests, which resembled a complex interplay that might provide a general picture of the honey bee pathosphere. Based on the Apis mellifera filamentous virus genome diversity (the most abundant detected DNA source) we obtained information that could define the origin of the honey at the apiary level. Mining Apis mellifera sequences made it possible to identify the honey bee subspecies both at the mitochondrial and nuclear genome levels.}, }
@article {pmid32517729, year = {2020}, author = {Pagliai, G and Dinu, M and Fiorillo, C and Becatti, M and Turroni, S and Emmi, G and Sofi, F}, title = {Modulation of gut microbiota through nutritional interventions in Behçet's syndrome patients (the MAMBA study): study protocol for a randomized controlled trial.}, journal = {Trials}, volume = {21}, number = {1}, pages = {511}, pmid = {32517729}, issn = {1745-6215}, support = {GR-2016-02361162//Italian Ministry of Health/ ; }, mesh = {Behcet Syndrome/*etiology/microbiology ; Body Composition ; Butyrates/*administration &amp; dosage ; Cross-Over Studies ; *Diet, Mediterranean ; *Diet, Vegetarian ; Dietary Supplements ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Randomized Controlled Trials as Topic ; Risk ; }, abstract = {BACKGROUND: Behçet's syndrome (BS) is a systemic inflammatory disorder of unknown etiology, and it is characterized by a wide range of potential clinical manifestations. Recent evidence suggests that the gut microbiota (GM) in BS has low biodiversity with a significant depletion in butyrate producers. The aim of the present project is to investigate whether a dietary intervention could ameliorate the clinical manifestations and modulate the GM of individuals with BS.<br><br>METHODS: This is a randomized, open, cross-over study that involves 90 individuals with BS, who will be randomly assigned to one of three different diets for 3 months: a lacto-ovo-vegetarian diet (VD), a Mediterranean diet (MD), or a Mediterranean diet supplemented with butyrate (MD-Bt). The VD will contain inulin-resistant and resistant-starch-rich foods, eggs, and dairy in addition to plant-based food, but it will not contain meat, poultry, or fish. The MD will contain all food categories and will provide two portions per week of fish and three portions per week of fresh and processed meat. The MD-Bt will be similar to the MD but supplemented with 1.8 g/day of oral butyrate. The three different diets will be isocaloric and related to the participants' nutritional requirements. Anthropometric measurements, body composition, blood, and fecal samples will be obtained from each participant at the beginning and the end of each intervention phase. The primary outcomes will be represented by the change from baseline of the BS gastrointestinal and systemic symptoms. Changes from baseline in GM composition, short-chain fatty acid (SCFA) production, and the inflammatory and antioxidant profile will be considered as secondary outcomes.<br><br>DISCUSSION: BS is a rare disease, and, actually, not all the available treatments are target therapies. A supportive treatment based on dietary and lifestyle issues, able to restore immune system homeostasis, could have a high impact on cost sustainability for the treatment of such a chronic and disabling inflammatory condition.<br><br>TRIAL REGISTRATION: clinicaltrials.gov: NCT03962335. Registered on 21 May 2019.}, }
@article {pmid32513310, year = {2020}, author = {Douglas, GM and Bielawski, JP and Langille, MGI}, title = {Re-evaluating the relationship between missing heritability and the microbiome.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {87}, pmid = {32513310}, issn = {2049-2618}, support = {CMF-108026//CIHR/Canada ; }, mesh = {Genetic Variation ; Genome, Human ; *Genome-Wide Association Study ; Humans ; *Microbiota/genetics ; Phenotype ; }, abstract = {Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typical GWASs. The human microbiome is potentially related to both of these explanations, but it has been more commonly considered as a source of unmeasured genetic variation. In particular, it has recently been argued that the genetic variation within the human microbiome should be included when estimating trait heritability. We outline issues with this argument, which in its strictest form depends on the holobiont model of human-microbiome interactions. Instead, we argue that the microbiome could be leveraged to help control for environmental variation across a population, although that remains to be determined. We discuss potential approaches that could be explored to determine whether integrating microbiome sequencing data into GWASs is useful. Video abstract.}, }
@article {pmid32510843, year = {2020}, author = {Alonso, P and Blondin, L and Gladieux, P and Mahé, F and Sanguin, H and Ferdinand, R and Filloux, D and Desmarais, E and Cerqueira, F and Jin, B and Huang, H and He, X and Morel, JB and Martin, DP and Roumagnac, P and Vernière, C}, title = {Heterogeneity of the rice microbial community of the Chinese centuries-old Honghe Hani rice terraces system.}, journal = {Environmental microbiology}, volume = {22}, number = {8}, pages = {3429-3445}, pmid = {32510843}, issn = {1462-2920}, support = {//National Research Foundation of South Africa/International ; //INRAE/Yunnan Agricultural University/International ; //International Associated Laboratory Plantomix/International ; //Yunnan Agricultural University/International ; ANR-17-CE32-0011//French National Research Agency/International ; //E-Space Flagship Program/International ; 1504-004//Agropolis Fondation/International ; //French International and Agricultural Research Agency (CIRAD)/International ; }, mesh = {Agriculture/methods ; *Biodiversity ; China ; Humans ; Microbiota/*genetics ; Oryza/*microbiology ; Plant Diseases/microbiology ; }, abstract = {The Honghe Hani rice terraces system (HHRTS) is a traditional rice cultivation system where Hani people cultivate remarkably diverse rice varieties. Recent introductions of modern rice varieties to the HHRTS have significantly increased the severity of rice diseases within the terraces. Here, we determine the impacts of these recent introductions on the composition of the rice-associated microbial communities. We confirm that the HHRTS contains a range of both traditional HHRTS landraces and introduced modern rice varieties and find differences between the microbial communities of these two groups. However, this introduction of modern rice varieties has not strongly impacted the overall diversity of the HHRTS rice microbial community. Furthermore, we find that the rice varieties (i.e. groups of closely related genotypes) have significantly structured the rice microbial community composition (accounting for 15%-22% of the variance) and that the core microbial community of HHRTS rice plants represents less than 3.3% of all the microbial taxa identified. Collectively, our study suggests a highly diverse HHRTS rice holobiont (host with its associated microbes) where the diversity of rice hosts mirrors the diversity of their microbial communities. Further studies will be needed to better determine how such changes might impact the sustainability of the HHRTS.}, }
@article {pmid32510361, year = {2020}, author = {Yu, X and Yu, K and Liao, Z and Liang, J and Deng, C and Huang, W and Huang, Y}, title = {Potential molecular traits underlying environmental tolerance of Pavona decussata and Acropora pruinosa in Weizhou Island, northern South China Sea.}, journal = {Marine pollution bulletin}, volume = {156}, number = {}, pages = {111199}, doi = {10.1016/j.marpolbul.2020.111199}, pmid = {32510361}, issn = {1879-3363}, mesh = {Animals ; *Anthozoa ; Bacteria ; China ; *Dinoflagellida ; Islands ; }, abstract = {Coral species display varying susceptibilities to biotic or abiotic stress. To address the causes underlying this phenomenon, we profiled the Symbiodiniaceae clade type, bacterial communities and coral transcriptome responses in Pavona decussata and Acropora pruinosa, two species displaying different environmental tolerances in the Weizhou Island. We found that C1 was the most dominant Symbiodiniaceae subclade, with no difference detected between A. pruinosa and P. decussata. Nevertheless, P. decussata exhibited higher microbial diversity and significantly different community structure compared with that of A. pruinosa. Transcriptome analysis revealed that coral genes with significantly high expression in P. decussata were mostly related to immune and stress-resistance responses, whereas, those with significantly low expression were metabolism-related. We postulate that the higher tolerance of P. decussata as compared with that of A. pruinosa is the result of several traits, such as higher microbial diversity, different dominant bacteria, higher immune and stress-resistant response, and lower metabolic rate.}, }
@article {pmid32508779, year = {2020}, author = {Jorge, F and Dheilly, NM and Poulin, R}, title = {Persistence of a Core Microbiome Through the Ontogeny of a Multi-Host Parasite.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {954}, pmid = {32508779}, issn = {1664-302X}, abstract = {Animal microbiomes influence their development, behavior and interactions with other organisms. Parasitic metazoans also harbor microbial communities; although they are likely to modulate host-parasite interactions, little is known about parasite microbiomes. The persistence of microbial communities throughout the life of a parasite is particularly challenging for helminths with complex life cycles. These parasites undergo major morphological changes during their life, and parasitize host species that are immunologically, physiologically, and phylogenetically very different. Here, using 16S amplicon sequencing, we characterize the microbiome of the trematode Coitocaecum parvum across four of its life stages: sporocysts, metacercariae and adults inhabiting (respectively) snails, crustaceans and fish, as well as free-living cercariae. Our results demonstrate that, at each life stage, the parasite possesses a phylogenetically diverse microbiome, distinct from that of its hosts or the external environment. The parasite's microbiome comprises bacterial taxa specific to each life stage in different hosts, as well as a small core set of taxa that persists across the parasite's whole life. The apparent existence of an ontogenetically and vertically transmitted core microbiome is supported by the findings that the diversity and taxonomic composition of the microbiome does not vary significantly among life stages, and that the main source of microbial taxa at any life stage is the previous life stage. Our results suggest that microbes are an integrated component of the trematode, possibly shaping its phenotype and host-parasite interactions.}, }
@article {pmid32504001, year = {2020}, author = {Gouveia, D and Pible, O and Culotta, K and Jouffret, V and Geffard, O and Chaumot, A and Degli-Esposti, D and Armengaud, J}, title = {Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {23}, pmid = {32504001}, issn = {2055-5008}, mesh = {Amphipoda/*microbiology ; Animals ; Bacteria/*classification/genetics/isolation &amp; purification/metabolism ; DNA Barcoding, Taxonomic ; Gastrointestinal Microbiome ; Phylogeny ; Proteogenomics/*methods ; Proteomics/*methods ; Sequence Analysis, RNA ; Tandem Mass Spectrometry ; }, abstract = {Metaproteomics of gut microbiomes from animal hosts lacking a reference genome is challenging. Here we describe a strategy combining high-resolution metaproteomics and host RNA sequencing (RNA-seq) with generalist database searching to survey the digestive tract of Gammarus fossarum, a small crustacean used as a sentinel species in ecotoxicology. This approach provides a deep insight into the full range of biomasses and metabolic activities of the holobiont components, and differentiates between the intestine and hepatopancreatic caecum.}, }
@article {pmid32498449, year = {2020}, author = {Murray, AE and Avalon, NE and Bishop, L and Davenport, KW and Delage, E and Dichosa, AEK and Eveillard, D and Higham, ML and Kokkaliari, S and Lo, CC and Riesenfeld, CS and Young, RM and Chain, PSG and Baker, BJ}, title = {Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica.}, journal = {Marine drugs}, volume = {18}, number = {6}, pages = {}, pmid = {32498449}, issn = {1660-3397}, support = {R21 CA205932/CA/NCI NIH HHS/United States ; OPP-0442857, ANT-0838776, PLR-1341339, ANT-0632389, DBI-0532893//National Science Foundation/ ; CA205932/NH/NIH HHS/United States ; }, mesh = {Animals ; Antarctic Regions ; Islands ; Macrolides/*analysis ; *Microbiota ; RNA, Ribosomal, 16S ; Urochordata/*microbiology ; }, abstract = {Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64° 46'S, 64° 03'W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3-V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)-20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.}, }
@article {pmid32498442, year = {2020}, author = {Gamalero, E and Bona, E and Todeschini, V and Lingua, G}, title = {Saline and Arid Soils: Impact on Bacteria, Plants, and their Interaction.}, journal = {Biology}, volume = {9}, number = {6}, pages = {}, pmid = {32498442}, issn = {2079-7737}, abstract = {Salinity and drought are the most important abiotic stresses hampering crop growth and yield. It has been estimated that arid areas cover between 41% and 45% of the total Earth area worldwide. At the same time, the world's population is going to soon reach 9 billion and the survival of this huge amount of people is dependent on agricultural products. Plants growing in saline/arid soil shows low germination rate, short roots, reduced shoot biomass, and serious impairment of photosynthetic efficiency, thus leading to a substantial loss of crop productivity, resulting in significant economic damage. However, plants should not be considered as single entities, but as a superorganism, or a holobiont, resulting from the intimate interactions occurring between the plant and the associated microbiota. Consequently, it is very complex to define how the plant responds to stress on the basis of the interaction with its associated plant growth-promoting bacteria (PGPB). This review provides an overview of the physiological mechanisms involved in plant survival in arid and saline soils and aims at describing the interactions occurring between plants and its bacteriome in such perturbed environments. The potential of PGPB in supporting plant survival and fitness in these environmental conditions has been discussed.}, }
@article {pmid32497352, year = {2020}, author = {Speare, L and Davies, SW and Balmonte, JP and Baumann, J and Castillo, KD}, title = {Patterns of environmental variability influence coral-associated bacterial and algal communities on the Mesoamerican Barrier Reef.}, journal = {Molecular ecology}, volume = {29}, number = {13}, pages = {2334-2348}, doi = {10.1111/mec.15497}, pmid = {32497352}, issn = {1365-294X}, mesh = {Animals ; Anthozoa/*microbiology ; *Bacteria/classification ; Belize ; Coral Reefs ; *Dinoflagellida/classification ; *Microbiota ; }, abstract = {A coral's capacity to alter its microbial symbionts may enhance its fitness in the face of climate change. Recent work predicts exposure to high environmental variability may increase coral resilience and adaptability to future climate conditions. However, how this heightened environmental variability impacts coral-associated microbial communities remains largely unexplored. Here, we examined the bacterial and algal symbionts associated with two coral species of the genus Siderastrea with distinct life history strategies from three reef sites on the Belize Mesoamerican Barrier Reef System with low or high environmental variability. Our results reveal bacterial community structure, as well as alpha- and beta-diversity patterns, vary by host species. Differences in bacterial communities between host species were partially explained by high abundance of Deltaproteobacteria and Rhodospirillales and high bacterial diversity in Siderastrea radians. Our findings also suggest Siderastrea spp. have dynamic core bacterial communities that likely drive differences observed in the entire bacterial community, which may play a critical role in rapid acclimatization to environmental change. Unlike the bacterial community, Symbiodiniaceae composition was only distinct between host species at high thermal variability sites, suggesting that different factors shape bacterial versus algal communities within the coral holobiont. Our findings shed light on how domain-specific shifts in dynamic microbiomes may allow for unique methods of enhanced host fitness.}, }
@article {pmid32484275, year = {2020}, author = {Hawksworth, DL and Grube, M}, title = {Lichens redefined as complex ecosystems.}, journal = {The New phytologist}, volume = {227}, number = {5}, pages = {1281-1283}, pmid = {32484275}, issn = {1469-8137}, mesh = {Biodiversity ; Ecosystem ; *Lichens ; Saccharomyces cerevisiae ; Symbiosis ; }, }
@article {pmid32483294, year = {2020}, author = {Calusinska, M and Marynowska, M and Bertucci, M and Untereiner, B and Klimek, D and Goux, X and Sillam-Dussès, D and Gawron, P and Halder, R and Wilmes, P and Ferrer, P and Gerin, P and Roisin, Y and Delfosse, P}, title = {Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {275}, pmid = {32483294}, issn = {2399-3642}, mesh = {Adaptation, Biological ; Animals ; Bacteria/*enzymology ; Diet ; Digestion ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/physiology ; *Gene Expression ; Isoptera/*physiology ; Poaceae/*chemistry ; }, abstract = {Miscanthus sp. biomass could satisfy future biorefinery value chains. However, its use is largely untapped due to high recalcitrance. The termite and its gut microbiome are considered the most efficient lignocellulose degrading system in nature. Here, we investigate at holobiont level the dynamic adaptation of Cortaritermes sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose recalcitrance. We use an integrative omics approach combined with enzymatic characterisation of carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Modified gene expression profiles of gut bacteria suggest a shift towards utilisation of cellulose and arabinoxylan, two main components of Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to closely related species supports the hypothesis of a strong phylogenetic relationship between host and its gut microbiome. This study provides a framework for better understanding the complex lignocellulose degradation by the higher termite gut system and paves a road towards its future bioprospecting.}, }
@article {pmid32482859, year = {2020}, author = {Roach, TNF and Little, M and Arts, MGI and Huckeba, J and Haas, AF and George, EE and Quinn, RA and Cobián-Güemes, AG and Naliboff, DS and Silveira, CB and Vermeij, MJA and Kelly, LW and Dorrestein, PC and Rohwer, F}, title = {A multiomic analysis of in situ coral-turf algal interactions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {24}, pages = {13588-13595}, pmid = {32482859}, issn = {1091-6490}, mesh = {Animals ; Anthozoa/chemistry/*metabolism/microbiology/parasitology ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Chlorophyta/chemistry/*metabolism ; Coral Reefs ; Ecosystem ; Metagenomics ; Microbiota ; }, abstract = {Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequencing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the holobiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral-turf algae interface displaying higher microbial abundances and larger microbial cells. This was consistent with previous studies showing that turf algae exudates feed interface and coral-associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabolites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further supported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut microbiome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral-turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral-associated microbes.}, }
@article {pmid32477316, year = {2020}, author = {Corbin, KR and Bolt, B and Rodríguez López, CM}, title = {Breeding for Beneficial Microbial Communities Using Epigenomics.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {937}, pmid = {32477316}, issn = {1664-302X}, }
@article {pmid32467160, year = {2020}, author = {Daybog, I and Kolodny, O}, title = {Simplified model assumptions artificially constrain the parameter range in which selection at the holobiont level can occur.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {11862-11863}, pmid = {32467160}, issn = {1091-6490}, mesh = {*Microbiota ; Symbiosis ; }, }
@article {pmid32467159, year = {2020}, author = {van Vliet, S and Doebeli, M}, title = {Reply to Daybog and Kolodny: Necessary requirements for holobiont-level selection are robust to model assumptions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {117}, number = {22}, pages = {11864}, pmid = {32467159}, issn = {1091-6490}, mesh = {*Microbiota ; Symbiosis ; }, }
@article {pmid32466246, year = {2020}, author = {Ben-Eliahu, N and Herut, B and Rahav, E and Abramovich, S}, title = {Shell Growth of Large Benthic Foraminifera under Heavy Metals Pollution: Implications for Geochemical Monitoring of Coastal Environments.}, journal = {International journal of environmental research and public health}, volume = {17}, number = {10}, pages = {}, pmid = {32466246}, issn = {1660-4601}, mesh = {Chlorophyll A ; Environmental Monitoring ; *Foraminifera ; Geologic Sediments ; Metals, Heavy/*analysis/toxicity ; Water Pollutants, Chemical/*analysis/toxicity ; }, abstract = {This study was promoted by the recent efforts using larger benthic foraminiferal (LBF) shells geochemistry for the monitoring of heavy metals (HMs) pollution in the marine environment. The shell itself acts as a recorder of the ambient water chemistry in low to extreme HMs-polluted environments, allowing the monitoring of recent-past pollution events. This concept, known as sclerochronology, requires the addition of new parts (i.e., new shell) even in extreme pollution events. We evaluated the physiological resilience of three LBF species with different shell types and symbionts to enriched concentrations of Cd, Cu, and Pb at levels several folds higher than the ecological criteria maximum concentration (CMC) (165-166, 33-43, 1001-1206 µg L-1, respectively), which is derived from aquatic organisms' toxicity tests. The physiological response of the holobiont was expressed by growth rates quantified by the addition of new chambers (new shell parts), and by the chlorophyll a of the algal symbionts. The growth rate decrease varied between 0% and 30% compared to the unamended control for all HMs tested, whereas the algal symbionts exhibited a general non-fatal but significant response to Pb and Cu. Our results highlight that shell growth inhibition of LBF is predicted in extreme concentrations of 57 × CMC of Cu and 523 × CMC of Cd, providing a proof of concept for shell geochemistry monitoring, which is currently not used in the regulatory sectors.}, }
@article {pmid32451122, year = {2020}, author = {Arif, I and Batool, M and Schenk, PM}, title = {Plant Microbiome Engineering: Expected Benefits for Improved Crop Growth and Resilience.}, journal = {Trends in biotechnology}, volume = {38}, number = {12}, pages = {1385-1396}, doi = {10.1016/j.tibtech.2020.04.015}, pmid = {32451122}, issn = {1879-3096}, mesh = {*Crops, Agricultural/microbiology ; *Microbiota ; Plant Roots/microbiology ; *Soil Microbiology ; }, abstract = {Plant-associated microbiomes can boost plant growth or control pathogens. Altering the microbiome by inoculation with a consortium of plant growth-promoting rhizobacteria (PGPR) can enhance plant development and mitigate against pathogens as well as abiotic stresses. Manipulating the plant holobiont by microbiome engineering is an emerging biotechnological strategy to improve crop yields and resilience. Indirect approaches to microbiome engineering include the use of soil amendments or selective substrates, and direct approaches include inoculation with specific probiotic microbes, artificial microbial consortia, and microbiome breeding and transplantation. We highlight why and how microbiome services could be incorporated into traditional agricultural practices and the gaps in knowledge that must be answered before these approaches can be commercialized in field applications.}, }
@article {pmid32446076, year = {2020}, author = {Yu, X and Yu, K and Huang, W and Liang, J and Qin, Z and Chen, B and Yao, Q and Liao, Z}, title = {Thermal acclimation increases heat tolerance of the scleractinian coral Acropora pruinosa.}, journal = {The Science of the total environment}, volume = {733}, number = {}, pages = {139319}, doi = {10.1016/j.scitotenv.2020.139319}, pmid = {32446076}, issn = {1879-1026}, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Symbiosis ; *Thermotolerance ; }, abstract = {Field ecological observations indicate that scleractinian coral exposed to early thermal stress are likely to develop higher tolerance to subsequent heat stress. The causes of this phenomenon, however, remain enigmatic. To unravel the mechanisms underlying the increased heat tolerance, we applied different thermal treatments to the scleractinian coral Acropora pruinosa and studied the resulting differences in appearance, physiological index, Symbiodiniaceae and bacterial communities, and transcriptome response. We found that early heat stress improved the thermal tolerance of the coral holobiont. After thermal acclimation, the community structure and symbiotic bacterial diversity in the microbiota were reorganized, whereas those of Symbiodiniaceae remained stable. RNA-seq analysis revealed that the downregulated coral host genes were mainly involved in pathways relating to metabolism, particularly the nitrogen metabolism pathway. This indicates that thermal acclimation led to decrease in the metabolism level in the coral host, which might be a self-protection mechanism. We suggest that thermal acclimation may increase scleractinian coral thermal tolerance by slowing host metabolism, altering the dominant bacterial population, and increasing bacterial diversity. This study offers new insights into the adaptive potential of scleractinian coral to heat stress from global warming.}, }
@article {pmid32431680, year = {2020}, author = {Newkirk, CR and Frazer, TK and Martindale, MQ and Schnitzler, CE}, title = {Adaptation to Bleaching: Are Thermotolerant Symbiodiniaceae Strains More Successful Than Other Strains Under Elevated Temperatures in a Model Symbiotic Cnidarian?.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {822}, pmid = {32431680}, issn = {1664-302X}, abstract = {The ability of some symbiotic cnidarians to resist and better withstand stress factors that cause bleaching is a trait that is receiving increased attention. The adaptive bleaching hypothesis postulates that cnidarians that can form a stable symbiosis with thermotolerant Symbiodiniaceae strains may cope better with increasing seawater temperatures. We used polyps of the scyphozoan, Cassiopea xamachana, as a model system to test symbiosis success under heat stress. We sought to determine: (1) if aposymbiotic C. xamachana polyps could establish and maintain a symbiosis with both native and non-native strains of Symbiodiniaceae that all exhibit different tolerances to heat, (2) whether polyps with these newly acquired Symbiodiniaceae strains would strobilate (produce ephyra), and (3) if thermally tolerant Symbiodiniaceae strains that established and maintained a symbiosis exhibited greater success in response to heat stress (even if they are not naturally occurring in Cassiopea). Following recolonization of aposymbiotic C. xamachana polyps with different strains, we found that: (1) strains Smic, Stri, Slin, and Spil all established a stable symbiosis that promoted strobilation and (2) strains Bmin1 and Bmin2 did not establish a stable symbiosis and strobilation did not occur. Strains Smic, Stri, Slin, and Spil were used in a subsequent bleaching experiment; each of the strains was introduced to a subset of aposymbiotic polyps and once polyp tissues were saturated with symbionts they were subjected to elevated temperatures - 32°C and 34°C - for 2 weeks. Our findings indicate that, in general, pairings of polyps with Symbiodiniaceae strains that are native to Cassiopea (Stri and Smic) performed better than a non-native strain (Slin) even though this strain has a high thermotolerance. This suggests a degree of partner specificity that may limit the adaptive potential of certain cnidarians to increased ocean warming. We also observed that the free-living, non-native thermotolerant strain Spil was relatively successful in resisting bleaching during experimental trials. This suggests that free-living Symbiodiniaceae may provide a supply of potentially "new" thermotolerant strains to cnidarians following a bleaching event.}, }
@article {pmid32429344, year = {2020}, author = {Sariola, S and Gilbert, SF}, title = {Toward a Symbiotic Perspective on Public Health: Recognizing the Ambivalence of Microbes in the Anthropocene.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32429344}, issn = {2076-2607}, support = {316941//Academy of Finland/ ; SFG//Swarthmore College Faculty Research/ ; }, abstract = {Microbes evolve in complex environments that are often fashioned, in part, by human desires. In a global perspective, public health has played major roles in structuring how microbes are perceived, cultivated, and destroyed. The germ theory of disease cast microbes as enemies of the body and the body politic. Antibiotics have altered microbial development by providing stringent natural selection on bacterial species, and this has led to the formation of antibiotic-resistant bacterial strains. Public health perspectives such as "Precision Public Health" and "One Health" have recently been proposed to further manage microbial populations. However, neither of these take into account the symbiotic relationships that exist between bacterial species and between bacteria, viruses, and their eukaryotic hosts. We propose a perspective on public health that recognizes microbial evolution through symbiotic associations (the hologenome theory) and through lateral gene transfer. This perspective has the advantage of including both the pathogenic and beneficial interactions of humans with bacteria, as well as combining the outlook of the "One Health" model with the genomic methodologies utilized in the "Precision Public Health" model. In the Anthropocene, the conditions for microbial evolution have been altered by human interventions, and public health initiatives must recognize both the beneficial (indeed, necessary) interactions of microbes with their hosts as well as their pathogenic interactions.}, }
@article {pmid32429044, year = {2020}, author = {Pavagadhi, S and Swarup, S}, title = {Metabolomics for Evaluating Flavor-Associated Metabolites in Plant-Based Products.}, journal = {Metabolites}, volume = {10}, number = {5}, pages = {}, pmid = {32429044}, issn = {2218-1989}, support = {NRF-CRP 16-2015-04//National Research Foundation Singapore/ ; Holobiont Cluster (core funding)//Singapore Centre for Environmental Life Sciences Engineering/ ; }, abstract = {Plant-based diets (PBDs) are associated with environmental benefits, human health promotion and animal welfare. There is a worldwide shift towards PBDs, evident from the increased global demand for fresh plant-based products (PBPs). Such shifts in dietary preferences accompanied by evolving food palates, create opportunities to leverage technological advancements and strict quality controls in developing PBPs that can drive consumer acceptance. Flavor, color and texture are important sensory attributes of a food product and, have the largest influence on consumer appeal and acceptance. Among these, flavor is considered the most dominating quality attribute that significantly affects overall eating experience. Current state-of-art technologies rely on physicochemical estimations and sensory-based tests to assess flavor-related attributes in fresh PBPs. However, these methodologies often do not provide any indication about the metabolic features associated with unique flavor profiles and, consequently, can be used in a limited way to define the quality attributes of PBPs. To this end, a systematic understanding of metabolites that contribute to the flavor profiles of PBPs is warranted to complement the existing methodologies. This review will discuss the use of metabolomics for evaluating flavor-associated metabolites in fresh PBPs at post-harvest stage, alongside its applications for quality assessment and grading. We will summarize the current research in this area, discuss technical challenges and considerations pertaining to sampling and analytical techniques, as well as s provide future perspectives and directions for government organizations, industries and other stakeholders associated with the quality assessment of fresh PBPs.}, }
@article {pmid32408381, year = {2020}, author = {Bonthond, G and Bayer, T and Krueger-Hadfield, SA and Barboza, FR and Nakaoka, M and Valero, M and Wang, G and Künzel, S and Weinberger, F}, title = {How do microbiota associated with an invasive seaweed vary across scales?.}, journal = {Molecular ecology}, volume = {29}, number = {11}, pages = {2094-2108}, doi = {10.1111/mec.15470}, pmid = {32408381}, issn = {1365-294X}, mesh = {Introduced Species ; *Microbiota/genetics ; Rhodophyta/*microbiology ; Seaweed/*microbiology ; }, abstract = {Communities are shaped by scale dependent processes. To study the diversity and variation of microbial communities across scales, the invasive and widespread seaweed Agarophyton vermiculophyllum presents a unique opportunity. We characterized pro- and eukaryotic communities associated with this holobiont across its known distribution range, which stretches over the northern hemisphere. Our data reveal that community composition and diversity in the holobiont vary at local but also larger geographic scales. While processes acting at the local scale (i.e., within population) are the main structuring drivers of associated microbial communities, changes in community composition also depend on processes acting at larger geographic scales. Interestingly, the largest analysed scale (i.e., native and non-native ranges) explained variation in the prevalence of predicted functional groups, which could suggest a functional shift in microbiota occurred over the course of the invasion process. While high variability in microbiota at the local scale supports A. vermiculophyllum to be a generalist host, we also identified a number of core taxa. These geographically independent holobiont members imply that cointroduction of specific microbiota may have additionally promoted the invasion process.}, }
@article {pmid32406121, year = {2020}, author = {Suárez, J and Stencel, A}, title = {A part-dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {95}, number = {5}, pages = {1308-1324}, doi = {10.1111/brv.12610}, pmid = {32406121}, issn = {1469-185X}, support = {FFI2016-76799-P//Ministerio de Economía y Competitividad/International ; FFU16/02570//Ministerio de Educación, Cultura y Deporte/International ; 2018/28/T/HS1/00201//Narodowe Centrum Nauki/International ; //University of Sydney/International ; //University of Bordeaux/International ; //University of Barcelona/International ; //University of Exeter/International ; }, mesh = {Biological Evolution ; Humans ; *Microbiota ; Symbiosis ; }, abstract = {Given one conception of biological individuality (evolutionary, physiological, etc.), can a holobiont - that is the host + its symbiotic (mutualistic, commensalist and parasitic) microbiome - be simultaneously a biological individual and an ecological community? Herein, we support this possibility by arguing that the notion of biological individuality is part-dependent. In our account, the individuality of a biological ensemble should not only be determined by the conception of biological individuality in use, but also by the biological characteristics of the part of the ensemble under investigation. In the specific case of holobionts, evaluations of their individuality should be made either host-relative or microbe-relative. We support the claim that biological individuality is part-dependent by drawing upon recent empirical evidence regarding the physiology of hosts and microbes, and the recent characterization of the 'demibiont'. Our account shows that contemporary disagreements about the individuality of the holobiont derive from an incorrect understanding of the ontology of biological individuality. We show that collaboration between philosophers and biologists can be very fruitful in attempts to solve some contemporary biological debates.}, }
@article {pmid32390975, year = {2020}, author = {Tong, H and Cai, L and Zhou, G and Zhang, W and Huang, H and Qian, PY}, title = {Correlations Between Prokaryotic Microbes and Stress-Resistant Algae in Different Corals Subjected to Environmental Stress in Hong Kong.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {686}, pmid = {32390975}, issn = {1664-302X}, abstract = {Coral reefs are extremely vulnerable to global climate change, as evidenced by increasing bleaching events. Previous studies suggest that both algal and microbial partners benefit coral hosts, but the nature of interactions between Symbiodiniaceae and prokaryotic microbes and their effects on coral hosts remains unclear. In the present study, we examined correlations between Symbiodiniaceae and prokaryotic microbes in Montipora spp. and Porites lutea sampled from two sites in Hong Kong with contrasting environmental conditions in March and October 2014. The results showed that the prokaryotic microbial communities had adaptable structures in both Montipora spp. and P. lutea, and environmental conditions had greater effects on the algal/microbial communities in Montipora spp. than in P. lutea. Further network analysis revealed a greater number of prokaryotic microbes were significantly correlated with potentially stress-resistant Symbiodiniaceae in P. lutea than in Montipora spp. Stress-resistant Symbiodiniaceae played more important roles in the community and in the algal-microbial correlations in P. lutea than in Montipora spp. Since P. lutea is faring better in Hong Kong as the seawater temperature gradually increases, the results suggest that the correlations between stress-resistant algae and prokaryotic microbes could provide a compensation mechanism allowing coral hosts to adapt to higher temperatures, particularly as the prokaryotic microbes correlated with Symbiodiniaceae provide the ecological functions of photosynthesis and nitrogen fixation.}, }
@article {pmid32390855, year = {2020}, author = {Zhang, R and Gao, X and Bai, H and Ning, K}, title = {Traditional Chinese Medicine and Gut Microbiome: Their Respective and Concert Effects on Healthcare.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {538}, pmid = {32390855}, issn = {1663-9812}, abstract = {Advances in systems biology, particularly based on the omics approaches, have resulted in a paradigm shift in both traditional Chinese medicine (TCM) and the gut microbiome research. In line with this paradigm shift, the importance of TCM and gut microbiome in healthcare, as well as their interplay, has become clearer. Firstly, we briefly summarize the current status of three topics in this review: microbiome, TCM, and relationship of TCM and microbiome. Second, we focused on TCM's therapeutic effects and gut microbiome's mediation roles, including the relationships among diet, gut microbiome, and health care. Third, we have summarized some databases and tools to help understand the impact of TCM and gut microbiome on diagnosis and treatment at the molecular level. Finally, we introduce the effects of gut microbiome on TCM and host health, with two case studies, one on the metabolic effect of gut microbiome on TCM, and another on cancer treatment. In summary, we have reviewed the current status of the two components of healthcare: TCM and gut microbiome, as well as their concert effects. It is quite clear that as the holobiont, the maintenance of the health status of human would depend heavily on TCM, gut microbiome, and their combined effects.}, }
@article {pmid32372688, year = {2020}, author = {Perry, WB and Lindsay, E and Payne, CJ and Brodie, C and Kazlauskaite, R}, title = {The role of the gut microbiome in sustainable teleost aquaculture.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1926}, pages = {20200184}, pmid = {32372688}, issn = {1471-2954}, mesh = {Animal Feed ; Animals ; *Aquaculture ; Fishes/*microbiology ; *Gastrointestinal Microbiome ; Sustainable Development ; }, abstract = {As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.}, }
@article {pmid32354088, year = {2020}, author = {Roberty, S and Béraud, E and Grover, R and Ferrier-Pagès, C}, title = {Coral Productivity Is Co-Limited by Bicarbonate and Ammonium Availability.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, pmid = {32354088}, issn = {2076-2607}, abstract = {The nitrogen environment and nitrogen status of reef-building coral endosymbionts is one of the important factors determining the optimal assimilation of phototrophic carbon and hence the growth of the holobiont. However, the impact of inorganic nutrient availability on the photosynthesis and physiological state of the coral holobiont is partly understood. This study aimed to determine if photosynthesis of the endosymbionts associated with the coral Stylophora pistillata and the overall growth of the holobiont were limited by the availability of dissolved inorganic carbon and nitrogen in seawater. For this purpose, colonies were incubated in absence or presence of 4 µM ammonium and/or 6 mM bicarbonate. Photosynthetic performances, pigments content, endosymbionts density and growth rate of the coral colonies were monitored for 3 weeks. Positive effects were observed on coral physiology with the supplementation of one or the other nutrient, but the most important changes were observed when both nutrients were provided. The increased availability of DIC and NH4+ significantly improved the photosynthetic efficiency and capacity of endosymbionts, in turn enhancing the host calcification rate. Overall, these results suggest that in hospite symbionts are co-limited by nitrogen and carbon availability for an optimal photosynthesis.}, }
@article {pmid32326359, year = {2020}, author = {Gong, S and Jin, X and Ren, L and Tan, Y and Xia, X}, title = {Unraveling Heterogeneity of Coral Microbiome Assemblages in Tropical and Subtropical Corals in the South China Sea.}, journal = {Microorganisms}, volume = {8}, number = {4}, pages = {}, pmid = {32326359}, issn = {2076-2607}, support = {GML2019ZD0405//Key Ecological Processes and Health Regulation Principles of Marine Ecosystem in Guangdong-Hong Kong-Macao Greater Bay Area/ ; Y8SL031001, Y9YB021001//the CAS Pioneer Hundred Talents Program and the South China Sea Institute of Oceanography/ ; 31971501//National Natural Science Foundation of China/ ; }, abstract = {Understanding the coral microbiome is critical for predicting the fidelity of coral symbiosis with growing surface seawater temperature (SST). However, how the coral microbiome will respond to increasing SST is still understudied. Here, we compared the coral microbiome assemblages among 73 samples across six typical South China Sea coral species in two thermal regimes. The results revealed that the composition of microbiome varied across both coral species and thermal regimes, except for Porites lutea. The tropical coral microbiome displayed stronger heterogeneity and had a more un-compacted ecological network than subtropical coral microbiome. The coral microbiome was more strongly determined by environmental factors than host specificity. γ- (32%) and α-proteobacteria (19%), Bacteroidetes (14%), Firmicutes (14%), Actinobacteria (6%) and Cyanobacteria (2%) dominated the coral microbiome. Additionally, bacteria inferred to play potential roles in host nutrients metabolism, several keystone bacteria detected in human and plant rhizospheric microbiome were retrieved in explored corals. This study not only disentangles how different host taxa and microbiome interact and how such an interaction is affected by thermal regimes, but also identifies previously unrecognized keystone bacteria in corals, and also infers the community structure of coral microbiome will be changed from a compacted to an un-compacted network under elevated SST.}, }
@article {pmid32314003, year = {2020}, author = {Parker, ES and Newton, ILG and Moczek, AP}, title = {(My Microbiome) Would Walk 10,000 miles: Maintenance and Turnover of Microbial Communities in Introduced Dung Beetles.}, journal = {Microbial ecology}, volume = {80}, number = {2}, pages = {435-446}, doi = {10.1007/s00248-020-01514-9}, pmid = {32314003}, issn = {1432-184X}, support = {1901680//Division of Integrative Organismal Systems/ ; 1256689//Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; }, mesh = {Animals ; Australian Capital Territory ; Bacteria/*isolation &amp; purification ; Coleoptera/*microbiology ; Introduced Species ; Italy ; *Microbiota ; *Symbiosis ; West Virginia ; }, abstract = {Host-associated microbes facilitate diverse biotic and abiotic interactions between hosts and their environments. Experimental alterations of host-associated microbial communities frequently decrease host fitness, yet much less is known about if and how host-microbiome interactions are altered by natural perturbations, such as introduction events. Here, we begin to assess this question in Onthophagus dung beetles, a species-rich and geographically widely distributed genus whose members rely on vertically transmitted microbiota to support normal development. Specifically, we investigated to what extent microbiome community membership shifts during host introduction events and the relative significance of ancestral associations and novel environmental conditions in the structuring of microbial communities of introduced host species. Our results demonstrate that both evolutionary history and local environmental forces structure the microbial communities of these animals, but that their relative importance is shaped by the specific circumstances that characterize individual introduction events. Furthermore, we identify microbial taxa such as Dysgonomonas that may constitute members of the core Onthophagus microbiome regardless of host population or species, but also Wolbachia which associates with Onthophagus beetles in a species or even population-specific manner. We discuss the implications of our results for our understanding of the evolutionary ecology of symbiosis in dung beetles and beyond.}, }
@article {pmid32307770, year = {2020}, author = {Kriaa, A and Jablaoui, A and Mkaouar, H and Akermi, N and Maguin, E and Rhimi, M}, title = {Serine proteases at the cutting edge of IBD: Focus on gastrointestinal inflammation.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {34}, number = {6}, pages = {7270-7282}, doi = {10.1096/fj.202000031RR}, pmid = {32307770}, issn = {1530-6860}, mesh = {Animals ; Bacteria/metabolism ; Gastrointestinal Microbiome/physiology ; Humans ; Inflammation/*metabolism ; Inflammatory Bowel Diseases/*metabolism ; Serine Proteases/*metabolism ; }, abstract = {Serine proteases have been long recognized to coordinate many physiological processes and play key roles in regulating the inflammatory response. Accordingly, their dysregulation has been regularly associated with several inflammatory disorders and suggested as a central mechanism in the pathophysiology of digestive inflammation. So far, studies addressing the proteolytic homeostasis in the gut have mainly focused on host serine proteases as candidates of interest, while largely ignoring the potential contribution of their bacterial counterparts. The human gut microbiota comprises a complex ecosystem that contributes to host health and disease. Yet, our understanding of microbially produced serine proteases and investigation of whether they are causally linked to IBD is still in its infancy. In this review, we highlight recent advances in the emerging roles of host and bacterial serine proteases in digestive inflammation. We also discuss the application of available tools in the gut to monitor disease-related serine proteases. An exhaustive representation and understanding of such functional potential would help in closing existing gaps in mechanistic knowledge.}, }
@article {pmid32294545, year = {2020}, author = {Muggia, L and Nelsen, MP and Kirika, PM and Barreno, E and Beck, A and Lindgren, H and Lumbsch, HT and Leavitt, SD and , }, title = {Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy.}, journal = {Molecular phylogenetics and evolution}, volume = {149}, number = {}, pages = {106821}, doi = {10.1016/j.ympev.2020.106821}, pmid = {32294545}, issn = {1095-9513}, mesh = {*Biodiversity ; Chlorophyta/anatomy &amp; histology/*classification/genetics/ultrastructure ; Genetic Loci ; Lichens/*classification/genetics/ultrastructure ; *Phylogeny ; Species Specificity ; }, abstract = {Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.}, }
@article {pmid32282951, year = {2020}, author = {Lin, D and Lacey, EA and Bach, BH and Bi, K and Conroy, CJ and Suvorov, A and Bowie, RCK}, title = {Gut microbial diversity across a contact zone for California voles: Implications for lineage divergence of hosts and mitonuclear mismatch in the assembly of the mammalian gut microbiome.}, journal = {Molecular ecology}, volume = {29}, number = {10}, pages = {1873-1889}, doi = {10.1111/mec.15443}, pmid = {32282951}, issn = {1365-294X}, mesh = {Animals ; Arvicolinae/*microbiology ; California ; *Gastrointestinal Microbiome/genetics ; Mammals ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbial diversity is thought to reflect the co-evolution of microbes and their hosts as well as current host-specific attributes such as genetic background and environmental setting. To explore interactions among these parameters, we characterized variation in gut microbiome composition of California voles (Microtus californicus) across a contact zone between two recently diverged lineages of this species. Because this contact zone contains individuals with mismatched mitochondrial-nuclear genomes (cybrids), it provides an important opportunity to explore how different components of the genotype contribute to gut microbial diversity. Analyses of bacterial 16S rRNA sequences and joint species distribution modelling revealed that host genotypes and genetic differentiation among host populations together explained more than 50% of microbial community variation across our sampling transect. The ranked importance (most to least) of factors contributing to gut microbial diversity in our study populations were: genome-wide population differentiation, local environmental conditions, and host genotypes. However, differences in microbial communities among vole populations (β-diversity) did not follow patterns of lineage divergence (i.e., phylosymbiosis). Instead, among-population variation was best explained by the spatial distribution of hosts, as expected if the environment is a primary source of gut microbial diversity (i.e., dispersal limitation hypothesis). Across the contact zone, several bacterial taxa differed in relative abundance between the two parental lineages as well as among individuals with mismatched mitochondrial and nuclear genomes. Thus, genetic divergence among host lineages and mitonuclear genomic mismatches may also contribute to microbial diversity by altering interactions between host genomes and gut microbiota (i.e., hologenome speciation hypothesis).}, }
@article {pmid32275303, year = {2020}, author = {Renoud, S and Bouffaud, ML and Dubost, A and Prigent-Combaret, C and Legendre, L and Moënne-Loccoz, Y and Muller, D}, title = {Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {5}, pages = {}, doi = {10.1093/femsec/fiaa062}, pmid = {32275303}, issn = {1574-6941}, mesh = {Deamination ; Nitrogen Fixation ; *Rhizosphere ; Soil Microbiology ; *Zea mays ; }, abstract = {The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.}, }
@article {pmid32275297, year = {2020}, author = {Simonin, M and Dasilva, C and Terzi, V and Ngonkeu, ELM and Diouf, D and Kane, A and Béna, G and Moulin, L}, title = {Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {6}, pages = {}, doi = {10.1093/femsec/fiaa067}, pmid = {32275297}, issn = {1574-6941}, mesh = {France ; Fungi ; Genotype ; Italy ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; }, abstract = {Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.}, }
@article {pmid32269559, year = {2020}, author = {Paix, B and Carriot, N and Barry-Martinet, R and Greff, S and Misson, B and Briand, JF and Culioli, G}, title = {A Multi-Omics Analysis Suggests Links Between the Differentiated Surface Metabolome and Epiphytic Microbiota Along the Thallus of a Mediterranean Seaweed Holobiont.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {494}, pmid = {32269559}, issn = {1664-302X}, abstract = {Marine macroalgae constitute an important living resource in marine ecosystems and complex ecological interactions occur at their surfaces with microbial communities. In this context, the present study aimed to investigate how the surface metabolome of the algal holobiont Taonia atomaria could drive epiphytic microbiota variations at the thallus scale. First, a clear discrimination was observed between algal surface, planktonic and rocky prokaryotic communities. These data strengthened the hypothesis of an active role of the algal host in the selection of epiphytic communities. Moreover, significant higher epibacterial density and α-diversity were found at the basal algal parts compared to the apical ones, suggesting a maturation gradient of the community along the thallus. In parallel, a multiplatform mass spectrometry-based metabolomics study, using molecular networking to annotate relevant metabolites, highlighted a clear chemical differentiation at the algal surface along the thallus with similar clustering as for microbial communities. In that respect, higher amounts of sesquiterpenes, phosphatidylcholines (PCs), and diacylglycerylhydroxymethyl-N,N,N-trimethyl-β-alanines (DGTAs) were observed at the apical regions while dimethylsulfoniopropionate (DMSP) and carotenoids were predominantly found at the basal parts of the thalli. A weighted UniFrac distance-based redundancy analysis linking the metabolomics and metabarcoding datasets indicated that these surface compounds, presumably of algal origin, may drive the zonal variability of the epibacterial communities. As only few studies were focused on microbiota and metabolome variation along a single algal thallus, these results improved our understanding about seaweed holobionts. Through this multi-omics approach at the thallus scale, we suggested a plausible scenario where the chemical production at the surface of T. atomaria, mainly induced by the algal physiology, could explain the specificity and the variations of the surface microbiota along the thallus.}, }
@article {pmid32266849, year = {2020}, author = {Boem, F and Nannini, G and Amedei, A}, title = {Not just 'immunity': how the microbiota can reshape our approach to cancer immunotherapy.}, journal = {Immunotherapy}, volume = {12}, number = {6}, pages = {407-416}, doi = {10.2217/imt-2019-0192}, pmid = {32266849}, issn = {1750-7448}, abstract = {Cancer immunotherapy refers to a set of approaches aiming at enhancing the immune system to fight cancer growth and spread. This variety of therapeutic approaches, especially those inhibiting immune checkpoints, have shown very promising results. Nevertheless, patients may respond differently to treatments and the efficacy of immunotherapy seems to be dependent on several factors that go beyond the molecular targeting of immune cells modulation. Here, we review how the activity of gut microbiota appears to be crucial in determining the effectiveness of some immunotherapeutic treatments, fostering or impeding the conditions under which treatments can work or not. Moreover, we discuss how these findings suggest not only extending the range of immunotherapeutic approaches but also reshaping our understanding of immunotherapy itself.}, }
@article {pmid32251879, year = {2020}, author = {Biagi, E and Caroselli, E and Barone, M and Pezzimenti, M and Teixido, N and Soverini, M and Rampelli, S and Turroni, S and Gambi, MC and Brigidi, P and Goffredo, S and Candela, M}, title = {Patterns in microbiome composition differ with ocean acidification in anatomic compartments of the Mediterranean coral Astroides calycularis living at CO2 vents.}, journal = {The Science of the total environment}, volume = {724}, number = {}, pages = {138048}, doi = {10.1016/j.scitotenv.2020.138048}, pmid = {32251879}, issn = {1879-1026}, mesh = {Animals ; *Anthozoa ; Carbon Dioxide ; Coral Reefs ; Hydrogen-Ion Concentration ; Italy ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Seawater ; }, abstract = {Coral microbiomes, the complex microbial communities associated with the different anatomic compartments of the coral, provide important functions for the host's survival, such as nutrient cycling at the host's surface, prevention of pathogens colonization, and promotion of nutrient uptake. Microbiomes are generally referred to as plastic entities, able to adapt their composition and functionality in response to environmental change, with a possible impact on coral acclimatization to phenomena related to climate change, such as ocean acidification. Ocean sites characterized by natural gradients of pCO2 provide models for investigating the ability of marine organisms to acclimatize to decreasing seawater pH. Here we compared the microbiome of the temperate, shallow water, non-symbiotic solitary coral Astroides calycularis that naturally lives at a volcanic CO2 vent in Ischia Island (Naples, Italy), with that of corals living in non-acidified sites at the same island. Bacterial DNA associated with the different anatomic compartments (mucus, tissue and skeleton) of A. calycularis was differentially extracted and a total of 68 samples were analyzed by 16S rRNA gene sequencing. In terms of phylogenetic composition, the microbiomes associated with the different coral anatomic compartments were different from each other and from the microbial communities of the surrounding seawater. Of all the anatomic compartments, the mucus-associated microbiome differed the most between the control and acidified sites. The differences detected in the microbial communities associated to the three anatomic compartments included a general increase in subdominant bacterial groups, some of which are known to be involved in different stages of the nitrogen cycle, such as potential nitrogen fixing bacteria and bacteria able to degrade organic nitrogen. Our data therefore suggests a potential increase of nitrogen fixation and recycling in A. calycularis living close to the CO2 vent system.}, }
@article {pmid32245478, year = {2020}, author = {Corona, G and Kreimes, A and Barone, M and Turroni, S and Brigidi, P and Keleszade, E and Costabile, A}, title = {Impact of lignans in oilseed mix on gut microbiome composition and enterolignan production in younger healthy and premenopausal women: an in vitro pilot study.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {82}, pmid = {32245478}, issn = {1475-2859}, mesh = {Case-Control Studies ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lignans/*chemistry ; Pilot Projects ; Plant Oils/*chemistry ; Premenopause ; }, abstract = {BACKGROUND: Dietary lignans belong to the group of phytoestrogens together with coumestans, stilbenes and isoflavones, and themselves do not exhibit oestrogen-like properties. Nonetheless, the gut microbiota converts them into enterolignans, which show chemical similarity to the human oestrogen molecule. One of the richest dietary sources of lignans are oilseeds, including flaxseed. The aim of this pilot study was to determine the concentration of the main dietary lignans in an oilseed mix, and explore the gut microbiota-dependent production of enterolignans for oestrogen substitution in young and premenopausal women. The oilseed mix was fermented in a pH-controlled batch culture system inoculated with women's faecal samples. The lignan content and enterolignan production were measured by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and the faecal-derived microbial communities were profiled by 16S rRNA gene-based next-generation sequencing.<br><br>RESULTS: In vitro batch culture fermentation of faecal samples inoculated with oilseed mix for 24 h resulted in a substantial increase in enterolactone production in younger women and an increase in enterodiol in the premenopausal group. As for the gut microbiota, different baseline profiles were observed as well as different temporal dynamics, mainly related to Clostridiaceae, and Klebsiella and Collinsella spp.<br><br>CONCLUSIONS: Despite the small sample size, our pilot study revealed that lignan-rich oilseeds could strongly influence the faecal microbiota of both younger and premenopausal females, leading to a different enterolignan profile being produced. Further studies in larger cohorts are needed to evaluate the long-term effects of lignan-rich diets on the gut microbiota and find out how enterolactone-producing bacterial species could be increased. Diets rich in lignans could potentially serve as a safe supplement of oestrogen analogues to meet the cellular needs of endogenous oestrogen and deliver numerous health benefits, provided that the premenopausal woman microbiota is capable of converting dietary precursors into enterolignans.}, }
@article {pmid32230931, year = {2020}, author = {Leitão, AL and Costa, MC and Gabriel, AF and Enguita, FJ}, title = {Interspecies Communication in Holobionts by Non-Coding RNA Exchange.}, journal = {International journal of molecular sciences}, volume = {21}, number = {7}, pages = {}, pmid = {32230931}, issn = {1422-0067}, mesh = {Animals ; Anthozoa/physiology ; Bacteria ; Bacterial Physiological Phenomena ; Cell Communication/*genetics/*physiology ; Dysbiosis ; Mammals ; Metagenome ; MicroRNAs ; Microbiota/physiology ; Plant Physiological Phenomena ; Plants ; RNA, Untranslated/*genetics/*metabolism ; *Signal Transduction ; Symbiosis/genetics/physiology ; Transcriptome ; }, abstract = {Complex organisms are associations of different cells that coexist and collaborate creating a living consortium, the holobiont. The relationships between the holobiont members are essential for proper homeostasis of the organisms, and they are founded on the establishment of complex inter-connections between all the cells. Non-coding RNAs are regulatory molecules that can also act as communication signals between cells, being involved in either homeostasis or dysbiosis of the holobionts. Eukaryotic and prokaryotic cells can transmit signals via non-coding RNAs while using specific extracellular conveyors that travel to the target cell and can be translated into a regulatory response by dedicated molecular machinery. Within holobionts, non-coding RNA regulatory signaling is involved in symbiotic and pathogenic relationships among the cells. This review analyzes current knowledge regarding the role of non-coding RNAs in cell-to-cell communication, with a special focus on the signaling between cells in multi-organism consortia.}, }
@article {pmid32209692, year = {2020}, author = {Storey, MA and Andreassend, SK and Bracegirdle, J and Brown, A and Keyzers, RA and Ackerley, DF and Northcote, PT and Owen, JG}, title = {Metagenomic Exploration of the Marine Sponge Mycale hentscheli Uncovers Multiple Polyketide-Producing Bacterial Symbionts.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32209692}, issn = {2150-7511}, mesh = {Animals ; Aquatic Organisms/microbiology ; Bacteria/*classification/isolation &amp; purification ; Biosynthetic Pathways ; Metabolome ; *Metagenomics ; Microbiota ; Multigene Family ; Phylogeny ; Polyketides/*metabolism ; Porifera/*microbiology ; Secondary Metabolism ; *Symbiosis ; }, abstract = {Marine sponges have been a prolific source of unique bioactive compounds that are presumed to act as a deterrent to predation. Many of these compounds have potential therapeutic applications; however, the lack of efficient and sustainable synthetic routes frequently limits clinical development. Here, we describe a metagenomic investigation of Mycale hentscheli, a chemically gifted marine sponge that possesses multiple distinct chemotypes. We applied shotgun metagenomic sequencing, hybrid assembly of short- and long-read data, and metagenomic binning to obtain a comprehensive picture of the microbiome of five specimens, spanning three chemotypes. Our data revealed multiple producing species, each having relatively modest secondary metabolomes, that contribute collectively to the chemical arsenal of the holobiont. We assembled complete genomes for multiple new genera, including two species that produce the cytotoxic polyketides pateamine and mycalamide, as well as a third high-abundance symbiont harboring a proteusin-type biosynthetic pathway that appears to encode a new polytheonamide-like compound. We also identified an additional 188 biosynthetic gene clusters, including a pathway for biosynthesis of peloruside. These results suggest that multiple species cooperatively contribute to defensive symbiosis in M. hentscheli and reveal that the taxonomic diversity of secondary-metabolite-producing sponge symbionts is larger and richer than previously recognized.IMPORTANCE Mycale hentscheli is a marine sponge that is rich in bioactive small molecules. Here, we use direct metagenomic sequencing to elucidate highly complete and contiguous genomes for the major symbiotic bacteria of this sponge. We identify complete biosynthetic pathways for the three potent cytotoxic polyketides which have previously been isolated from M. hentscheli Remarkably, and in contrast to previous studies of marine sponges, we attribute each of these metabolites to a different producing microbe. We also find that the microbiome of M. hentscheli is stably maintained among individuals, even over long periods of time. Collectively, our data suggest a cooperative mode of defensive symbiosis in which multiple symbiotic bacterial species cooperatively contribute to the defensive chemical arsenal of the holobiont.}, }
@article {pmid32208346, year = {2020}, author = {Vanwonterghem, I and Webster, NS}, title = {Coral Reef Microorganisms in a Changing Climate.}, journal = {iScience}, volume = {23}, number = {4}, pages = {100972}, pmid = {32208346}, issn = {2589-0042}, abstract = {Coral reefs are one of the most diverse and productive ecosystems on the planet, yet they have suffered tremendous losses due to anthropogenic disturbances and are predicted to be one of the most adversely affected habitats under future climate change conditions. Coral reefs can be viewed as microbially driven ecosystems that rely on the efficient capture, retention, and recycling of nutrients in order to thrive in oligotrophic waters. Microorganisms play vital roles in maintaining holobiont health and ecosystem resilience under environmental stress; however, they are also key players in positive feedback loops that intensify coral reef decline, with cascading effects on biogeochemical cycles and marine food webs. There is an urgent need to develop a fundamental understanding of the complex microbial interactions within coral reefs and their role in ecosystem acclimatization, and it is important to include microorganisms in reef conservation in order to secure a future for these unique environments.}, }
@article {pmid32194470, year = {2020}, author = {Suárez, J and Triviño, V}, title = {What Is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems.}, journal = {Frontiers in psychology}, volume = {11}, number = {}, pages = {187}, pmid = {32194470}, issn = {1664-1078}, abstract = {Contemporary biological research has suggested that some host-microbiome multispecies systems (referred to as "holobionts") can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology.}, }
@article {pmid32190114, year = {2020}, author = {Bredon, M and Herran, B and Bertaux, J and Grève, P and Moumen, B and Bouchon, D}, title = {Isopod holobionts as promising models for lignocellulose degradation.}, journal = {Biotechnology for biofuels}, volume = {13}, number = {}, pages = {49}, pmid = {32190114}, issn = {1754-6834}, abstract = {BACKGROUND: Isopods have colonized all environments, partly thanks to their ability to decompose the organic matter. Their enzymatic repertoire, as well as the one of their associated microbiota, has contributed to their colonization success. Together, these holobionts have evolved several interesting life history traits to degrade the plant cell walls, mainly composed of lignocellulose. It has been shown that terrestrial isopods achieve lignocellulose degradation thanks to numerous and diverse CAZymes provided by both the host and its microbiota. Nevertheless, the strategies for lignocellulose degradation seem more diversified in isopods, in particular in aquatic species which are the least studied. Isopods could be an interesting source of valuable enzymes for biotechnological industries of biomass conversion.<br><br>RESULTS: To provide new features on the lignocellulose degradation in isopod holobionts, shotgun sequencing of 36 metagenomes of digestive and non-digestive tissues was performed from several populations of four aquatic and terrestrial isopod species. Combined to the 15 metagenomes of an additional species from our previous study, as well as the host transcriptomes, this large dataset allowed us to identify the CAZymes in both the host and the associated microbial communities. Analyses revealed the dominance of Bacteroidetes and Proteobacteria in the five species, covering 36% and 56% of the total bacterial community, respectively. The identification of CAZymes and new enzymatic systems for lignocellulose degradation, such as PULs, cellulosomes and LPMOs, highlights the richness of the strategies used by the isopods and their associated microbiota.<br><br>CONCLUSIONS: Altogether, our results show that the isopod holobionts are promising models to study lignocellulose degradation. These models can provide new enzymes and relevant lignocellulose-degrading bacteria strains for the biotechnological industries of biomass conversion.}, }
@article {pmid32181589, year = {2020}, author = {Gaona, O and Cerqueda-García, D and Moya, A and Neri-Barrios, X and Falcón, LI}, title = {Geographical separation and physiology drive differentiation of microbial communities of two discrete populations of the bat Leptonycteris yerbabuenae.}, journal = {MicrobiologyOpen}, volume = {9}, number = {6}, pages = {1113-1127}, pmid = {32181589}, issn = {2045-8827}, mesh = {Animals ; Bacteria/*classification/*genetics/isolation &amp; purification ; Chiroptera/*microbiology ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Genetic Variation/genetics ; Geography ; High-Throughput Nucleotide Sequencing ; Lactation ; Mexico ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Social Isolation ; }, abstract = {In this paper, we explore how two discrete and geographically separated populations of the lesser long-nosed bat (Leptonycteris yerbabuenae)-one in central and the other in the Pacific region of Mexico-differ in their fecal microbiota composition. Considering the microbiota-host as a unity, in which extrinsic (as food availability and geography) or intrinsic factors (as physiology) play an important role in the microbiota composition, we would expect differentiation in the microbiota of two geographically separated populations. The Amplicon Sequences Variants (ASVs) of the V4 region of the 16s rRNA gene from 68 individuals were analyzed using alpha and beta diversity metrics. We obtained a total of 11 566 (ASVs). The bacterial communities in the Central and Pacific populations had a diversity of 6,939 and 4,088 ASVs, respectively, sharing a core microbiota of 539 ASVs accounting for 75% of the relative abundance, suggesting stability over evolutionary time. The Weighted UniFrac metrics tested by a PERMANOVA showed that lactating and pregnant females had significant beta diversity differences in the two populations compared with other reproductive stages. This could be a consequence of the increased energy requirements of these physiological stages, more than the variation due to geographical separation. In contrast, a positive correlation of the observed ASVs of fecal microbiota with the observed ASVs of plastids related to the diet was observed in the juveniles and adults, suggesting that in these physiological stages an extrinsic factor as the diet shapes the microbiota composition. The results provide a baseline for future studies of the microbiome in these two wild populations of the lesser long-nosed bat, the main pollinator of the Agaves from which the beverages tequila and mezcal are made.}, }
@article {pmid32174904, year = {2020}, author = {Clerissi, C and de Lorgeril, J and Petton, B and Lucasson, A and Escoubas, JM and Gueguen, Y and Dégremont, L and Mitta, G and Toulza, E}, title = {Microbiota Composition and Evenness Predict Survival Rate of Oysters Confronted to Pacific Oyster Mortality Syndrome.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {311}, pmid = {32174904}, issn = {1664-302X}, abstract = {Pacific Oyster Mortality Syndrome (POMS) affects Crassostrea gigas oysters worldwide and causes important economic losses. Disease dynamic was recently deciphered and revealed a multiple and progressive infection caused by the Ostreid herpesvirus OsHV-1 μVar, triggering an immunosuppression followed by microbiota destabilization and bacteraemia by opportunistic bacterial pathogens. However, it remains unknown if microbiota might participate to protect oysters against POMS, and if microbiota characteristics might be predictive of oyster mortalities. To tackle this issue, we transferred full-sib progenies of resistant and susceptible oyster families from hatchery to the field during a period in favor of POMS. After 5 days of transplantation, oysters from each family were either sampled for individual microbiota analyses using 16S rRNA gene-metabarcoding or transferred into facilities to record their survival using controlled condition. As expected, all oysters from susceptible families died, and all oysters from the resistant family survived. Quantification of OsHV-1 and bacteria showed that 5 days of transplantation were long enough to contaminate oysters by POMS, but not for entering the pathogenesis process. Thus, it was possible to compare microbiota characteristics between resistant and susceptible oysters families at the early steps of infection. Strikingly, we found that microbiota evenness and abundances of Cyanobacteria (Subsection III, family I), Mycoplasmataceae, Rhodobacteraceae, and Rhodospirillaceae were significantly different between resistant and susceptible oyster families. We concluded that these microbiota characteristics might predict oyster mortalities.}, }
@article {pmid32167987, year = {2020}, author = {Donovan, SM}, title = {Evolution of the gut microbiome in infancy within an ecological context.}, journal = {Current opinion in clinical nutrition and metabolic care}, volume = {23}, number = {3}, pages = {223-227}, pmid = {32167987}, issn = {1473-6519}, support = {R01 DK107561/DK/NIDDK NIH HHS/United States ; }, mesh = {Ecological and Environmental Phenomena/*physiology ; Feeding Behavior/*physiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Male ; Pregnancy ; *Prenatal Nutritional Physiological Phenomena ; }, abstract = {PURPOSE OF REVIEW: Humans and their commensal microbiota coexist in a complex ecosystem molded by evolutionary and ecological factors. Ecological opportunity is the prospective, lineage-specific characteristic of an environment that contains both niche availability leading to persistence coupled with niche discordance that drives selection within that lineage. The newborn gut ecosystem presents vast ecological opportunity. Herein, factors affecting perinatal infant microbiome composition are discussed.<br><br>RECENT FINDINGS: Establishing a healthy microbiota in early life is required for immunological programming and prevention of both short-term and long-term health outcomes. The holobiont theory infers that host genetics contributes to microbiome composition. However, in most human studies, environmental factors are predominantly responsible for microbiome composition and function. Key perinatal elements are route of delivery, diet and the environment in which that infant resides. Vaginal delivery seeds an initial microbiome, and breastfeeding refines the community by providing additional microbes, human milk oligosaccharides and immunological proteins.<br><br>SUMMARY: Early life represents an opportunity to implement clinical practices that promote the optimal seeding and feeding of the gut microbial ecosystem. These include reducing nonemergent cesarean deliveries, avoiding the use of antibiotics, and promoting exclusive breastfeeding.}, }
@article {pmid32155796, year = {2020}, author = {Meron, D and Maor-Landaw, K and Eyal, G and Elifantz, H and Banin, E and Loya, Y and Levy, O}, title = {The Complexity of the Holobiont in the Red Sea Coral Euphyllia paradivisa under Heat Stress.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, pmid = {32155796}, issn = {2076-2607}, abstract = {The recognition of the microbiota complexity and their role in the evolution of their host is leading to the popularization of the holobiont concept. However, the coral holobiont (host and its microbiota) is still enigmatic and unclear. Here, we explore the complex relations between different holobiont members of a mesophotic coral Euphyllia paradivisa. We subjected two lines of the coral-with photosymbionts, and without photosymbionts (apo-symbiotic)-to increasing temperatures and to antibiotics. The different symbiotic states were characterized using transcriptomics, microbiology and physiology techniques. The bacterial community's composition is dominated by bacteroidetes, alphaproteobacteria, and gammaproteobacteria, but is dependent upon the symbiont state, colony, temperature treatment, and antibiotic exposure. Overall, the most important parameter determining the response was whether the coral was a symbiont/apo-symbiotic, while the colony and bacterial composition were secondary factors. Enrichment Gene Ontology analysis of coral host's differentially expressed genes demonstrated the cellular differences between symbiotic and apo-symbiotic samples. Our results demonstrate the significance of each component of the holobiont consortium and imply a coherent link between them, which dramatically impacts the molecular and cellular processes of the coral host, which possibly affect its fitness, particularly under environmental stress.}, }
@article {pmid32146404, year = {2020}, author = {Robinson, JM and Breed, MF}, title = {The Lovebug Effect: Is the human biophilic drive influenced by interactions between the host, the environment, and the microbiome?.}, journal = {The Science of the total environment}, volume = {720}, number = {}, pages = {137626}, doi = {10.1016/j.scitotenv.2020.137626}, pmid = {32146404}, issn = {1879-1026}, mesh = {Brain ; Humans ; *Microbiota ; }, abstract = {Psychological frameworks are often used to investigate the mechanisms involved with our affinity towards, and connection with nature--such as the Biophilia Hypothesis and Nature Connectedness. Recent revelations from microbiome science suggest that animal behaviour can be strongly influenced by the host's microbiome--for example, via the bidirectional communication properties of the gut-brain axis. Here, we build on this theory to hypothesise that a microbially-influenced mechanism could also contribute to the human biophilic drive - the tendency for humans to affiliate and connect with nature. Humans may be at an evolutionary advantage through health-regulating exchange of environmental microbiota, which in turn could influence our nature affinity. We present a conceptual model for microbially-influenced nature affinity, calling it the Lovebug Effect. We present an overview of the potential mechanistic pathways involved in the Lovebug Effect, and consider its dependence on the hologenome concept of evolution, direct behavioural manipulation, and host-microbiota associated phenotypes independent of these concepts. We also discuss its implications for human health and ecological resilience. Finally, we highlight several possible approaches to scrutinise the hypothesis. The Lovebug Effect could have important implications for our understanding of exposure to natural environments for health and wellbeing, and could contribute to an ecologically resilient future.}, }
@article {pmid32132275, year = {2020}, author = {Gignoux-Wolfsohn, SA and Precht, WF and Peters, EC and Gintert, BE and Kaufman, LS}, title = {Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis.}, journal = {Diseases of aquatic organisms}, volume = {137}, number = {3}, pages = {217-237}, doi = {10.3354/dao03441}, pmid = {32132275}, issn = {0177-5103}, mesh = {Animals ; *Anthozoa ; Bacteria ; Coral Reefs ; Disease Outbreaks ; Ecosystem ; Florida ; }, abstract = {This study is a multi-pronged description of a temperature-induced outbreak of white-band disease (WBD) that occurred in Acropora cervicornis off northern Miami Beach, Florida (USA), from July to October 2014. We describe the ecology of the disease and examine diseased corals using both histopathology and next-generation bacterial 16S gene sequencing, making it possible to better understand the effect this disease has on the coral holobiont, and to address some of the seeming contradictions among previous studies of WBD that employed either a purely histological or molecular approach. The outbreak began in July 2014, as sea surface temperatures reached 29°C, and peaked in mid-September, a month after the sea surface temperature maximum. The microscopic anatomy of apparently healthy portions of colonies displaying active disease signs appeared normal except for some tissue atrophy and dissociation of mesenterial filaments deep within the branch. Structural changes were more pronounced in visibly diseased fragments, with atrophy, necrosis, and lysing of surface and basal body wall and polyp structures at the tissue-loss margin. The only bacteria evident microscopically in both diseased and apparently healthy tissues with Giemsa staining was a Rickettsiales-like organism (RLO) occupying mucocytes. Sequencing also identified bacteria belonging to the order Rickettsiales in all fragments. When compared to apparently healthy fragments, diseased fragments had more diverse bacterial communities made up of many previously suggested potential primary pathogens and secondary (opportunistic) colonizers. Interactions between elevated seawater temperatures, the coral host, and pathogenic members of the diseased microbiome all contribute to the coral displaying signs of WBD.}, }
@article {pmid32130695, year = {2020}, author = {Baffy, G}, title = {Gut Microbiota and Cancer of the Host: Colliding Interests.}, journal = {Advances in experimental medicine and biology}, volume = {1219}, number = {}, pages = {93-107}, doi = {10.1007/978-3-030-34025-4_5}, pmid = {32130695}, issn = {0065-2598}, mesh = {Dysbiosis ; Gastrointestinal Microbiome/immunology/*physiology ; Humans ; Intestines/immunology/microbiology ; Neoplasms/immunology/*metabolism/therapy ; Tumor Microenvironment ; }, abstract = {Cancer develops in multicellular organisms from cells that ignore the rules of cooperation and escape the mechanisms of anti-cancer surveillance. Tumorigenesis is jointly encountered by the host and microbiota, a vast collection of microorganisms that live on the external and internal epithelial surfaces of the body. The largest community of human microbiota resides in the gastrointestinal tract where commensal, symbiotic and pathogenic microorganisms interact with the intestinal barrier and gut mucosal lymphoid tissue, creating a tumor microenvironment in which cancer cells thrive or perish. Aberrant composition and function of the gut microbiota (dysbiosis) has been associated with tumorigenesis by inducing inflammation, promoting cell growth and proliferation, weakening immunosurveillance, and altering food and drug metabolism or other biochemical functions of the host. However, recent research has also identified several mechanisms through which gut microbiota support the host in the fight against cancer. These mechanisms include the use of antigenic mimicry, biotransformation of chemotherapeutic agents, and other mechanisms to boost anti-cancer immune responses and improve the efficacy of cancer immunotherapy. Further research in this rapidly advancing field is expected to identify additional microbial metabolites with tumor suppressing properties, map the complex interactions of host-microbe 'transkingdom network' with cancer cells, and elucidate cellular and molecular pathways underlying the impact of specific intestinal microbial configurations on immune checkpoint inhibitor therapy.}, }
@article {pmid32127450, year = {2020}, author = {Lima, LFO and Weissman, M and Reed, M and Papudeshi, B and Alker, AT and Morris, MM and Edwards, RA and de Putron, SJ and Vaidya, NK and Dinsdale, EA}, title = {Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network.}, journal = {mBio}, volume = {11}, number = {2}, pages = {}, pmid = {32127450}, issn = {2150-7511}, mesh = {Animals ; Anthozoa/*microbiology ; Bermuda ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Models, Theoretical ; Mucus/microbiology ; *Temperature ; }, abstract = {Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.}, }
@article {pmid32126507, year = {2020}, author = {Yin, J and Yu, Y and Zhang, Z and Chen, L and Ruan, L}, title = {Enrichment of potentially beneficial bacteria from the consistent microbial community confers canker resistance on tomato.}, journal = {Microbiological research}, volume = {234}, number = {}, pages = {126446}, doi = {10.1016/j.micres.2020.126446}, pmid = {32126507}, issn = {1618-0623}, abstract = {The soil microbiota interacts with plants closely and exerts strong influences on plant health and productivity. However, the relationship between the microbiota and the bacterial canker of tomato that is caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is still unclear. In order to establish causal relationship between the microbiota and plant phenotypes, the microbial communities of 49 tomato samples (including 15 cultivars) with different canker symptoms collected from the greenhouse in Gansu province, China were investigated via 16S ribosomal RNA sequencing. Roots exhibited a strong filter effect in the process of root colonization by microorganisms according to the α-diversity and the separation patterns of the microbiota in bulk soil, rhizosphere and endosphere. In addition, the gradually decreased cluster extent from bulk soil to endosphere indicating the selective effect of tomato on microbiota. Although the composition of the microbiota is similar, the potential beneficial bacteria and functions (e.g. antibiotics production, pollution degradation, nutrition acquisition) enriched in the rhizosphere and endosphere of healthy samples compared to those in the diseased ones. Furthermore, more robust networks occurred in the rhizosphere and endosphere of healthy samples compared to the diseased ones. Our research provided substantial evidence that although the plant genotype is the dominant factor of phenotype, the rhizosphere and endosphere microbiota, as part of phytobiomes or holobiont, could contribute to the host's phenotype. This causal relationship between microbiota and host phenotypes could guide us in rationally designing novel synthetic communities (SynComs) for tomato canker biocontrol in the near future.}, }
@article {pmid32123705, year = {2020}, author = {Butina, TV and Khanaev, IV and Kravtsova, LS and Maikova, OO and Bukin, YS}, title = {Metavirome datasets from two endemic Baikal sponges Baikalospongia bacillifera.}, journal = {Data in brief}, volume = {29}, number = {}, pages = {105260}, pmid = {32123705}, issn = {2352-3409}, abstract = {Sponges are ecologically important components of marine and freshwater benthic environments; these holobionts contain a variety of microorganisms and viruses. For the metagenomic characterization of potential taxonomic and functional diversity of sponge-associated dsDNA viruses, we surveyed two samples of Baikal endemic sponge Baikalospongia bacillifera (diseased and visually healthy). In total, after quality processing, we have obtained 3 375 063 and 4 063 311 reads; of these 97 557 and 88 517 sequences, accounting for ca. 2.9 and 2.2% of datasets, have been identified as viral. We have revealed approximately 28 viral families, among which the bacteriophages of the Myoviridae, Siphoviridae and Podoviridae families, as well as the viruses of the Phycodnaviridae and Poxviridae families, dominated in the samples. Analysis of viral sequences using the COG database has indicated 22 functional categories of proteins. Viral communities of visually healthy and diseased Baikal sponges were significantly different. The metagenome sequence data were deposited to NCBI SRA as BioProject PRJNA577390.}, }
@article {pmid32123297, year = {2020}, author = {Glasl, B and Robbins, S and Frade, PR and Marangon, E and Laffy, PW and Bourne, DG and Webster, NS}, title = {Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes.}, journal = {The ISME journal}, volume = {14}, number = {6}, pages = {1435-1450}, pmid = {32123297}, issn = {1751-7370}, mesh = {Animals ; Archaea/genetics ; Bacteria/classification/*genetics/isolation &amp; purification ; Biomass ; Coral Reefs ; Metagenome ; *Microbiota ; Porifera/*microbiology ; Seasons ; Seawater/microbiology ; Seaweed/classification/*genetics ; }, abstract = {Microbially mediated processes contribute to coral reef resilience yet, despite extensive characterisation of microbial community variation following environmental perturbation, the effect on microbiome function is poorly understood. We undertook metagenomic sequencing of sponge, macroalgae and seawater microbiomes from a macroalgae-dominated inshore coral reef to define their functional potential and evaluate seasonal shifts in microbially mediated processes. In total, 125 high-quality metagenome-assembled genomes were reconstructed, spanning 15 bacterial and 3 archaeal phyla. Multivariate analysis of the genomes relative abundance revealed changes in the functional potential of reef microbiomes in relation to seasonal environmental fluctuations (e.g. macroalgae biomass, temperature). For example, a shift from Alphaproteobacteria to Bacteroidota-dominated seawater microbiomes occurred during summer, resulting in an increased genomic potential to degrade macroalgal-derived polysaccharides. An 85% reduction of Chloroflexota was observed in the sponge microbiome during summer, with potential consequences for nutrition, waste product removal, and detoxification in the sponge holobiont. A shift in the Firmicutes:Bacteroidota ratio was detected on macroalgae over summer with potential implications for polysaccharide degradation in macroalgal microbiomes. These results highlight that seasonal shifts in the dominant microbial taxa alter the functional repertoire of host-associated and seawater microbiomes, and highlight how environmental perturbation can affect microbially mediated processes in coral reef ecosystems.}, }
@article {pmid32117798, year = {2020}, author = {Jablaoui, A and Kriaa, A and Mkaouar, H and Akermi, N and Soussou, S and Wysocka, M and Wołoszyn, D and Amouri, A and Gargouri, A and Maguin, E and Lesner, A and Rhimi, M}, title = {Fecal Serine Protease Profiling in Inflammatory Bowel Diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {21}, pmid = {32117798}, issn = {2235-2988}, mesh = {Feces ; Humans ; *Inflammatory Bowel Diseases ; Pancreatic Elastase ; *Serine Proteases ; }, abstract = {Serine proteases are extensively known to play key roles in many physiological processes. However, their dysregulation is often associated to several diseases including inflammatory bowel diseases (IBD). Here, we used specific substrates to monitor fecal protease activities in a large cohort of healthy and IBD patients. Of interest, serine protease activity was 10-fold higher in IBD fecal samples compared to healthy controls. Moreover, functional analysis of these fecal proteolytic activities revealed that the most increased activities are trypsin-like, elastase-like and cathepsin G-like. We also show for the first time, an increase of proteinase 3-like activity in these samples compared to controls. Results presented here will guide further investigations to better understand the relevance of these peptidases in IBD.}, }
@article {pmid32115438, year = {2020}, author = {Urayama, SI and Takaki, Y and Hagiwara, D and Nunoura, T}, title = {dsRNA-seq Reveals Novel RNA Virus and Virus-Like Putative Complete Genome Sequences from Hymeniacidon sp. Sponge.}, journal = {Microbes and environments}, volume = {35}, number = {2}, pages = {}, pmid = {32115438}, issn = {1347-4405}, mesh = {Animals ; Aquatic Organisms/virology ; *Genome, Viral ; Phylogeny ; Porifera/*virology ; RNA Viruses/*classification/isolation &amp; purification ; RNA, Double-Stranded/*genetics ; RNA, Viral/genetics ; RNA-Seq ; Sequence Analysis, DNA ; }, abstract = {Invertebrates are a source of previously unknown RNA viruses that fill gaps in the viral phylogenetic tree. Although limited information is currently available on RNA viral diversity in the marine sponge, a primordial multicellular animal that belongs to the phylum Porifera, the marine sponge is one of the well-studied holobiont systems. In the present study, we elucidated the putative complete genome sequences of five novel RNA viruses from Hymeniacidon sponge using a combination of double-stranded RNA sequencing, called fragmented and primer ligated dsRNA sequencing, and a conventional transcriptome method targeting single-stranded RNA. We identified highly diverged RNA-dependent RNA polymerase sequences, including a potential novel RNA viral lineage, in the sponge and three viruses presumed to infect sponge cells.}, }
@article {pmid32108224, year = {2020}, author = {Shoguchi, E and Yoshioka, Y and Shinzato, C and Arimoto, A and Bhattacharya, D and Satoh, N}, title = {Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera.}, journal = {Genome biology and evolution}, volume = {12}, number = {3}, pages = {203-209}, pmid = {32108224}, issn = {1759-6653}, mesh = {Animals ; *Anthozoa ; Dinoflagellida/*genetics ; Genes, Mitochondrial ; *Genome, Mitochondrial ; *Genome, Plastid ; Polymorphism, Single Nucleotide ; *RNA Editing ; }, abstract = {In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.}, }
@article {pmid32103386, year = {2020}, author = {Suárez, J}, title = {The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality.}, journal = {History and philosophy of the life sciences}, volume = {42}, number = {1}, pages = {11}, doi = {10.1007/s40656-020-00305-2}, pmid = {32103386}, issn = {1742-6316}, support = {FFU16/02570//Spanish Ministry of Education/ ; FFI2016-76799-P//Ministerio de Economía y Competitividad/ ; Bursary//Royal Institute of Philosophy/ ; }, mesh = {*Genome, Human ; Humans ; *Individuality ; *Phenotype ; }, abstract = {Bourrat and Griffiths (Hist Philos Life Sci 40(2):33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that allows divorcing true multispecies evolutionary individuals from other multispecies assemblages and provides an adequate criterion to single out genuine evolutionary multispecies assemblages. A consequence of their criterion is that holobionts, as conventionally defined by hologenome defenders, are not evolutionary individuals except in very rare cases, and for very specific host-symbiont associations. This paper is a critical response to Bourrat and Griffiths' arguments and a defence of the arguments presented by holobiont defenders. Drawing upon the case of the hologenomic basis of the evolution of sanguivory in vampire bats (Nat Ecol Evol 2:659-668, 2018), I argue that Bourrat and Griffiths overlook some aspects of the biological nature of the microbiome that justifies the thesis that holobionts are evolutionarily different to other multispecies assemblages. I argue that the hologenome theory of evolution should not define the hologenome as a collection of genomes, but as the sum of the host genome plus some traits of the microbiome which together constitute an evolutionary individual, a conception I refer to as the stability of traits conception of the hologenome. Based on that conception I argue that the evidence presented by holobiont defenders is to the point, and supports the thesis that holobionts are evolutionary individuals. In this sense, the paper offers an account of the holobiont that aims to foster a dialogue between hologenome advocates and hologenome critics.}, }
@article {pmid32097591, year = {2020}, author = {Greyson-Gaito, CJ and Bartley, TJ and Cottenie, K and Jarvis, WMC and Newman, AEM and Stothart, MR}, title = {Into the wild: microbiome transplant studies need broader ecological reality.}, journal = {Proceedings. Biological sciences}, volume = {287}, number = {1921}, pages = {20192834}, pmid = {32097591}, issn = {1471-2954}, mesh = {Ecology ; Gastrointestinal Microbiome ; *Microbiota ; *Symbiosis ; }, abstract = {Gut microbial communities (microbiomes) profoundly shape the ecology and evolution of multicellular life. Interactions between host and microbiome appear to be reciprocal, and ecological theory is now being applied to better understand how hosts and their microbiome influence each other. However, some ecological processes that underlie reciprocal host-microbiome interactions may be obscured by the current convention of highly controlled transplantation experiments. Although these approaches have yielded invaluable insights, there is a need for a broader array of approaches to fully understand host-microbiome reciprocity. Using a directed review, we surveyed the breadth of ecological reality in the current literature on gut microbiome transplants with non-human recipients. For 55 studies, we categorized nine key experimental conditions that impact the ecological reality (EcoReality) of the transplant, including host taxon match and donor environment. Using these categories, we rated the EcoReality of each transplant. Encouragingly, the breadth of EcoReality has increased over time, but some components of EcoReality are still relatively unexplored, including recipient host environment and microbiome state. The conceptual framework we develop here maps the landscape of possible EcoReality to highlight where fundamental ecological processes can be considered in future transplant experiments.}, }
@article {pmid32093216, year = {2020}, author = {Saurav, K and Borbone, N and Burgsdorf, I and Teta, R and Caso, A and Bar-Shalom, R and Esposito, G and Britstein, M and Steindler, L and Costantino, V}, title = {Identification of Quorum Sensing Activators and Inhibitors in The Marine Sponge Sarcotragus spinosulus.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32093216}, issn = {1660-3397}, support = {1243/16//Israel Science Foundation/ ; B61G18000470007//Regione Campania/ ; 2015-2018//Planning and Budgeting Committee of the Council for Higher Education of Israel/ ; }, mesh = {Animals ; Escherichia coli/*drug effects/physiology ; Luminescent Measurements ; Peptide Hydrolases/chemistry/pharmacology ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; Pyocyanine/chemistry/pharmacology ; Quorum Sensing/*drug effects ; Virulence Factors ; }, abstract = {Marine sponges, a well-documented prolific source of natural products, harbor highly diverse microbial communities. Their extracts were previously shown to contain quorum sensing (QS) signal molecules of the N-acyl homoserine lactone (AHL) type, known to orchestrate bacterial gene regulation. Some bacteria and eukaryotic organisms are known to produce molecules that can interfere with QS signaling, thus affecting microbial genetic regulation and function. In the present study, we established the production of both QS signal molecules as well as QS inhibitory (QSI) molecules in the sponge species Sarcotragus spinosulus. A total of eighteen saturated acyl chain AHLs were identified along with six unsaturated acyl chain AHLs. Bioassay-guided purification led to the isolation of two brominated metabolites with QSI activity. The structures of these compounds were elucidated by comparative spectral analysis of 1HNMR and HR-MS data and were identified as 3-bromo-4-methoxyphenethylamine (1) and 5,6-dibromo-N,N-dimethyltryptamine (2). The QSI activity of compounds 1 and 2 was evaluated using reporter gene assays for long- and short-chain AHL signals (Escherichia coli pSB1075 and E. coli pSB401, respectively). QSI activity was further confirmed by measuring dose-dependent inhibition of proteolytic activity and pyocyanin production in Pseudomonas aeruginosa PAO1. The obtained results show the coexistence of QS and QSI in S. spinosulus, a complex signal network that may mediate the orchestrated function of the microbiome within the sponge holobiont.}, }
@article {pmid32092934, year = {2020}, author = {Mohanty, I and Podell, S and Biggs, JS and Garg, N and Allen, EE and Agarwal, V}, title = {Multi-Omic Profiling of Melophlus Sponges Reveals Diverse Metabolomic and Microbiome Architectures that Are Non-overlapping with Ecological Neighbors.}, journal = {Marine drugs}, volume = {18}, number = {2}, pages = {}, pmid = {32092934}, issn = {1660-3397}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; R01-ES030316/NH/NIH HHS/United States ; R00-ES026620/NH/NIH HHS/United States ; OCE-1837116//National Science Foundation/ ; }, mesh = {Animals ; *Ecosystem ; *Metabolomics ; *Microbiota ; Phylogeny ; Porifera/genetics/*metabolism/*microbiology ; }, abstract = {Marine sponge holobionts, defined as filter-feeding sponge hosts together with their associated microbiomes, are prolific sources of natural products. The inventory of natural products that have been isolated from marine sponges is extensive. Here, using untargeted mass spectrometry, we demonstrate that sponges harbor a far greater diversity of low-abundance natural products that have evaded discovery. While these low-abundance natural products may not be feasible to isolate, insights into their chemical structures can be gleaned by careful curation of mass fragmentation spectra. Sponges are also some of the most complex, multi-organismal holobiont communities in the oceans. We overlay sponge metabolomes with their microbiome structures and detailed metagenomic characterization to discover candidate gene clusters that encode production of sponge-derived natural products. The multi-omic profiling strategy for sponges that we describe here enables quantitative comparison of sponge metabolomes and microbiomes to address, among other questions, the ecological relevance of sponge natural products and for the phylochemical assignment of previously undescribed sponge identities.}, }
@article {pmid32084687, year = {2020}, author = {Musella, M and Wathsala, R and Tavella, T and Rampelli, S and Barone, M and Palladino, G and Biagi, E and Brigidi, P and Turroni, S and Franzellitti, S and Candela, M}, title = {Tissue-scale microbiota of the Mediterranean mussel (Mytilus galloprovincialis) and its relationship with the environment.}, journal = {The Science of the total environment}, volume = {717}, number = {}, pages = {137209}, doi = {10.1016/j.scitotenv.2020.137209}, pmid = {32084687}, issn = {1879-1026}, mesh = {Animals ; Gills ; Hemolymph ; *Microbiota ; *Mytilus ; Seafood ; }, abstract = {In this study, we characterize the structural variation of the microbiota of Mytilus galloprovincialis at the tissue scale, also exploring the connection with the microbial ecosystem of the surrounding water. Mussels were sampled within a farm located in the North-Western Adriatic Sea and microbiota composition was analyzed in gills, hemolymph, digestive glands, stomach and foot by Next Generation Sequencing marker gene approach. Mussels showed a distinctive microbiota structure, with specific declinations at the tissue level. Indeed, each tissue is characterized by a distinct pattern of dominant families, reflecting a peculiar adaptation to the respective tissue niche. For instance, the microbiota of the digestive gland is characterized by Ruminococcaceae and Lachnospiraceae, being shaped to ferment complex polysaccharides of dietary origin into short-chain fatty acids, well matching the general asset of the animal gut microbiota. Conversely, the gill and hemolymph ecosystems are dominated by marine microorganisms with aerobic oxidative metabolism, consistent with the role played by these tissues as an interface with the external environment. Our findings highlight the putative importance of mussel microbiota for different aspects of host physiology, with ultimate repercussions on mussel health and productivity.}, }
@article {pmid32075325, year = {2020}, author = {Lewandowska, M and Hazan, Y and Moran, Y}, title = {Initial Virome Characterization of the Common Cnidarian Lab Model Nematostella vectensis.}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, pmid = {32075325}, issn = {1999-4915}, mesh = {Animals ; Female ; Life Cycle Stages ; Phylogeny ; RNA-Seq ; Sea Anemones/*virology ; *Transcriptome ; Viral Load ; *Virome ; Viruses/*classification ; }, abstract = {The role of viruses in forming a stable holobiont has been the subject of extensive research in recent years. However, many emerging model organisms still lack any data on the composition of the associated viral communities. Here, we re-analyzed seven publicly available transcriptome datasets of the starlet sea anemone Nematostella vectensis, the most commonly used anthozoan lab model, and searched for viral sequences. We applied a straightforward, yet powerful approach of de novo assembly followed by homology-based virus identification and a multi-step, thorough taxonomic validation. The comparison of different lab populations of N. vectensis revealed the existence of the core virome composed of 21 viral sequences, present in all adult datasets. Unexpectedly, we observed an almost complete lack of viruses in the samples from the early developmental stages, which together with the identification of the viruses shared with the major source of the food in the lab, the brine shrimp Artemia salina, shed new light on the course of viral species acquisition in N. vectensis. Our study provides an initial, yet comprehensive insight into N. vectensis virome and sets the first foundation for the functional studies of viruses and antiviral systems in this lab model cnidarian.}, }
@article {pmid32051527, year = {2020}, author = {Miyazaki, J and Ikuta, T and Watsuji, TO and Abe, M and Yamamoto, M and Nakagawa, S and Takaki, Y and Nakamura, K and Takai, K}, title = {Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica.}, journal = {The ISME journal}, volume = {14}, number = {5}, pages = {1273-1289}, pmid = {32051527}, issn = {1751-7370}, mesh = {Animals ; Bacteria/genetics ; Campylobacter/*physiology ; Energy Metabolism ; Gills/microbiology ; In Situ Hybridization, Fluorescence ; Indian Ocean ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Snails/*microbiology/physiology ; *Symbiosis ; }, abstract = {Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.}, }
@article {pmid32048447, year = {2020}, author = {Howe-Kerr, LI and Bachelot, B and Wright, RM and Kenkel, CD and Bay, LK and Correa, AMS}, title = {Symbiont community diversity is more variable in corals that respond poorly to stress.}, journal = {Global change biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/gcb.14999}, pmid = {32048447}, issn = {1365-2486}, support = {G2016100191023671//Sigma Xi Grant-in-Aid of Research/ ; G11/34671.1//Australian Institute of Marine Science/ ; G14/37318.1//Australian Institute of Marine Science/ ; 1635798//US National Science Foundation/ ; 1800914//US National Science Foundation/ ; 1928609//US National Science Foundation/ ; 1401165//US National Science Foundation/ ; 2000009651//National Academies of Sciences, Engineering, and Medicine/ ; }, abstract = {Coral reefs are declining globally as climate change and local water quality press environmental conditions beyond the physiological tolerances of holobionts-the collective of the host and its microbial symbionts. To assess the relationship between symbiont composition and holobiont stress tolerance, community diversity metrics were quantified for dinoflagellate endosymbionts (Family: Symbiodiniaceae) from eight Acropora millepora genets that thrived under or responded poorly to various stressors. These eight selected genets represent the upper and lower tails of the response distribution of 40 coral genets that were exposed to four stress treatments (and control conditions) in a 10-day experiment. Specifically, four 'best performer' coral genets were analyzed at the end of the experiment because they survived high temperature, high pCO2 , bacterial exposure, or combined stressors, whereas four 'worst performer' genets were characterized because they experienced substantial mortality under these stressors. At the end of the experiment, seven of eight coral genets mainly hosted Cladocopium symbionts, whereas the eighth genet was dominated by both Cladocopium and Durusdinium symbionts. Symbiodiniaceae alpha and beta diversity were higher in worst performing genets than in best performing genets. Symbiont communities in worst performers also differed more after stress exposure relative to their controls (based on normalized proportional differences in beta diversity), than did best performers. A generalized joint attribute model estimated the influence of host genet and treatment on Symbiodiniaceae community composition and identified strong associations among particular symbionts and host genet performance, as well as weaker associations with treatment. Although dominant symbiont physiology and function contribute to host performance, these findings emphasize the importance of symbiont community diversity and stochasticity as components of host performance. Our findings also suggest that symbiont community diversity metrics may function as indicators of resilience and have potential applications in diverse disciplines from climate change adaptation to agriculture and medicine.}, }
@article {pmid32040614, year = {2020}, author = {Brodin, P}, title = {New approaches to the study of immune responses in humans.}, journal = {Human genetics}, volume = {139}, number = {6-7}, pages = {795-799}, pmid = {32040614}, issn = {1432-1203}, support = {Born-Immune//H2020 European Research Council/ ; }, mesh = {Animals ; *Cell Communication ; *Homeostasis ; Humans ; Immune System/*immunology ; Infections/*etiology ; Signal Transduction ; }, abstract = {The human immune system consists of multiple, layered mechanisms of sensing and responding to cellular stress, infection and tissue damage to ensure defense from pathogens, maintenance of tissue homeostasis, and the integrity of the holobiont. Every single cell in the body has a role to play, but a few dozen, specialized white blood cells are particularly important in this respect. Understanding the overall state of this multifaceted system in a single individual is challenging, and we are only beginning to do this across populations of individuals, to understand the vast range of inter-individual variation, and the influences of genes and environmental factors that collectively shape the immune system in a given individual. We are also only beginning to understand the changes occurring within this system over time, and how this relates to health and disease susceptibility. Several technological breakthroughs in recent years have enabled these developments and the emergence of a new, complementary approach to studying human immune systems, namely systems immunology. In this paradigm, the focus is shifted from the understanding of individual immune system components and their mechanisms of action, towards analyses of cell-cell interactions, and mechanisms of coordination and regulation within the human immune system.}, }
@article {pmid32039567, year = {2020}, author = {Baedke, J and Fábregas-Tejeda, A and Nieves Delgado, A}, title = {The holobiont concept before Margulis.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {334}, number = {3}, pages = {149-155}, doi = {10.1002/jez.b.22931}, pmid = {32039567}, issn = {1552-5015}, mesh = {Animals ; *Biological Evolution ; Eukaryota/*cytology/*genetics ; History, 20th Century ; *Host Microbial Interactions ; Microbiota ; Selection, Genetic ; Symbiosis/*genetics/*physiology ; }, abstract = {In recent years, Lynn Margulis has been credited in various articles as the person who introduced the concept of holobiont into biology in the early 1990s. Today, the origin of evolutionary studies on holobionts is closely linked to her name. However, Margulis was not the first person to use this concept in its current context. That honor goes to the German theoretical biologist Adolf Meyer-Abich, who introduced the holobiont concept nearly 50 years before her (in 1943). Although nearly completely forgotten today, in the 1940-60s he developed a comprehensive theory of evolutionary change through "holobiosis." It had a surprisingly modern outlook, as it not only addressed tenets of today's evolutionary developmental biology (evo-devo), like the origin of form and production of variation, but also anticipated key elements of Margulis' later endosymbiotic theory. As the holobiont concept has become an important guiding concept for organizing research, labeling conferences, and publishing articles on host-microbiota collectives and hologenomes, the field should become aware of the independent origin of this concept in the context of holistic biology of the 1940s.}, }
@article {pmid32023487, year = {2020}, author = {Wang, GH and Berdy, BM and Velasquez, O and Jovanovic, N and Alkhalifa, S and Minbiole, KPC and Brucker, RM}, title = {Changes in Microbiome Confer Multigenerational Host Resistance after Sub-toxic Pesticide Exposure.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {2}, pages = {213-224.e7}, doi = {10.1016/j.chom.2020.01.009}, pmid = {32023487}, issn = {1934-6069}, mesh = {Animals ; Atrazine/metabolism/toxicity ; Bacteria/genetics/isolation &amp; purification/metabolism ; Directed Molecular Evolution ; Drug Resistance/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; Genes, Bacterial ; Maternal Inheritance ; Metagenomics ; Pesticides/metabolism/*toxicity ; Pseudomonas/genetics/isolation &amp; purification/metabolism ; Serratia marcescens/genetics/isolation &amp; purification/metabolism ; Wasps/drug effects/*microbiology ; Xenobiotics/metabolism/toxicity ; }, abstract = {The gut is a first point of contact with ingested xenobiotics, where chemicals are metabolized directly by the host or microbiota. Atrazine is a widely used pesticide, but the role of the microbiome metabolism of this xenobiotic and the impact on host responses is unclear. We exposed successive generations of the wasp Nasonia vitripennis to subtoxic levels of atrazine and observed changes in the structure and function of the gut microbiome that conveyed atrazine resistance. This microbiome-mediated resistance was maternally inherited and increased over successive generations, while also heightening the rate of host genome selection. The rare gut bacteria Serratia marcescens and Pseudomonas protegens contributed to atrazine metabolism. Both of these bacteria contain genes that are linked to atrazine degradation and were sufficient to confer resistance in experimental wasp populations. Thus, pesticide exposure causes functional, inherited changes in the microbiome that should be considered when assessing xenobiotic exposure and as potential countermeasures to toxicity.}, }
@article {pmid32021942, year = {2020}, author = {Mondo, E and Barone, M and Soverini, M and D'Amico, F and Cocchi, M and Petrulli, C and Mattioli, M and Marliani, G and Candela, M and Accorsi, PA}, title = {Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders.}, journal = {Heliyon}, volume = {6}, number = {1}, pages = {e03311}, pmid = {32021942}, issn = {2405-8440}, abstract = {Accompanying human beings since the Paleolithic period, dogs has been recently regarded as a reliable model for the study of the gut microbiome connections with health and disease. In order to provide some glimpses on the connections between the gut microbiome layout and host behavior, we profiled the phylogenetic composition and structure of the canine gut microbiome of dogs with aggressive (n = 11), phobic (n = 13) and normal behavior (n = 18). Hormones' determination was made through Radio Immuno-Assay (RIA), and next generation sequencing of the V3-V4 gene region of the bacterial 16S rRNA was employed to determine gut microbiome composition. Our results did not evidence any significant differences of hormonal levels between the three groups. According to our findings, aggressive behavioral disorder was found to be characterized by a peculiar gut microbiome structure, with high biodiversity and enrichment in generally subdominant bacterial genera (i.e. Catenibacterium and Megamonas). On the other hand, phobic dogs were enriched in Lactobacillus, a bacterial genus with known probiotic and psychobiotic properties. Although further studies are needed to validate our findings, our work supports the intriguing opportunity that different behavioral phenotypes in dogs may be associated with peculiar gut microbiome layouts, suggesting possible connections between the gut microbiome and the central nervous system and indicating the possible adoption of probiotic interventions aimed at restoring a balanced host-symbiont interplay for mitigating behavioral disorders.}, }
@article {pmid32011756, year = {2020}, author = {Kennedy, SR and Tsau, S and Gillespie, R and Krehenwinkel, H}, title = {Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua.}, journal = {Molecular ecology}, volume = {29}, number = {5}, pages = {1001-1015}, doi = {10.1111/mec.15370}, pmid = {32011756}, issn = {1365-294X}, mesh = {Animals ; Bacteria/*classification ; Bacterial Load ; California ; *Diet ; *Gastrointestinal Microbiome ; Predatory Behavior ; RNA, Ribosomal, 16S/genetics ; Spiders/*microbiology ; }, abstract = {Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven. This assumption is supported by a feeding experiment, in which two types of prey-crickets and fruit flies-both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.}, }
@article {pmid32010100, year = {2019}, author = {Flores-Núñez, VM and Fonseca-García, C and Desgarennes, D and Eloe-Fadrosh, E and Woyke, T and Partida-Martínez, LP}, title = {Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {3044}, pmid = {32010100}, issn = {1664-302X}, abstract = {Microbial symbionts account for survival, development, fitness and evolution of eukaryotic hosts. These microorganisms together with their host form a biological unit known as holobiont. Recent studies have revealed that the holobiont of agaves and cacti comprises a diverse and structured microbiome, which might be important for its adaptation to drylands. Here, we investigated the functional signatures of the prokaryotic communities of the soil and the episphere, that includes the rhizosphere and phyllosphere, associated with the cultivated Agave tequilana and the native and sympatric Agave salmiana, Opuntia robusta and Myrtillocactus geometrizans by mining shotgun metagenomic data. Consistent with previous phylogenetic profiling, we found that Proteobacteria, Actinobacteria and Firmicutes were the main represented phyla in the episphere of agaves and cacti, and that clustering of metagenomes correlated with the plant compartment. In native plants, genes related to aerobic anoxygenic phototrophy and photosynthesis were enriched in the phyllosphere and soil, while genes coding for biofilm formation and quorum sensing were enriched in both epiphytic communities. In the episphere of cultivated A. tequilana fewer genes were identified, but they belonged to similar pathways than those found in native plants. A. tequilana showed a depletion in several genes belonging to carbon metabolism, secondary metabolite biosynthesis and xenobiotic degradation suggesting that its lower microbial diversity might be linked to functional losses. However, this species also showed an enrichment in biofilm and quorum sensing in the epiphytic compartments, and evidence for nitrogen fixation in the rhizosphere. Aerobic anoxygenic phototrophic markers were represented by Rhizobiales (Methylobacterium) and Rhodospirillales (Belnapia) in the phyllosphere, while photosystem genes were widespread in Bacillales and Cyanobacteria. Nitrogen fixation and biofilm formation genes were mostly related to Proteobacteria. These analyses support the idea of niche differentiation in the rhizosphere and phyllosphere of agaves and cacti and shed light on the potential mechanisms by which epiphytic microbial communities survive and colonize plants of arid and semiarid ecosystems. This study establishes a guideline for testing the relevance of the identified functional traits on the microbial community and the plant fitness.}, }
@article {pmid32008576, year = {2020}, author = {Osman, EO and Suggett, DJ and Voolstra, CR and Pettay, DT and Clark, DR and Pogoreutz, C and Sampayo, EM and Warner, ME and Smith, DJ}, title = {Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {8}, pmid = {32008576}, issn = {2049-2618}, mesh = {Acclimatization ; Animals ; Anthozoa/*microbiology ; Bacteria/*classification ; Coral Reefs ; Dinoflagellida/classification/*physiology ; *Host Specificity ; Hot Temperature ; Indian Ocean ; *Microbiota ; *Symbiosis ; }, abstract = {BACKGROUND: The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.<br><br>RESULTS: We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.<br><br>CONCLUSION: The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.}, }
@article {pmid31983620, year = {2020}, author = {Bettenfeld, P and Fontaine, F and Trouvelot, S and Fernandez, O and Courty, PE}, title = {Woody Plant Declines. What's Wrong with the Microbiome?.}, journal = {Trends in plant science}, volume = {25}, number = {4}, pages = {381-394}, doi = {10.1016/j.tplants.2019.12.024}, pmid = {31983620}, issn = {1878-4372}, mesh = {Carbon ; *Microbiota ; Nitrogen ; Plants ; Rhizosphere ; Soil Microbiology ; }, abstract = {Woody plant (WP) declines have multifactorial determinants as well as a biological and economic reality. The vascular system of WPs involved in the transport of carbon, nitrogen, and water from sources to sinks has a seasonal activity, which places it at a central position for mediating plant-environment interactions from nutrient cycling to community assembly and for regulating a variety of processes. To limit effects and to fight against declines, we propose: (i) to consider the WP and its associated microbiota as an holobiont and as a set of functions; (ii) to consider simultaneously, without looking at what comes first, the physiological or pathogenic disorders; and (iii) to define pragmatic strategies, including preventive and curative agronomical practices based on microbiota engineering.}, }
@article {pmid31969889, year = {2019}, author = {Vincent, D and Rafiqi, M and Job, D}, title = {The Multiple Facets of Plant-Fungal Interactions Revealed Through Plant and Fungal Secretomics.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1626}, pmid = {31969889}, issn = {1664-462X}, abstract = {The plant secretome is usually considered in the frame of proteomics, aiming at characterizing extracellular proteins, their biological roles and the mechanisms accounting for their secretion in the extracellular space. In this review, we aim to highlight recent results pertaining to secretion through the conventional and unconventional protein secretion pathways notably those involving plant exosomes or extracellular vesicles. Furthermore, plants are well known to actively secrete a large array of different molecules from polymers (e.g. extracellular RNA and DNA) to small compounds (e.g. ATP, phytochemicals, secondary metabolites, phytohormones). All of these play pivotal roles in plant-fungi (or oomycetes) interactions, both for beneficial (mycorrhizal fungi) and deleterious outcomes (pathogens) for the plant. For instance, recent work reveals that such secretion of small molecules by roots is of paramount importance to sculpt the rhizospheric microbiota. Our aim in this review is to extend the definition of the plant and fungal secretomes to a broader sense to better understand the functioning of the plant/microorganisms holobiont. Fundamental perspectives will be brought to light along with the novel tools that should support establishing an environment-friendly and sustainable agriculture.}, }
@article {pmid31964724, year = {2020}, author = {Motone, K and Takagi, T and Aburaya, S and Miura, N and Aoki, W and Ueda, M}, title = {A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress.}, journal = {mBio}, volume = {11}, number = {1}, pages = {}, pmid = {31964724}, issn = {2150-7511}, mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/classification/genetics/*isolation &amp; purification/*metabolism ; Microbiota ; Open Reading Frames ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Zeaxanthins/*biosynthesis ; }, abstract = {Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [Fv/Fm]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the Fv/Fm and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the Fv/Fm and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.IMPORTANCE Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions.}, }
@article {pmid31960895, year = {2019}, author = {Bovio, E and Sfecci, E and Poli, A and Gnavi, G and Prigione, V and Lacour, T and Mehiri, M and Varese, GC}, title = {The culturable mycobiota associated with the Mediterranean sponges Aplysina cavernicola, Crambe crambe and Phorbas tenacior.}, journal = {FEMS microbiology letters}, volume = {366}, number = {24}, pages = {}, doi = {10.1093/femsle/fnaa014}, pmid = {31960895}, issn = {1574-6968}, mesh = {Animals ; Biodiversity ; Crambe Sponge/*microbiology ; Fungi/isolation &amp; purification ; Mediterranean Sea ; *Microbiota ; Phylogeny ; Porifera/microbiology ; Seawater/microbiology ; }, abstract = {Marine fungi are part of the huge and understudied biodiversity hosted in the sea. To broaden the knowledge on fungi inhabiting the Mediterranean Sea and their role in sponge holobiont, three sponges namely Aplysina cavernicola, Crambe crambe and Phorbas tenacior were collected in Villefranche sur Mer, (France) at about 25 m depth. The fungal communities associated with the sponges were isolated using different techniques to increase the numbers of fungi isolated. All fungi were identified to species level giving rise to 19, 13 and 3 species for P. tenacior, A. cavernicola and C. crambe, respectively. Of note, 35.7% and 50.0% of the species detected were either reported for the first time in the marine environment or in association with sponges. The mini-satellite analysis confirmed the uniqueness of the mycobiota of each sponge, leading to think that the sponge, with its metabolome, may shape the microbial community.}, }
@article {pmid31945519, year = {2020}, author = {Meenatchi, R and Thinesh, T and Brindangnanam, P and Hassan, S and Kiran, GS and Selvin, J}, title = {Revealing the impact of global mass bleaching on coral microbiome through 16S rRNA gene-based metagenomic analysis.}, journal = {Microbiological research}, volume = {233}, number = {}, pages = {126408}, doi = {10.1016/j.micres.2019.126408}, pmid = {31945519}, issn = {1618-0623}, mesh = {Animals ; Anthozoa/*microbiology/physiology ; Bacteria/*classification ; Coral Reefs ; *Heat-Shock Response ; High-Throughput Nucleotide Sequencing ; India ; *Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Coral bleaching, a phenomenon by which the expulsion of corals' alveolate endosymbiont (zooxanthellae) occurs when experiencing thermal stress is the major cause for devastation of corals. However, apart from this obligate symbiont of Scleractinian corals, there are different kinds of microbes that exist as stable, transient or sporadic members of the holobiont which reside within various microhabitats in the coral structures. Thus, this study aims to profile the coral bacterial community composition among different coral genera (thermally-sensitive (Acropora digetifera and A. noblis) and thermally resistant (Favites abdita) coral genera analyzed by field monitoring surveys) and also in a particular coral genus (thermally sensitive coral-A. digetifera) at two different sampling times (March 2016 and January 2017). A total of about 608695 paired end reads were obtained through Illumina MiSeq Sequencing platform. The alpha diversity indices (ACE, Chao1 and Shannon) were found to be higher in A. nobilis, followed by A. digetifera and Favites abdita, and the corresponding Simpson values were also found to follow the same trend, indicating that the samples are both rich in species diversity and species evenness. Proteobacteria was found to be the most dominant phylum and Gammaproteobacteria was the predominant class present in all the coral genera studied as also during different sampling time periods. As Vibrionaceae was previously reported to increase its abundance during bleaching stress conditions, bacterial profiling among different coral genera showed the presence of 86 % Vibrionaceae in A. digetifera colonies, and it was 93 % in A. digetifera samples collected during March 2016 whereas, it was found to decrease significantly (7 %) in same tagged colonies collected during January 2017. Thus, profiling of microbiome is of prime importance while studying the holobiont organism like the corals. Stress levels experienced by Palk Bay are even depicted in this microbiome study showing high alpha diversity indices that should alarm reef managers to pay attention to this precious stress tolerant reef community.}, }
@article {pmid31943674, year = {2020}, author = {Matthews, JL and Raina, JB and Kahlke, T and Seymour, JR and van Oppen, MJH and Suggett, DJ}, title = {Symbiodiniaceae-bacteria interactions: rethinking metabolite exchange in reef-building corals as multi-partner metabolic networks.}, journal = {Environmental microbiology}, volume = {22}, number = {5}, pages = {1675-1687}, doi = {10.1111/1462-2920.14918}, pmid = {31943674}, issn = {1462-2920}, support = {DP180100074//Australian Research Council/International ; DP180100838//Australian Research Council/International ; FL180100036//Australian Research Council/International ; LT000625/2018‐L//Human Frontier Science Program/International ; }, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/*metabolism ; Bacteria/genetics/*metabolism ; Coral Reefs ; Dinoflagellida/*microbiology ; Ecosystem ; Fungi/genetics/*metabolism ; Metabolic Networks and Pathways ; Symbiosis/*physiology ; }, abstract = {The intimate relationship between scleractinian corals and their associated microorganisms is fundamental to healthy coral reef ecosystems. Coral-associated microbes (Symbiodiniaceae and other protists, bacteria, archaea, fungi and viruses) support coral health and resilience through metabolite transfer, inter-partner signalling, and genetic exchange. However, much of our understanding of the coral holobiont relationship has come from studies that have investigated either coral-Symbiodiniaceae or coral-bacteria interactions in isolation, while relatively little research has focused on other ecological and metabolic interactions potentially occurring within the coral multi-partner symbiotic network. Recent evidences of intimate coupling between phytoplankton and bacteria have demonstrated that obligate resource exchange between partners fundamentally drives their ecological success. Here, we posit that similar associations with bacterial consortia regulate Symbiodiniaceae productivity and are in turn central to the health of corals. Indeed, we propose that this bacteria-Symbiodiniaceae-coral relationship underpins the coral holobiont's nutrition, stress tolerance and potentially influences the future survival of coral reef ecosystems under changing environmental conditions. Resolving Symbiodiniaceae-bacteria associations is therefore a logical next step towards understanding the complex multi-partner interactions occurring in the coral holobiont.}, }
@article {pmid31925332, year = {2020}, author = {Gibbin, E and Banc-Prandi, G and Fine, M and Comment, A and Meibom, A}, title = {A method to disentangle and quantify host anabolic turnover in photosymbiotic holobionts with subcellular resolution.}, journal = {Communications biology}, volume = {3}, number = {1}, pages = {14}, pmid = {31925332}, issn = {2399-3642}, mesh = {Animals ; Anthozoa/metabolism/ultrastructure ; Carbohydrate Metabolism ; Microbiology ; *Photosynthesis ; Pyruvic Acid/metabolism ; *Symbiosis ; }, abstract = {A wide range of organisms host photosynthesizing symbionts. In these animals the metabolic exchange between host and symbionts has prevented in situ host anabolic turnover to be studied without the confounding effect of translocated photosynthates. Using the symbiotic coral Stylophora pistillata as a model organism and [1-13C]-pyruvate and [2,3-13C]-pyruvate in different incubation conditions (light, light + DCMU, and darkness), we employed NanoSIMS isotopic imaging to quantify host anabolism, with and without translocated metabolites from their photosynthesizing dinoflagellate symbionts. Under our experimental conditions, host de novo lipid synthesis accounted for ~40% of the total holobiont lipid reserve, and dinoflagellate recycling of metabolic 13CO2 enhanced host tissue 13C-enrichment by 13-22% in the epidermis, 40-58% in the gastrodermis, and 135-169% in host lipid bodies. Furthermore, we show that host anabolic turnover in different tissue structures differs, in a manner consistent with the localisation, function and cellular composition of these structures.}, }
@article {pmid31921931, year = {2020}, author = {Pontarollo, G and Kiouptsi, K and Reinhardt, C}, title = {A holobiont view on thrombosis: unravelling the microbiota's influence on arterial thrombus growth.}, journal = {Microbial cell (Graz, Austria)}, volume = {7}, number = {1}, pages = {28-31}, doi = {10.15698/mic2020.01.704}, pmid = {31921931}, issn = {2311-2638}, abstract = {The commensal microbiota has co-evolved with its host, colonizing all body surfaces. Therefore, this microbial ecosystem is intertwined with host physiology at multiple levels. While it is evident that microbes that reach the blood stream can trigger thrombus formation, it remains poorly explored if the wealth of microbes that colonize the body surfaces of the mammalian host can be regarded as a modifier of cardiovascular disease (CVD) development. To experimentally address the microbiota's role in the development of atherosclerotic lesions and arterial thrombosis, we generated a germ-free (GF) low-density lipoprotein receptor-deficient (Ldlr-/-) atherosclerosis mouse model (Kiouptsi et al., mBio, 2019) and explored the role of nutritional composition on arterial thrombogenesis.}, }
@article {pmid31878183, year = {2019}, author = {Chialva, M and Ghignone, S and Novero, M and Hozzein, WN and Lanfranco, L and Bonfante, P}, title = {Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota.}, journal = {Microorganisms}, volume = {8}, number = {1}, pages = {}, pmid = {31878183}, issn = {2076-2607}, support = {TO_call03_2012_0039//Compagnia di San Paolo/ ; 727929//Horizon 2020 Framework Programme/ ; RSP-2019/53//King Saud University/ ; }, abstract = {Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early "omics" experiments focused mainly on the species composition of microbial communities, new "meta-omics" approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research.}, }
@article {pmid31866971, year = {2019}, author = {Pausan, MR and Csorba, C and Singer, G and Till, H and Schöpf, V and Santigli, E and Klug, B and Högenauer, C and Blohs, M and Moissl-Eichinger, C}, title = {Exploring the Archaeome: Detection of Archaeal Signatures in the Human Body.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2796}, pmid = {31866971}, issn = {1664-302X}, abstract = {Due to their fundamentally different biology, archaea are consistently overlooked in conventional microbiome surveys. Using amplicon sequencing, we evaluated methodological set-ups to detect archaea in samples from five different body sites: respiratory tract (nasal cavity), digestive tract (mouth, appendix, and stool) and skin. With optimized protocols, the detection of archaeal ribosomal sequence variants (RSVs) was increased from one (found in currently used, so-called "universal" approach) to 81 RSVs in a representative sample set. The results from this extensive primer-evaluation led to the identification of the primer pair combination 344f-1041R/519F-806R which performed superior for the analysis of the archaeome of gastrointestinal tract, oral cavity and skin. The proposed protocol might not only prove useful for analyzing the human archaeome in more detail but could also be used for other holobiont samples.}, }
@article {pmid31857601, year = {2019}, author = {Tilstra, A and El-Khaled, YC and Roth, F and Rädecker, N and Pogoreutz, C and Voolstra, CR and Wild, C}, title = {Denitrification Aligns with N2 Fixation in Red Sea Corals.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19460}, pmid = {31857601}, issn = {2045-2322}, support = {Wi 2677/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/International ; }, mesh = {Animals ; Anthozoa/genetics/*metabolism ; Denitrification/*physiology ; Dinoflagellida/*metabolism ; Gene Dosage ; Indian Ocean ; Nitrogen/metabolism ; Nitrogen Fixation/*physiology ; Photosynthesis ; Symbiosis ; }, abstract = {Denitrification may potentially alleviate excess nitrogen (N) availability in coral holobionts to maintain a favourable N to phosphorous ratio in the coral tissue. However, little is known about the abundance and activity of denitrifiers in the coral holobiont. The present study used the nirS marker gene as a proxy for denitrification potential along with measurements of denitrification rates in a comparative coral taxonomic framework from the Red Sea: Acropora hemprichii, Millepora dichotoma, and Pleuractis granulosa. Relative nirS gene copy numbers associated with the tissues of these common corals were assessed and compared with denitrification rates on the holobiont level. In addition, dinitrogen (N2) fixation rates, Symbiodiniaceae cell density, and oxygen evolution were assessed to provide an environmental context for denitrification. We found that relative abundances of the nirS gene were 16- and 17-fold higher in A. hemprichii compared to M. dichotoma and P. granulosa, respectively. In concordance, highest denitrification rates were measured in A. hemprichii, followed by M. dichotoma and P. granulosa. Denitrification rates were positively correlated with N2 fixation rates and Symbiodiniaceae cell densities. Our results suggest that denitrification may counterbalance the N input from N2 fixation in the coral holobiont, and we hypothesize that these processes may be limited by photosynthates released by the Symbiodiniaceae.}, }
@article {pmid31849163, year = {2020}, author = {Singh, BK and Liu, H and Trivedi, P}, title = {Eco-holobiont: A new concept to identify drivers of host-associated microorganisms.}, journal = {Environmental microbiology}, volume = {22}, number = {2}, pages = {564-567}, doi = {10.1111/1462-2920.14900}, pmid = {31849163}, issn = {1462-2920}, support = {DP170104634//Australian Research Council/International ; DP190103714//Australian Research Council/International ; }, mesh = {Animals ; Biological Evolution ; Humans ; Microbiota/*physiology ; Plants ; Symbiosis/*physiology ; }, abstract = {Host microbiomes play a critical role in host fitness and health. Whilst the current 'holobiont' concept framework has greatly expanded eco-evolutionary and functional understanding of host-microbiome interactions, the important role of biotic interactions and microbial loop (compositional linkage between soil, plant and animal) in shaping host-microbiome are poorly understood. We proposed an 'eco-holobiont' concept to fill the knowledge gap.}, }
@article {pmid31848270, year = {2019}, author = {Hinzke, T and Kleiner, M and Breusing, C and Felbeck, H and Häsler, R and Sievert, SM and Schlüter, R and Rosenstiel, P and Reusch, TBH and Schweder, T and Markert, S}, title = {Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31848270}, issn = {2150-7511}, mesh = {Adaptation, Biological ; Animal Nutritional Physiological Phenomena ; Animals ; Aquatic Organisms ; Energy Metabolism ; Metabolic Networks and Pathways ; Metabolome ; *Microbiota ; Oxidation-Reduction ; Polychaeta/*metabolism/*microbiology/ultrastructure ; Proteome ; Proteomics/methods ; Seawater ; *Symbiosis ; }, abstract = {The deep-sea tubeworm Riftia pachyptila lacks a digestive system but completely relies on bacterial endosymbionts for nutrition. Although the symbiont has been studied in detail on the molecular level, such analyses were unavailable for the animal host, because sequence information was lacking. To identify host-symbiont interaction mechanisms, we therefore sequenced the Riftia transcriptome, which served as a basis for comparative metaproteomic analyses of symbiont-containing versus symbiont-free tissues, both under energy-rich and energy-limited conditions. Our results suggest that metabolic interactions include nutrient allocation from symbiont to host by symbiont digestion and substrate transfer to the symbiont by abundant host proteins. We furthermore propose that Riftia maintains its symbiont by protecting the bacteria from oxidative damage while also exerting symbiont population control. Eukaryote-like symbiont proteins might facilitate intracellular symbiont persistence. Energy limitation apparently leads to reduced symbiont biomass and increased symbiont digestion. Our study provides unprecedented insights into host-microbe interactions that shape this highly efficient symbiosis.IMPORTANCE All animals are associated with microorganisms; hence, host-microbe interactions are of fundamental importance for life on earth. However, we know little about the molecular basis of these interactions. Therefore, we studied the deep-sea Riftia pachyptila symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition. Using a metaproteomics approach, we identified both metabolic interaction processes, such as substrate transfer between the two partners, and interactions that serve to maintain the symbiotic balance, e.g., host efforts to control the symbiont population or symbiont strategies to modulate these host efforts. We suggest that these interactions are essential principles of mutualistic animal-microbe associations.}, }
@article {pmid31844749, year = {2019}, author = {Hussien, E and Juhmani, AS and AlMasri, R and Al-Horani, F and Al-Saghir, M}, title = {Metagenomic analysis of microbial community associated with coral mucus from the Gulf of Aqaba.}, journal = {Heliyon}, volume = {5}, number = {11}, pages = {e02876}, pmid = {31844749}, issn = {2405-8440}, abstract = {Coral-associated microbial communities contribute to a wide variety of useful roles regarding the their host, and therefore, the arrangement of the general microbiome network can emphatically impact coral wellbeing and survival. Various pollution sources can interfere and disrupt the microbial relationship with corals. Here, we adopted the bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP®) technique to investigate the shift of microbial communities associated with the mucus of the coral Stylophora pistillata collected from five sites (Marine Science Station, Industrial Complex, Oil Terminal, Public Beach, and Phosphate Port) along the Gulf of Aqaba (Red Sea). Our results revealed a high diversity in bacterial populations associated with coral mucus. Proteobacteria were observed to be the dominating phylum among all sampling sites. The identified bacterial taxa belong to the pathogenic bacteria from the genus Vibrio was presented in varying abundances at all sampling sites. Diversity and similarity analysis of microbial communists based on rarefaction curve and UniFrac cluster respectively demonstrated that there are variances in microbial groups associated with coral mucus along sites. The pollution sources among different locations along the Gulf of Aqaba seem to affect the coral-associated holobiont leading to changes in bacterial populations due to increasing human activities.}, }
@article {pmid31843471, year = {2020}, author = {Edwards, JM and Roy, S and Tomcho, JC and Schreckenberger, ZJ and Chakraborty, S and Bearss, NR and Saha, P and McCarthy, CG and Vijay-Kumar, M and Joe, B and Wenceslau, CF}, title = {Microbiota are critical for vascular physiology: Germ-free status weakens contractility and induces sex-specific vascular remodeling in mice.}, journal = {Vascular pharmacology}, volume = {125-126}, number = {}, pages = {106633}, pmid = {31843471}, issn = {1879-3649}, support = {R00 GM118885/GM/NIGMS NIH HHS/United States ; R01 HL143082/HL/NHLBI NIH HHS/United States ; R01 CA219144/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Elastic Modulus ; Female ; Gastrointestinal Microbiome/*physiology ; Germ-Free Life ; Host Microbial Interactions ; Male ; Mesenteric Arteries/metabolism/*physiology ; Mice, Inbred C57BL ; Neutrophils/metabolism ; Reactive Oxygen Species/metabolism ; Sex Factors ; *Vascular Remodeling ; Vascular Resistance ; Vascular Stiffness ; *Vasoconstriction ; }, abstract = {Commensal microbiota within a holobiont contribute to the overall health of the host via mutualistic symbiosis. Disturbances in such symbiosis is prominently correlated with a variety of diseases affecting the modern society of humans including cardiovascular diseases, which are the number one contributors to human mortality. Given that a hallmark of all cardiovascular diseases is changes in vascular function, we hypothesized that depleting microbiota from a holobiont would induce vascular dysfunction. To test this hypothesis, young mice of both sexes raised in germ-free conditions were examined vascular contractility and structure. Here we observed that male and female germ-free mice presented a decrease in contraction of resistance arteries. These changes were more pronounced in germ-free males than in germ-free females mice. Furthermore, there was a distinct change in vascular remodeling between males and females germ-free mice. Resistance arteries from male germ-free mice demonstrated increased vascular stiffness, as shown by the leftward shift in the stress-strain curve and inward hypotrophic remodeling, a characteristic of chronic reduction in blood flow. On the other hand, resistance arteries from germ-free female mice were similar in the stress-strain curves to that of conventionally raised mice, but were distinctly different and showed outward hypertrophic remodeling, a characteristic seen in aging. Interestingly, we observed that reactive oxygen species (ROS) generation from bone marrow derived neutrophils is blunted in female germ-free mice, but it is exacerbated in male germ-free mice. In conclusion, these observations indicate that commensal microbiota of a holobiont are central to maintain proper vascular function and structure homeostasis, especially in males.}, }
@article {pmid31841144, year = {2020}, author = {Martin, BC and Alarcon, MS and Gleeson, D and Middleton, JA and Fraser, MW and Ryan, MH and Holmer, M and Kendrick, GA and Kilminster, K}, title = {Root microbiomes as indicators of seagrass health.}, journal = {FEMS microbiology ecology}, volume = {96}, number = {2}, pages = {}, doi = {10.1093/femsec/fiz201}, pmid = {31841144}, issn = {1574-6941}, mesh = {Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Biomass ; Environmental Biomarkers/*genetics ; Estuaries ; Hydrocharitaceae/growth &amp; development/metabolism/*microbiology/*physiology ; Microbiota/*genetics ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; South Australia ; Sulfides/metabolism ; }, abstract = {The development of early warning indicators that identify ecosystem stress is a priority for improving ecosystem management. As microbial communities respond rapidly to environmental disturbance, monitoring their composition could prove one such early indicator of environmental stress. We combined 16S rRNA gene sequencing of the seagrass root microbiome of Halophila ovalis with seagrass health metrics (biomass, productivity and Fsulphide) to develop microbial indicators for seagrass condition across the Swan-Canning Estuary and the Leschenault Estuary (south-west Western Australia); the former had experienced an unseasonal rainfall event leading to declines in seagrass health. Microbial indicators detected sites of potential stress that other seagrass health metrics failed to detect. Genera that were more abundant in 'healthy' seagrasses included putative methylotrophic bacteria (e.g. Methylotenera and Methylophaga), iron cycling bacteria (e.g. Deferrisoma and Geothermobacter) and N2 fixing bacteria (e.g. Rhizobium). Conversely, genera that were more abundant in 'stressed' seagrasses were dominated by putative sulphur-cycling bacteria, both sulphide-oxidising (e.g. Candidatus Thiodiazotropha and Candidatus Electrothrix) and sulphate-reducing (e.g. SEEP-SRB1, Desulfomonile and Desulfonema). The sensitivity of the microbial indicators developed here highlights their potential to be further developed for use in adaptive seagrass management, and emphasises their capacity to be effective early warning indicators of stress.}, }
@article {pmid31841132, year = {2020}, author = {Karimi, E and Geslain, E and KleinJan, H and Tanguy, G and Legeay, E and Corre, E and Dittami, SM}, title = {Genome Sequences of 72 Bacterial Strains Isolated from Ectocarpus subulatus: A Resource for Algal Microbiology.}, journal = {Genome biology and evolution}, volume = {12}, number = {1}, pages = {3647-3655}, pmid = {31841132}, issn = {1759-6653}, mesh = {Bacteria/genetics/isolation &amp; purification/metabolism ; *Genome, Bacterial ; Phaeophyta/*microbiology ; Phylogeny ; Secondary Metabolism/genetics ; Symbiosis ; Vitamins/biosynthesis ; }, abstract = {Brown algae are important primary producers and ecosystem engineers in the ocean, and Ectocarpus has been established as a laboratory model for this lineage. Like most multicellular organisms, Ectocarpus is associated with a community of microorganisms, a partnership frequently referred to as holobiont due to the tight interconnections between the components. Although genomic resources for the algal host are well established, its associated microbiome is poorly characterized from a genomic point of view, limiting the possibilities of using these types of data to study host-microbe interactions. To address this gap in knowledge, we present the annotated draft genome sequences of seventy-two cultivable Ectocarpus-associated bacteria. A screening of gene clusters related to the production of secondary metabolites revealed terpene, bacteriocin, NRPS, PKS-t3, siderophore, PKS-t1, and homoserine lactone clusters to be abundant among the sequenced genomes. These compounds may be used by the bacteria to communicate with the host and other microbes. Moreover, detoxification and provision of vitamin B pathways have been observed in most sequenced genomes, highlighting potential contributions of the bacterial metabolism toward host fitness and survival. The genomes sequenced in this study form a valuable resource for comparative genomic analyses and evolutionary surveys of alga-associated bacteria. They help establish Ectocarpus as a model for brown algal holobionts and will enable the research community to produce testable hypotheses about the molecular interactions within this complex system.}, }
@article {pmid31831078, year = {2019}, author = {Ricci, F and Rossetto Marcelino, V and Blackall, LL and Kühl, M and Medina, M and Verbruggen, H}, title = {Beneath the surface: community assembly and functions of the coral skeleton microbiome.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {159}, pmid = {31831078}, issn = {2049-2618}, mesh = {Animals ; Anthozoa/*microbiology ; Archaea/classification ; Bacteria/classification ; Biodiversity ; *Coral Reefs ; Microbiota/*physiology ; }, abstract = {Coral microbial ecology is a burgeoning field, driven by the urgency of understanding coral health and slowing reef loss due to climate change. Coral resilience depends on its microbiota, and both the tissue and the underlying skeleton are home to a rich biodiversity of eukaryotic, bacterial and archaeal species that form an integral part of the coral holobiont. New techniques now enable detailed studies of the endolithic habitat, and our knowledge of the skeletal microbial community and its eco-physiology is increasing rapidly, with multiple lines of evidence for the importance of the skeletal microbiota in coral health and functioning. Here, we review the roles these organisms play in the holobiont, including nutritional exchanges with the coral host and decalcification of the host skeleton. Microbial metabolism causes steep physico-chemical gradients in the skeleton, creating micro-niches that, along with dispersal limitation and priority effects, define the fine-scale microbial community assembly. Coral bleaching causes drastic changes in the skeletal microbiome, which can mitigate bleaching effects and promote coral survival during stress periods, but may also have detrimental effects. Finally, we discuss the idea that the skeleton may function as a microbial reservoir that can promote recolonization of the tissue microbiome following dysbiosis and help the coral holobiont return to homeostasis.}, }
@article {pmid31824548, year = {2019}, author = {Maréchal, E}, title = {Marine and Freshwater Plants: Challenges and Expectations.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1545}, pmid = {31824548}, issn = {1664-462X}, abstract = {The past decades have seen an increasing interest on the biology of photosynthetic species living in aquatic environments, including diverse organisms collectively called "algae." If we consider the relative size of scientific communities, marine and freshwater plants have been overall less studied than terrestrial ones. The efforts put on land plants were motivated by agriculture and forestry, applications for human industry, easy access to terrestrial ecosystems, and convenient cultivation methods in fields or growth chambers. By contrast, the fragmentary knowledge on the biology of algae, the hope to find in this biodiversity inspiration for biotechnologies, and the emergency created by the environmental crisis affecting oceans, lakes, rivers, or melting glaciers, have stressed the importance to make up for lost time. Needed efforts embrace a broad spectrum of disciplines, from environmental and evolutionary sciences, to molecular and cell biology. In this multiscale view, functional genomics and ecophysiology occupy a pivotal position linking molecular and cellular analyses and ecosystem-level studies. Without pretending to be exhaustive and with few selected references, six grand challenges, requiring multidisciplinary approaches, are introduced below.}, }
@article {pmid31822603, year = {2019}, author = {Luter, HM and Whalan, S and Andreakis, N and Abdul Wahab, M and Botté, ES and Negri, AP and Webster, NS}, title = {The Effects of Crude Oil and Dispersant on the Larval Sponge Holobiont.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31822603}, issn = {2379-5077}, abstract = {Accidental oil spills from shipping and during extraction can threaten marine biota, particularly coral reef species which are already under pressure from anthropogenic disturbances. Marine sponges are an important structural and functional component of coral reef ecosystems; however, despite their ecological importance, little is known about how sponges and their microbial symbionts respond to petroleum products. Here, we use a systems biology-based approach to assess the effects of water-accommodated fractions (WAF) of crude oil, chemically enhanced water-accommodated fractions of crude oil (CWAF), and dispersant (Corexit EC9500A) on the survival, metamorphosis, gene expression, and microbial symbiosis of the abundant reef sponge Rhopaloeides odorabile in larval laboratory-based assays. Larval survival was unaffected by the 100% WAF treatment (107 μg liter-1 polycyclic aromatic hydrocarbon [PAH]), whereas significant decreases in metamorphosis were observed at 13% WAF (13.9 μg liter-1 PAH). The CWAF and dispersant treatments were more toxic, with decreases in metamorphosis identified at 0.8% (0.58 μg liter-1 PAH) and 1.6% (38 mg liter-1 Corexit EC9500A), respectively. In addition to the negative impact on larval settlement, significant changes in host gene expression and disruptions to the microbiome were evident, with microbial shifts detected at the lowest treatment level (1.6% WAF; 1.7 μg liter-1 PAH), including a significant reduction in the relative abundance of a previously described thaumarchaeal symbiont. The responsiveness of the R. odorabile microbial community to the lowest level of hydrocarbon treatment highlights the utility of the sponge microbiome as a sensitive marker for exposure to crude oils and dispersants.IMPORTANCE Larvae of the sponge R. odorabile survived exposure to high concentrations of petroleum hydrocarbons; however, their ability to settle and metamorphose was adversely affected at environmentally relevant concentrations, and these effects were paralleled by marked changes in sponge gene expression and preceded by disruption of the symbiotic microbiome. Given the ecological importance of sponges, uncontrolled hydrocarbon releases from shipping accidents or production could affect sponge recruitment, which would have concomitant consequences for reef ecosystem function.}, }
@article {pmid31802185, year = {2020}, author = {Walker, DM and Hill, AJ and Albecker, MA and McCoy, MW and Grisnik, M and Romer, A and Grajal-Puche, A and Camp, C and Kelehear, C and Wooten, J and Rheubert, J and Graham, SP}, title = {Variation in the Slimy Salamander (Plethodon spp.) Skin and Gut-Microbial Assemblages Is Explained by Geographic Distance and Host Affinity.}, journal = {Microbial ecology}, volume = {79}, number = {4}, pages = {985-997}, doi = {10.1007/s00248-019-01456-x}, pmid = {31802185}, issn = {1432-184X}, mesh = {Animal Distribution ; Animals ; Bacteria/isolation &amp; purification ; *Bacterial Physiological Phenomena ; Fungi/isolation &amp; purification/*physiology ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; *Microbiota ; Mycobiome ; Skin/*microbiology ; Southeastern United States ; Spatial Analysis ; Tennessee ; Urodela/*microbiology ; }, abstract = {A multicellular host and its microbial communities are recognized as a metaorganism-a composite unit of evolution. Microbial communities have a variety of positive and negative effects on the host life history, ecology, and evolution. This study used high-throughput amplicon sequencing to characterize the complete skin and gut microbial communities, including both bacteria and fungi, of a terrestrial salamander, Plethodon glutinosus (Family Plethodontidae). We assessed salamander populations, representing nine mitochondrial haplotypes ('clades'), for differences in microbial assemblages across 13 geographic locations in the Southeastern United States. We hypothesized that microbial assemblages were structured by both host factors and geographic distance. We found a strong correlation between all microbial assemblages at close geographic distances, whereas, as spatial distance increases, the patterns became increasingly discriminate. Network analyses revealed that gut-bacterial communities have the highest degree of connectedness across geographic space. Host salamander clade was explanatory of skin-bacterial and gut-fungal assemblages but not gut-bacterial assemblages, unless the latter were analyzed within a phylogenetic context. We also inferred the function of gut-fungal assemblages to understand how an understudied component of the gut microbiome may influence salamander life history. We concluded that dispersal limitation may in part describe patterns in microbial assemblages across space and also that the salamander host may select for skin and gut communities that are maintained over time in closely related salamander populations.}, }
@article {pmid31801294, year = {2019}, author = {Alex, A and Antunes, A}, title = {Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses.}, journal = {Microorganisms}, volume = {7}, number = {12}, pages = {}, pmid = {31801294}, issn = {2076-2607}, support = {PTDC/BIA-BMA/29985/2017 (POCI-01-0145-FEDER-029985)//Fundação para a Ciência e a Tecnologia/International ; PTDC/CTA-AMB/31774/2017 (POCI-01-0145-FEDER/031774/2017).//Fundação para a Ciência e a Tecnologia/International ; UID/Multi/04423/2019//Fundação para a Ciência e a Tecnologia/International ; }, abstract = {The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.}, }
@article {pmid31795848, year = {2019}, author = {Achlatis, M and Pernice, M and Green, K and de Goeij, JM and Guagliardo, P and Kilburn, MR and Hoegh-Guldberg, O and Dove, S}, title = {Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter.}, journal = {Proceedings. Biological sciences}, volume = {286}, number = {1916}, pages = {20192153}, pmid = {31795848}, issn = {1471-2954}, mesh = {Animals ; Coral Reefs ; Dinoflagellida/physiology ; Nitrogen/metabolism ; Porifera/*physiology ; *Symbiosis ; }, abstract = {Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known, however, about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most other invertebrates. Here, we examine the cellular capacity for direct processing of DOM, and the fate of the processed matter, inside a dinoflagellate-hosting bioeroding sponge that is prominent on Indo-Pacific coral reefs. Integrating transmission electron microscopy with nanoscale secondary ion mass spectrometry, we track 15N- and 13C-enriched DOM over time at the individual cell level of an intact sponge holobiont. We show initial high enrichment in the filter-feeding cells of the sponge, providing visual evidence of their capacity to process DOM through pinocytosis without mediation of resident bacteria. Subsequent enrichment of the endosymbiotic dinoflagellates also suggests sharing of host nitrogenous wastes. Our results shed light on the physiological mechanism behind the ecologically important ability of sponges to cycle DOM via the recently described sponge loop.}, }
@article {pmid31788212, year = {2019}, author = {McIlroy, SE and Cunning, R and Baker, AC and Coffroth, MA}, title = {Competition and succession among coral endosymbionts.}, journal = {Ecology and evolution}, volume = {9}, number = {22}, pages = {12767-12778}, pmid = {31788212}, issn = {2045-7758}, abstract = {Host species often support a genetically diverse guild of symbionts, the identity and performance of which can determine holobiont fitness under particular environmental conditions. These symbiont communities are structured by a complex set of potential interactions, both positive and negative, between the host and symbionts and among symbionts. In reef-building corals, stable associations with specific symbiont species are common, and we hypothesize that this is partly due to ecological mechanisms, such as succession and competition, which drive patterns of symbiont winnowing in the initial colonization of new generations of coral recruits. We tested this hypothesis using the experimental framework of the de Wit replacement series and found that competitive interactions occurred among symbionts which were characterized by unique ecological strategies. Aposymbiotic octocoral recruits within high- and low-light environments were inoculated with one of three Symbiodiniaceae species as monocultures or with cross-paired mixtures, and we tracked symbiont uptake using quantitative genetic assays. Priority effects, in which early colonizers excluded competitive dominants, were evidenced under low light, but these early opportunistic species were later succeeded by competitive dominants. Under high light, a more consistent competitive hierarchy was established in which competitive dominants outgrew and limited the abundance of others. These findings provide insight into mechanisms of microbial community organization and symbiosis breakdown and recovery. Furthermore, transitions in competitive outcomes across spatial and temporal environmental variation may improve lifetime host fitness.}, }
@article {pmid31772223, year = {2019}, author = {Kamm, K and Osigus, HJ and Stadler, PF and DeSalle, R and Schierwater, B}, title = {Genome analyses of a placozoan rickettsial endosymbiont show a combination of mutualistic and parasitic traits.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {17561}, pmid = {31772223}, issn = {2045-2322}, mesh = {Amino Acids/biosynthesis ; Animals ; Evolution, Molecular ; Genome/genetics ; Genome, Bacterial/genetics ; Metabolic Networks and Pathways/genetics ; Phylogeny ; Placozoa/*genetics/microbiology/physiology ; Rickettsia/*genetics/physiology ; Symbiosis/*genetics ; }, abstract = {Symbiotic relationships between eukaryotic hosts and bacteria range from parasitism to mutualism and may deeply influence both partners' fitness. The presence of intracellular bacteria in the metazoan phylum Placozoa has been reported several times, but without any knowledge about the nature of this relationship and possible implications for the placozoan holobiont. This information may be of crucial significance since little is known about placozoan ecology and how different species adapt to different environmental conditions, despite being almost invariable at the morphological level. We here report on the novel genome of the rickettsial endosymbiont of Trichoplax sp. H2 (strain "Panama"). The combination of eliminated and retained metabolic pathways of the bacterium indicates a potential for a mutualistic as well as for a parasitic relationship, whose outcome could depend on the environmental context. In particular we show that the endosymbiont is dependent on the host for growth and reproduction and that the latter could benefit from a supply with essential amino acids and important cofactors. These findings call for further studies to clarify the actual benefit for the placozoan host and to investigate a possible role of the endosymbiont for ecological separation between placozoan species.}, }
@article {pmid31762410, year = {2020}, author = {Zhang, Y and Kumarasamy, S and Mell, B and Cheng, X and Morgan, EE and Britton, SL and Vijay-Kumar, M and Koch, LG and Joe, B}, title = {Vertical selection for nuclear and mitochondrial genomes shapes gut microbiota and modifies risks for complex diseases.}, journal = {Physiological genomics}, volume = {52}, number = {1}, pages = {1-14}, pmid = {31762410}, issn = {1531-2267}, support = {P40 OD021331/OD/NIH HHS/United States ; }, mesh = {Adiposity/genetics ; Animals ; Behavior, Animal ; Blood Pressure/genetics ; Body Weight/genetics ; Cardiovascular Diseases/genetics ; Cell Nucleus/*genetics ; Cognition ; DNA, Mitochondrial/genetics ; Gastrointestinal Microbiome/*genetics ; *Genetic Predisposition to Disease ; *Genome, Mitochondrial ; Physical Conditioning, Animal ; Rats ; Risk Factors ; Selection, Genetic ; Ventricular Remodeling/genetics ; }, abstract = {Here we postulate that the heritability of complex disease traits previously ascribed solely to the inheritance of the nuclear and mitochondrial genomes is broadened to encompass a third component of the holobiome, the microbiome. To test this, we expanded on the selectively bred low capacity runner/high capacity runner (LCR/HCR) rat exercise model system into four distinct rat holobiont model frameworks including matched and mismatched host nuclear and mitochondrial genomes. Vertical selection of varying nuclear and mitochondrial genomes resulted in differential acquisition of the microbiome within each of these holobiont models. Polygenic disease risk of these novel models were assessed and subsequently correlated with patterns of acquisition and contributions of their microbiomes in controlled laboratory settings. Nuclear-mitochondrial-microbiotal interactions were not for exercise as a reporter of health, but significantly noted for increased adiposity, increased blood pressure, compromised cardiac function, and loss of long-term memory as reporters of disease susceptibility. These findings provide evidence for coselection of the microbiome with nuclear and mitochondrial genomes as an important feature impacting the heritability of complex diseases.}, }
@article {pmid31759226, year = {2019}, author = {Cooke, I and Mead, O and Whalen, C and Boote, C and Moya, A and Ying, H and Robbins, S and Strugnell, JM and Darling, A and Miller, D and Voolstra, CR and Adamska, M and , }, title = {Molecular techniques and their limitations shape our view of the holobiont.}, journal = {Zoology (Jena, Germany)}, volume = {137}, number = {}, pages = {125695}, doi = {10.1016/j.zool.2019.125695}, pmid = {31759226}, issn = {1873-2720}, mesh = {*Environmental Microbiology ; *Microbiota ; *Symbiosis ; }, abstract = {It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.}, }
@article {pmid31752998, year = {2019}, author = {Sweet, M and Burian, A and Fifer, J and Bulling, M and Elliott, D and Raymundo, L}, title = {Compositional homogeneity in the pathobiome of a new, slow-spreading coral disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {139}, pmid = {31752998}, issn = {2049-2618}, mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/*pathogenicity ; *Coral Reefs ; Microbial Interactions/*physiology ; Microbiota/*physiology ; Micronesia ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Coral reefs face unprecedented declines in diversity and cover, a development largely attributed to climate change-induced bleaching and subsequent disease outbreaks. Coral-associated microbiomes may strongly influence the fitness of their hosts and alter heat tolerance and disease susceptibility of coral colonies. Here, we describe a new coral disease found in Micronesia and present a detailed assessment of infection-driven changes in the coral microbiome.<br><br>RESULTS: Combining field monitoring and histological, microscopic and next-generation barcoding assessments, we demonstrate that the outbreak of the disease, named 'grey-patch disease', is associated with the establishment of cyanobacterial biofilm overgrowing coral tissue. The disease is characterised by slow progression rates, with coral tissue sometimes growing back over the GPD biofilm. Network analysis of the corals' microbiome highlighted the clustering of specific microbes which appeared to benefit from the onset of disease, resulting in the formation of 'infection clusters' in the microbiomes of apparently healthy corals.<br><br>CONCLUSIONS: Our results appear to be in contrast to the recently proposed Anna-Karenina principle, which states that disturbances (such as disease) trigger chaotic dynamics in microbial communities and increase β-diversity. Here, we show significantly higher community similarity (compositional homogeneity) in the pathobiome of diseased corals, compared to the microbiome associated with apparently healthy tissue. A possible explanation for this pattern is strong competition between the pathogenic community and those associated with the 'healthy' coral holobiont, homogenising the composition of the pathobiome. Further, one of our key findings is that multiple agents appear to be involved in degrading the corals' defences causing the onset of this disease. This supports recent findings indicating a need for a shift from the one-pathogen-one-disease paradigm to exploring the importance of multiple pathogenic players in any given disease.}, }
@article {pmid31739792, year = {2019}, author = {Li, Y and Tassia, MG and Waits, DS and Bogantes, VE and David, KT and Halanych, KM}, title = {Genomic adaptations to chemosymbiosis in the deep-sea seep-dwelling tubeworm Lamellibrachia luymesi.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {91}, pmid = {31739792}, issn = {1741-7007}, mesh = {Animals ; *Chemoautotrophic Growth ; Genome/*physiology ; Hydrothermal Vents ; Polychaeta/*genetics/*microbiology ; Symbiosis/*physiology ; }, abstract = {BACKGROUND: Symbiotic relationships between microbes and their hosts are widespread and diverse, often providing protection or nutrients, and may be either obligate or facultative. However, the genetic mechanisms allowing organisms to maintain host-symbiont associations at the molecular level are still mostly unknown, and in the case of bacterial-animal associations, most genetic studies have focused on adaptations and mechanisms of the bacterial partner. The gutless tubeworms (Siboglinidae, Annelida) are obligate hosts of chemoautotrophic endosymbionts (except for Osedax which houses heterotrophic Oceanospirillales), which rely on the sulfide-oxidizing symbionts for nutrition and growth. Whereas several siboglinid endosymbiont genomes have been characterized, genomes of hosts and their adaptations to this symbiosis remain unexplored.<br><br>RESULTS: Here, we present and characterize adaptations of the cold seep-dwelling tubeworm Lamellibrachia luymesi, one of the longest-lived solitary invertebrates. We sequenced the worm's ~ 688-Mb haploid genome with an overall completeness of ~ 95% and discovered that L. luymesi lacks many genes essential in amino acid biosynthesis, obligating them to products provided by symbionts. Interestingly, the host is known to carry hydrogen sulfide to thiotrophic endosymbionts using hemoglobin. We also found an expansion of hemoglobin B1 genes, many of which possess a free cysteine residue which is hypothesized to function in sulfide binding. Contrary to previous analyses, the sulfide binding mediated by zinc ions is not conserved across tubeworms. Thus, the sulfide-binding mechanisms in sibgolinids need to be further explored, and B1 globins might play a more important role than previously thought. Our comparative analyses also suggest the Toll-like receptor pathway may be essential for tolerance/sensitivity to symbionts and pathogens. Several genes related to the worm's unique life history which are known to play important roles in apoptosis, cell proliferation, and aging were also identified. Last, molecular clock analyses based on phylogenomic data suggest modern siboglinid diversity originated in 267 mya (± 70 my) support previous hypotheses indicating a Late Mesozoic or Cenozoic origins of approximately 50-126 mya for vestimentiferans.<br><br>CONCLUSIONS: Here, we elucidate several specific adaptations along various molecular pathways that link phenome to genome to improve understanding of holobiont evolution. Our findings of adaptation in genomic mechanisms to reducing environments likely extend to other chemosynthetic symbiotic systems.}, }
@article {pmid31731227, year = {2019}, author = {Mitter, B and Brader, G and Pfaffenbichler, N and Sessitsch, A}, title = {Next generation microbiome applications for crop production - limitations and the need of knowledge-based solutions.}, journal = {Current opinion in microbiology}, volume = {49}, number = {}, pages = {59-65}, doi = {10.1016/j.mib.2019.10.006}, pmid = {31731227}, issn = {1879-0364}, mesh = {Agricultural Inoculants ; Crop Production/*methods/*trends ; Crops, Agricultural/growth &amp; development/*microbiology ; Knowledge Bases ; *Microbiota ; }, abstract = {Plants are associated with highly diverse microbiota, which are crucial partners for their host carrying out important functions. Essentially, they are involved in nutrient supply, pathogen antagonism and protection of their host against different types of stress. The potential of microbial inoculants has been demonstrated in numerous studies, primarily under greenhouse conditions. However, field application, for example, as biofertilizer or biocontrol agent, is still a challenge as the applied microorganisms often are not provided in sufficiently high cell numbers, are rapidly outcompeted and cannot establish or require specific conditions to mediate the desired effects. We still have limited understanding on the fate of inoculants and on holobiont interactions, that is, interactions between plants, micro-biota and macro-biota and the environment, under field conditions. A better understanding will provide the basis for establishing models predicting the behaviour of strains or consortia and will help identifying microbiome members being able to establish and to mediate desired effects under certain conditions. Such models may also inform about the best management practices modulating microbiota in a desired way. Also, smart delivery approaches of microbial inoculants as well as the selection or breeding of plant genotypes better able to interact with microbiota may represent promising avenues.}, }
@article {pmid31722669, year = {2019}, author = {Sauvage, T and Schmidt, WE and Yoon, HS and Paul, VJ and Fredericq, S}, title = {Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery.}, journal = {BMC genomics}, volume = {20}, number = {1}, pages = {850}, pmid = {31722669}, issn = {1471-2164}, support = {GIAR 2013&amp;2014//Phycological Society of America/ ; }, mesh = {Caulerpa/*genetics ; Genome, Bacterial ; *Genome, Chloroplast ; Genome, Mitochondrial ; Genomics/methods ; Nanopore Sequencing/*methods ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/*methods ; }, abstract = {BACKGROUND: The MinION Access Program (MAP, 2014-2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches.<br><br>RESULTS: The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii's nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope's estimate (> 26.3 Mbp, including 4.8 Mbp in repeat).<br><br>CONCLUSION: Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic 'chlorotypes' in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii's nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.}, }
@article {pmid31709760, year = {2019}, author = {Collens, A and Kelley, E and Katz, LA}, title = {The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis.}, journal = {Journal of experimental zoology. Part B, Molecular and developmental evolution}, volume = {332}, number = {8}, pages = {349-355}, pmid = {31709760}, issn = {1552-5015}, support = {R15 GM113177/GM/NIGMS NIH HHS/United States ; R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Adaptation, Biological ; *Biological Evolution ; *Epigenesis, Genetic ; Genome ; Microbiota ; Symbiosis/*genetics ; }, abstract = {John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.}, }
@article {pmid31708944, year = {2019}, author = {Lucaciu, R and Pelikan, C and Gerner, SM and Zioutis, C and Köstlbacher, S and Marx, H and Herbold, CW and Schmidt, H and Rattei, T}, title = {A Bioinformatics Guide to Plant Microbiome Analysis.}, journal = {Frontiers in plant science}, volume = {10}, number = {}, pages = {1313}, pmid = {31708944}, issn = {1664-462X}, abstract = {Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.}, }
@article {pmid31701649, year = {2020}, author = {Staples, R and LaDuca, RL and Roze, LV and Laivenieks, M and Linz, JE and Beaudry, R and Fryday, A and Schilmiller, AL and Koptina, AV and Smith, B and Trail, F}, title = {Structure and Chemical Analysis of Major Specialized Metabolites Produced by the Lichen Evernia prunastri.}, journal = {Chemistry &amp; biodiversity}, volume = {17}, number = {1}, pages = {e1900465}, doi = {10.1002/cbdv.201900465}, pmid = {31701649}, issn = {1612-1880}, support = {//MSU Office of the Vice President of Research and Graduate Studies/ ; //AgBioResearch and the College of Natural Sciences/ ; }, mesh = {Benzofurans/*analysis/metabolism ; Hydroxybenzoates/*analysis/metabolism ; Lichens/*chemistry/metabolism ; Models, Molecular ; Salicylates/*analysis/metabolism ; }, abstract = {We performed comparative profiling of four specialized metabolites in the lichen Evernia prunastri, collected at three different geographic locations, California and Maine, USA, and Yoshkar Ola, Mari El, Russia. Among the compounds produced at high concentrations that were identified in all three specimens, evernic acid, usnic acid, lecanoric acid and chloroatranorin, evernic acid was the most abundant. Two depsidones, salazinic acid and physodic acid, were detected in the Yoshkar-Ola collection only. The crystalline structure of evernic acid (2-hydroxy-4-[(2-hydroxy-4-methoxy-6-methylbenzoyl)oxy]-6-methylbenzoate) (hmb) revealed two crystallographically and conformationally distinct hmb anions, along with two monovalent sodium atoms. One hmb moiety contained an exotetradentate binding mode to sodium, whereas the other exhibited an exohexadentate binding mode to sodium. Embedded edge-sharing {Na2 O8 }n sodium-oxygen chains connected the hmb anions into the full three-dimensional crystal structure of the title compound. The crystal used for single-crystal X-ray diffraction exhibited non-merohedral twinning. The data suggest the importance of the acetyl-polymalonyl pathway products to processes of maintaining integrity of the lichen holobiont community.}, }
@article {pmid31701578, year = {2020}, author = {Weishaar, R and Wellmann, R and Camarinha-Silva, A and Rodehutscord, M and Bennewitz, J}, title = {Selecting the hologenome to breed for an improved feed efficiency in pigs-A novel selection index.}, journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie}, volume = {137}, number = {1}, pages = {14-22}, doi = {10.1111/jbg.12447}, pmid = {31701578}, issn = {1439-0388}, mesh = {Animals ; Breeding/*methods ; Female ; *Genomics ; Male ; Microbiota ; Models, Genetic ; Swine/*genetics/microbiology ; }, abstract = {Most traits in animal breeding, including feed efficiency traits in pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 and 0.5, which enables efficient selection. Since the microbiota composition in the gastrointestinal tract is also partly heritable and was shown to have a substantial effect on feed efficiency, the host genes affect the phenotype not only directly by altering metabolic pathways, but also indirectly by changing the microbiota composition. The effect m i of the microbiota composition on the breeding value g i of an animal i is the conditional expectation of its breeding value, given the vector φ i with microbiota frequencies, that is m i = E g i | φ i . The breeding value g i of an animal can therefore be decomposed into a heritable contribution m i that arises from an altered microbiota composition and a heritable contribution p i that arises from altered metabolic pathways within the animal, so g i = m i + p i . Instead of selecting for breeding value g ^ i , an index comprising the two components m ^ i and p ^ i with appropriate weights, that is I i = λ 1 m ^ i + λ 2 p ^ i , can be used. The present study shows how this breeding strategy can be applied in pig genomic selection breeding scheme for two feed efficiency traits and daily gain.}, }
@article {pmid31692206, year = {2020}, author = {Alves Monteiro, HJ and Brahmi, C and Mayfield, AB and Vidal-Dupiol, J and Lapeyre, B and Le Luyer, J}, title = {Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses.}, journal = {Global change biology}, volume = {26}, number = {3}, pages = {1271-1284}, doi = {10.1111/gcb.14907}, pmid = {31692206}, issn = {1365-2486}, support = {//Labex CORAIL/International ; //IFREMER/International ; }, mesh = {Acclimatization ; Animals ; *Anthozoa ; Coral Reefs ; *Dinoflagellida ; Polynesia ; Symbiosis ; Temperature ; }, abstract = {Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.